0s autopkgtest [06:54:54]: starting date and time: 2026-01-30 06:54:54+0000 0s autopkgtest [06:54:54]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [06:54:54]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5es1kukl/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-s390x-4.secgroup --name adt-resolute-s390x-toil-20260130-055139-juju-7f2275-prod-proposed-migration-environment-15-e63756b8-c1a0-4fd7-8737-17863babdcb8 --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-s390x-toil-20260130-055139-juju-7f2275-prod-proposed-migration-environment-15-e63756b8-c1a0-4fd7-8737-17863babdcb8 from image adt/ubuntu-resolute-s390x-server-20260129.img (UUID 0fdc3f45-c7c7-4a2c-aa6d-edc1dbbf6141)... 70s autopkgtest [06:56:04]: testbed dpkg architecture: s390x 70s autopkgtest [06:56:04]: testbed apt version: 3.1.14 71s autopkgtest [06:56:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 71s autopkgtest [06:56:05]: testbed release detected to be: None 72s autopkgtest [06:56:06]: updating testbed package index (apt update) 73s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 73s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 73s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 73s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 73s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 73s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [33.0 kB] 73s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [103 kB] 73s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1600 kB] 73s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [117 kB] 73s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [1102 kB] 73s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [12.0 kB] 75s Fetched 3095 kB in 2s (1786 kB/s) 77s Reading package lists... 79s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 79s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 79s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 79s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 83s Reading package lists... 83s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Calculating upgrade... 85s The following packages will be upgraded: 85s bzip2 gcc-15-base inetutils-telnet libatomic1 libbz2-1.0 libgcc-s1 85s libsgutils2-1.48 libsqlite3-0 libstdc++6 sg3-utils sg3-utils-udev telnet 85s 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s Need to get 3103 kB of archives. 85s After this operation, 3072 B of additional disk space will be used. 85s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libatomic1 s390x 15.2.0-12ubuntu1 [9486 B] 85s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libstdc++6 s390x 15.2.0-12ubuntu1 [907 kB] 85s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15-base s390x 15.2.0-12ubuntu1 [59.6 kB] 85s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libgcc-s1 s390x 15.2.0-12ubuntu1 [35.7 kB] 85s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x bzip2 s390x 1.0.8-6build2 [35.2 kB] 85s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libbz2-1.0 s390x 1.0.8-6build2 [41.6 kB] 85s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x libsqlite3-0 s390x 3.46.1-9 [748 kB] 85s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x inetutils-telnet s390x 2:2.7-2ubuntu1 [112 kB] 85s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x telnet all 0.17+2.7-2ubuntu1 [3636 B] 85s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x libsgutils2-1.48 s390x 1.48-3ubuntu2 [120 kB] 85s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x sg3-utils s390x 1.48-3ubuntu2 [1025 kB] 86s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x sg3-utils-udev all 1.48-3ubuntu2 [6610 B] 88s dpkg-preconfigure: unable to re-open stdin: No such file or directory 88s Fetched 3103 kB in 1s (4085 kB/s) 90s (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 ... 87720 files and directories currently installed.) 90s Preparing to unpack .../libatomic1_15.2.0-12ubuntu1_s390x.deb ... 91s Unpacking libatomic1:s390x (15.2.0-12ubuntu1) over (15.2.0-11ubuntu1) ... 91s Preparing to unpack .../libstdc++6_15.2.0-12ubuntu1_s390x.deb ... 92s Unpacking libstdc++6:s390x (15.2.0-12ubuntu1) over (15.2.0-11ubuntu1) ... 92s Preparing to unpack .../gcc-15-base_15.2.0-12ubuntu1_s390x.deb ... 92s Unpacking gcc-15-base:s390x (15.2.0-12ubuntu1) over (15.2.0-11ubuntu1) ... 93s Setting up gcc-15-base:s390x (15.2.0-12ubuntu1) ... 93s (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 ... 87720 files and directories currently installed.) 93s Preparing to unpack .../libgcc-s1_15.2.0-12ubuntu1_s390x.deb ... 94s Unpacking libgcc-s1:s390x (15.2.0-12ubuntu1) over (15.2.0-11ubuntu1) ... 94s Setting up libgcc-s1:s390x (15.2.0-12ubuntu1) ... 94s (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 ... 87720 files and directories currently installed.) 94s Preparing to unpack .../bzip2_1.0.8-6build2_s390x.deb ... 94s Unpacking bzip2 (1.0.8-6build2) over (1.0.8-6build1) ... 94s Preparing to unpack .../libbz2-1.0_1.0.8-6build2_s390x.deb ... 94s Unpacking libbz2-1.0:s390x (1.0.8-6build2) over (1.0.8-6build1) ... 94s Setting up libbz2-1.0:s390x (1.0.8-6build2) ... 94s (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 ... 87720 files and directories currently installed.) 94s Preparing to unpack .../0-libsqlite3-0_3.46.1-9_s390x.deb ... 95s Unpacking libsqlite3-0:s390x (3.46.1-9) over (3.46.1-8) ... 95s Preparing to unpack .../1-inetutils-telnet_2%3a2.7-2ubuntu1_s390x.deb ... 95s Unpacking inetutils-telnet (2:2.7-2ubuntu1) over (2:2.6-4ubuntu1) ... 95s Preparing to unpack .../2-telnet_0.17+2.7-2ubuntu1_all.deb ... 95s Unpacking telnet (0.17+2.7-2ubuntu1) over (0.17+2.6-4ubuntu1) ... 96s Preparing to unpack .../3-libsgutils2-1.48_1.48-3ubuntu2_s390x.deb ... 96s Unpacking libsgutils2-1.48:s390x (1.48-3ubuntu2) over (1.48-3ubuntu1) ... 96s Preparing to unpack .../4-sg3-utils_1.48-3ubuntu2_s390x.deb ... 97s Unpacking sg3-utils (1.48-3ubuntu2) over (1.48-3ubuntu1) ... 97s Preparing to unpack .../5-sg3-utils-udev_1.48-3ubuntu2_all.deb ... 97s Unpacking sg3-utils-udev (1.48-3ubuntu2) over (1.48-3ubuntu1) ... 97s Setting up libsqlite3-0:s390x (3.46.1-9) ... 97s Setting up inetutils-telnet (2:2.7-2ubuntu1) ... 97s Setting up libsgutils2-1.48:s390x (1.48-3ubuntu2) ... 98s Setting up bzip2 (1.0.8-6build2) ... 98s Setting up libatomic1:s390x (15.2.0-12ubuntu1) ... 98s Setting up libstdc++6:s390x (15.2.0-12ubuntu1) ... 98s Setting up sg3-utils (1.48-3ubuntu2) ... 98s Setting up telnet (0.17+2.7-2ubuntu1) ... 98s Setting up sg3-utils-udev (1.48-3ubuntu2) ... 98s update-initramfs: deferring update (trigger activated) 98s Processing triggers for libc-bin (2.42-2ubuntu4) ... 98s Processing triggers for man-db (2.13.1-1) ... 105s Processing triggers for initramfs-tools (0.150ubuntu7) ... 105s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 114s Using config file '/etc/zipl.conf' 114s Building bootmap in '/boot' 114s Adding IPL section 'ubuntu' (default) 114s Preparing boot device: vda. 114s Done. 115s autopkgtest [06:56:49]: upgrading testbed (apt dist-upgrade and autopurge) 116s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Calculating upgrade... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 119s Solving dependencies... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s autopkgtest [06:56:53]: rebooting testbed after setup commands that affected boot 160s autopkgtest [06:57:34]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP Mon Jan 12 15:39:23 UTC 2026 163s autopkgtest [06:57:37]: @@@@@@@@@@@@@@@@@@@@ apt-source toil 166s Get:1 http://ftpmaster.internal/ubuntu resolute/universe toil 9.1.0-1 (dsc) [2872 B] 166s Get:2 http://ftpmaster.internal/ubuntu resolute/universe toil 9.1.0-1 (tar) [7876 kB] 166s Get:3 http://ftpmaster.internal/ubuntu resolute/universe toil 9.1.0-1 (diff) [17.1 kB] 167s gpgv: Signature made Fri Oct 17 09:42:43 2025 UTC 167s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 167s gpgv: issuer "crusoe@debian.org" 167s gpgv: Can't check signature: No public key 167s dpkg-source: warning: cannot verify inline signature for ./toil_9.1.0-1.dsc: no acceptable signature found 167s autopkgtest [06:57:41]: testing package toil version 9.1.0-1 168s autopkgtest [06:57:42]: build not needed 171s autopkgtest [06:57:45]: test smoke-test: preparing testbed 171s Reading package lists... 171s Building dependency tree... 171s Reading state information... 171s Solving dependencies... 172s The following NEW packages will be installed: 172s cwl-upgrader cwltool fontconfig fontconfig-config fonts-dejavu-core 172s fonts-dejavu-mono fonts-glyphicons-halflings graphviz libaom3 libcairo2 172s libcdt6 libcgraph8 libdatrie1 libde265-0 libdeflate0 libfontconfig1 172s libfreetype6 libgd3 libgomp1 libgraphite2-3 libgvc7 libgvplugin-gd8 172s libgvplugin-pango8 libgvpr2 libharfbuzz0b libheif-plugin-aomdec 172s libheif-plugin-libde265 libheif1 libimagequant0 libjbig0 libjpeg-turbo8 172s libjpeg8 libjs-bootstrap libltdl7 libpango-1.0-0 libpangocairo-1.0-0 172s libpangoft2-1.0-0 libpathplan4 libpixman-1-0 libsharpyuv0 libthai-data 172s libthai0 libtiff6 libwebp7 libxcb-render0 libxcb-shm0 libxdot4 libxpm4 172s libxrender1 libxslt1.1 python3-arcp python3-argcomplete python3-blessed 172s python3-cachecontrol python3-coloredlogs python3-configargparse 172s python3-cwl-utils python3-dill python3-docker python3-enlighten 172s python3-filelock python3-humanfriendly python3-lxml python3-mistune 172s python3-msgpack python3-mypy-extensions python3-networkx python3-prefixed 172s python3-prompt-toolkit python3-prov python3-psutil python3-pubsub 172s python3-pydot python3-rdflib python3-rich-argparse python3-ruamel.yaml 172s python3-ruamel.yaml.clib python3-schema-salad python3-spython 172s python3-wcwidth toil 172s 0 upgraded, 81 newly installed, 0 to remove and 0 not upgraded. 172s Need to get 28.9 MB of archives. 172s After this operation, 165 MB of additional disk space will be used. 172s Get:1 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-ruamel.yaml.clib s390x 0.2.15+ds-1 [214 kB] 172s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x python3-ruamel.yaml all 0.18.10+ds-1build1 [127 kB] 172s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x python3-msgpack s390x 1.1.2-1 [117 kB] 172s Get:4 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-cachecontrol all 0.14.3-1 [18.7 kB] 172s Get:5 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mistune all 3.1.4-1 [35.0 kB] 172s Get:6 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mypy-extensions all 1.1.0-1 [6716 B] 172s Get:7 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-rdflib all 7.4.0-1 [431 kB] 172s Get:8 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-filelock all 3.20.3-1 [13.5 kB] 172s Get:9 http://ftpmaster.internal/ubuntu resolute/universe s390x fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 172s Get:10 http://ftpmaster.internal/ubuntu resolute/universe s390x libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 172s Get:11 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-schema-salad s390x 8.9.20251102115403-1 [1941 kB] 173s Get:12 http://ftpmaster.internal/ubuntu resolute/universe s390x cwl-upgrader all 1.2.14-1 [16.6 kB] 173s Get:13 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-argcomplete all 3.6.3-1 [36.1 kB] 173s Get:14 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-humanfriendly all 10.0-6build1 [70.9 kB] 173s Get:15 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-coloredlogs all 15.0.1-1build1 [38.4 kB] 173s Get:16 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-cwl-utils all 0.40-1 [140 kB] 173s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x libxslt1.1 s390x 1.1.43-0.3 [163 kB] 173s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x python3-lxml s390x 6.0.2-1 [2478 kB] 174s Get:19 http://ftpmaster.internal/ubuntu resolute/main s390x python3-networkx all 3.2.1-4ubuntu2 [11.8 MB] 177s Get:20 http://ftpmaster.internal/ubuntu resolute/universe s390x libcdt6 s390x 14.1.1-2ubuntu2 [20.7 kB] 177s Get:21 http://ftpmaster.internal/ubuntu resolute/universe s390x libcgraph8 s390x 14.1.1-2ubuntu2 [55.2 kB] 177s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x libltdl7 s390x 2.5.4-9 [44.4 kB] 177s Get:23 http://ftpmaster.internal/ubuntu resolute/universe s390x libpathplan4 s390x 14.1.1-2ubuntu2 [27.6 kB] 177s Get:24 http://ftpmaster.internal/ubuntu resolute/universe s390x libxdot4 s390x 14.1.1-2ubuntu2 [23.1 kB] 177s Get:25 http://ftpmaster.internal/ubuntu resolute/universe s390x libgvc7 s390x 14.1.1-2ubuntu2 [415 kB] 177s Get:26 http://ftpmaster.internal/ubuntu resolute/universe s390x libgvpr2 s390x 14.1.1-2ubuntu2 [131 kB] 177s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x libfreetype6 s390x 2.14.1+dfsg-2 [443 kB] 177s Get:28 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-dejavu-mono all 2.37-8build1 [502 kB] 177s Get:29 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-dejavu-core all 2.37-8build1 [834 kB] 177s Get:30 http://ftpmaster.internal/ubuntu resolute/main s390x fontconfig-config s390x 2.17.1-3ubuntu1 [38.5 kB] 177s Get:31 http://ftpmaster.internal/ubuntu resolute/main s390x libfontconfig1 s390x 2.17.1-3ubuntu1 [152 kB] 177s Get:32 http://ftpmaster.internal/ubuntu resolute/main s390x libpixman-1-0 s390x 0.46.4-1 [217 kB] 177s Get:33 http://ftpmaster.internal/ubuntu resolute/main s390x libxcb-render0 s390x 1.17.0-2ubuntu1 [16.9 kB] 178s Get:34 http://ftpmaster.internal/ubuntu resolute/main s390x libxcb-shm0 s390x 1.17.0-2ubuntu1 [5926 B] 178s Get:35 http://ftpmaster.internal/ubuntu resolute/main s390x libxrender1 s390x 1:0.9.12-1 [20.9 kB] 178s Get:36 http://ftpmaster.internal/ubuntu resolute/main s390x libcairo2 s390x 1.18.4-3 [578 kB] 178s Get:37 http://ftpmaster.internal/ubuntu resolute/main s390x libsharpyuv0 s390x 1.5.0-0.1build1 [16.6 kB] 178s Get:38 http://ftpmaster.internal/ubuntu resolute/main s390x libaom3 s390x 3.13.1-2 [1513 kB] 178s Get:39 http://ftpmaster.internal/ubuntu resolute/main s390x libheif-plugin-aomdec s390x 1.21.2-1 [14.4 kB] 178s Get:40 http://ftpmaster.internal/ubuntu resolute/main s390x libde265-0 s390x 1.0.16-1build1 [182 kB] 178s Get:41 http://ftpmaster.internal/ubuntu resolute/main s390x libheif-plugin-libde265 s390x 1.21.2-1 [10.0 kB] 178s Get:42 http://ftpmaster.internal/ubuntu resolute/main s390x libheif1 s390x 1.21.2-1 [557 kB] 178s Get:43 http://ftpmaster.internal/ubuntu resolute/main s390x libgomp1 s390x 15.2.0-12ubuntu1 [154 kB] 178s Get:44 http://ftpmaster.internal/ubuntu resolute/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 178s Get:45 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg-turbo8 s390x 2.1.5-4ubuntu2 [147 kB] 178s Get:46 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 178s Get:47 http://ftpmaster.internal/ubuntu resolute/main s390x libdeflate0 s390x 1.23-2 [46.0 kB] 178s Get:48 http://ftpmaster.internal/ubuntu resolute/main s390x libjbig0 s390x 2.1-6.1ubuntu3 [32.8 kB] 178s Get:49 http://ftpmaster.internal/ubuntu resolute/main s390x libwebp7 s390x 1.5.0-0.1build1 [227 kB] 178s Get:50 http://ftpmaster.internal/ubuntu resolute/main s390x libtiff6 s390x 4.7.0-3ubuntu3 [222 kB] 178s Get:51 http://ftpmaster.internal/ubuntu resolute/main s390x libxpm4 s390x 1:3.5.17-1build3 [41.5 kB] 178s Get:52 http://ftpmaster.internal/ubuntu resolute/main s390x libgd3 s390x 2.3.3-13ubuntu1 [142 kB] 178s Get:53 http://ftpmaster.internal/ubuntu resolute/universe s390x libgvplugin-gd8 s390x 14.1.1-2ubuntu2 [26.1 kB] 178s Get:54 http://ftpmaster.internal/ubuntu resolute/main s390x fontconfig s390x 2.17.1-3ubuntu1 [180 kB] 178s Get:55 http://ftpmaster.internal/ubuntu resolute/main s390x libgraphite2-3 s390x 1.3.14-11ubuntu1 [80.5 kB] 178s Get:56 http://ftpmaster.internal/ubuntu resolute/main s390x libharfbuzz0b s390x 12.3.1-1 [563 kB] 178s Get:57 http://ftpmaster.internal/ubuntu resolute/main s390x libthai-data all 0.1.30-1 [155 kB] 178s Get:58 http://ftpmaster.internal/ubuntu resolute/main s390x libdatrie1 s390x 0.2.14-1 [20.7 kB] 178s Get:59 http://ftpmaster.internal/ubuntu resolute/main s390x libthai0 s390x 0.1.30-1 [20.8 kB] 178s Get:60 http://ftpmaster.internal/ubuntu resolute/main s390x libpango-1.0-0 s390x 1.57.0-1 [255 kB] 178s Get:61 http://ftpmaster.internal/ubuntu resolute/main s390x libpangoft2-1.0-0 s390x 1.57.0-1 [52.9 kB] 178s Get:62 http://ftpmaster.internal/ubuntu resolute/main s390x libpangocairo-1.0-0 s390x 1.57.0-1 [28.4 kB] 178s Get:63 http://ftpmaster.internal/ubuntu resolute/universe s390x libgvplugin-pango8 s390x 14.1.1-2ubuntu2 [23.9 kB] 178s Get:64 http://ftpmaster.internal/ubuntu resolute/universe s390x graphviz s390x 14.1.1-2ubuntu2 [58.6 kB] 178s Get:65 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pydot all 4.0.1-1 [35.8 kB] 178s Get:66 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-prov all 2.1.1-1 [101 kB] 178s Get:67 http://ftpmaster.internal/ubuntu resolute/main s390x python3-psutil s390x 7.1.0-1ubuntu1 [191 kB] 178s Get:68 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-rich-argparse all 1.6.0-2 [17.2 kB] 178s Get:69 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-spython all 0.3.13-2build1 [56.4 kB] 178s Get:70 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-arcp all 0.2.1-7build1 [14.1 kB] 178s Get:71 http://ftpmaster.internal/ubuntu resolute/universe s390x cwltool all 3.1.20251031082601-1 [533 kB] 178s Get:72 http://ftpmaster.internal/ubuntu resolute/main s390x python3-wcwidth all 0.2.14+dfsg1-1build1 [26.5 kB] 178s Get:73 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-blessed all 1.21.0-1 [50.4 kB] 178s Get:74 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-configargparse all 1.7-2 [31.7 kB] 178s Get:75 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-dill all 0.4.0-1 [84.8 kB] 178s Get:76 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-docker all 7.1.0-2ubuntu1 [91.0 kB] 178s Get:77 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-prefixed all 0.7.0-1build1 [8352 B] 178s Get:78 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-enlighten s390x 1.11.2-1build1 [42.4 kB] 178s Get:79 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-prompt-toolkit all 3.0.52-2 [258 kB] 178s Get:80 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pubsub all 4.0.3-7build1 [45.0 kB] 178s Get:81 http://ftpmaster.internal/ubuntu resolute/universe s390x toil all 9.1.0-1 [1104 kB] 179s Fetched 28.9 MB in 6s (4831 kB/s) 179s Selecting previously unselected package python3-ruamel.yaml.clib. 180s (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 ... 87720 files and directories currently installed.) 180s Preparing to unpack .../00-python3-ruamel.yaml.clib_0.2.15+ds-1_s390x.deb ... 180s Unpacking python3-ruamel.yaml.clib (0.2.15+ds-1) ... 180s Selecting previously unselected package python3-ruamel.yaml. 180s Preparing to unpack .../01-python3-ruamel.yaml_0.18.10+ds-1build1_all.deb ... 180s Unpacking python3-ruamel.yaml (0.18.10+ds-1build1) ... 180s Selecting previously unselected package python3-msgpack. 180s Preparing to unpack .../02-python3-msgpack_1.1.2-1_s390x.deb ... 180s Unpacking python3-msgpack (1.1.2-1) ... 180s Selecting previously unselected package python3-cachecontrol. 180s Preparing to unpack .../03-python3-cachecontrol_0.14.3-1_all.deb ... 180s Unpacking python3-cachecontrol (0.14.3-1) ... 180s Selecting previously unselected package python3-mistune. 180s Preparing to unpack .../04-python3-mistune_3.1.4-1_all.deb ... 180s Unpacking python3-mistune (3.1.4-1) ... 180s Selecting previously unselected package python3-mypy-extensions. 180s Preparing to unpack .../05-python3-mypy-extensions_1.1.0-1_all.deb ... 180s Unpacking python3-mypy-extensions (1.1.0-1) ... 180s Selecting previously unselected package python3-rdflib. 180s Preparing to unpack .../06-python3-rdflib_7.4.0-1_all.deb ... 180s Unpacking python3-rdflib (7.4.0-1) ... 181s Selecting previously unselected package python3-filelock. 181s Preparing to unpack .../07-python3-filelock_3.20.3-1_all.deb ... 181s Unpacking python3-filelock (3.20.3-1) ... 181s Selecting previously unselected package fonts-glyphicons-halflings. 181s Preparing to unpack .../08-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 181s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 181s Selecting previously unselected package libjs-bootstrap. 181s Preparing to unpack .../09-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 181s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 181s Selecting previously unselected package python3-schema-salad. 181s Preparing to unpack .../10-python3-schema-salad_8.9.20251102115403-1_s390x.deb ... 181s Unpacking python3-schema-salad (8.9.20251102115403-1) ... 181s Selecting previously unselected package cwl-upgrader. 181s Preparing to unpack .../11-cwl-upgrader_1.2.14-1_all.deb ... 181s Unpacking cwl-upgrader (1.2.14-1) ... 181s Selecting previously unselected package python3-argcomplete. 181s Preparing to unpack .../12-python3-argcomplete_3.6.3-1_all.deb ... 181s Unpacking python3-argcomplete (3.6.3-1) ... 182s Selecting previously unselected package python3-humanfriendly. 182s Preparing to unpack .../13-python3-humanfriendly_10.0-6build1_all.deb ... 182s Unpacking python3-humanfriendly (10.0-6build1) ... 182s Selecting previously unselected package python3-coloredlogs. 182s Preparing to unpack .../14-python3-coloredlogs_15.0.1-1build1_all.deb ... 182s Unpacking python3-coloredlogs (15.0.1-1build1) ... 182s Selecting previously unselected package python3-cwl-utils. 182s Preparing to unpack .../15-python3-cwl-utils_0.40-1_all.deb ... 182s Unpacking python3-cwl-utils (0.40-1) ... 182s Selecting previously unselected package libxslt1.1:s390x. 182s Preparing to unpack .../16-libxslt1.1_1.1.43-0.3_s390x.deb ... 182s Unpacking libxslt1.1:s390x (1.1.43-0.3) ... 182s Selecting previously unselected package python3-lxml:s390x. 182s Preparing to unpack .../17-python3-lxml_6.0.2-1_s390x.deb ... 182s Unpacking python3-lxml:s390x (6.0.2-1) ... 182s Selecting previously unselected package python3-networkx. 182s Preparing to unpack .../18-python3-networkx_3.2.1-4ubuntu2_all.deb ... 182s Unpacking python3-networkx (3.2.1-4ubuntu2) ... 184s Selecting previously unselected package libcdt6:s390x. 184s Preparing to unpack .../19-libcdt6_14.1.1-2ubuntu2_s390x.deb ... 184s Unpacking libcdt6:s390x (14.1.1-2ubuntu2) ... 184s Selecting previously unselected package libcgraph8:s390x. 184s Preparing to unpack .../20-libcgraph8_14.1.1-2ubuntu2_s390x.deb ... 184s Unpacking libcgraph8:s390x (14.1.1-2ubuntu2) ... 184s Selecting previously unselected package libltdl7:s390x. 184s Preparing to unpack .../21-libltdl7_2.5.4-9_s390x.deb ... 184s Unpacking libltdl7:s390x (2.5.4-9) ... 184s Selecting previously unselected package libpathplan4:s390x. 184s Preparing to unpack .../22-libpathplan4_14.1.1-2ubuntu2_s390x.deb ... 184s Unpacking libpathplan4:s390x (14.1.1-2ubuntu2) ... 184s Selecting previously unselected package libxdot4:s390x. 184s Preparing to unpack .../23-libxdot4_14.1.1-2ubuntu2_s390x.deb ... 184s Unpacking libxdot4:s390x (14.1.1-2ubuntu2) ... 184s Selecting previously unselected package libgvc7:s390x. 184s Preparing to unpack .../24-libgvc7_14.1.1-2ubuntu2_s390x.deb ... 184s Unpacking libgvc7:s390x (14.1.1-2ubuntu2) ... 184s Selecting previously unselected package libgvpr2:s390x. 184s Preparing to unpack .../25-libgvpr2_14.1.1-2ubuntu2_s390x.deb ... 184s Unpacking libgvpr2:s390x (14.1.1-2ubuntu2) ... 184s Selecting previously unselected package libfreetype6:s390x. 184s Preparing to unpack .../26-libfreetype6_2.14.1+dfsg-2_s390x.deb ... 184s Unpacking libfreetype6:s390x (2.14.1+dfsg-2) ... 184s Selecting previously unselected package fonts-dejavu-mono. 184s Preparing to unpack .../27-fonts-dejavu-mono_2.37-8build1_all.deb ... 184s Unpacking fonts-dejavu-mono (2.37-8build1) ... 184s Selecting previously unselected package fonts-dejavu-core. 184s Preparing to unpack .../28-fonts-dejavu-core_2.37-8build1_all.deb ... 184s Unpacking fonts-dejavu-core (2.37-8build1) ... 184s Selecting previously unselected package fontconfig-config. 184s Preparing to unpack .../29-fontconfig-config_2.17.1-3ubuntu1_s390x.deb ... 185s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 185s Selecting previously unselected package libfontconfig1:s390x. 185s Preparing to unpack .../30-libfontconfig1_2.17.1-3ubuntu1_s390x.deb ... 185s Unpacking libfontconfig1:s390x (2.17.1-3ubuntu1) ... 185s Selecting previously unselected package libpixman-1-0:s390x. 185s Preparing to unpack .../31-libpixman-1-0_0.46.4-1_s390x.deb ... 185s Unpacking libpixman-1-0:s390x (0.46.4-1) ... 185s Selecting previously unselected package libxcb-render0:s390x. 185s Preparing to unpack .../32-libxcb-render0_1.17.0-2ubuntu1_s390x.deb ... 185s Unpacking libxcb-render0:s390x (1.17.0-2ubuntu1) ... 185s Selecting previously unselected package libxcb-shm0:s390x. 185s Preparing to unpack .../33-libxcb-shm0_1.17.0-2ubuntu1_s390x.deb ... 185s Unpacking libxcb-shm0:s390x (1.17.0-2ubuntu1) ... 185s Selecting previously unselected package libxrender1:s390x. 185s Preparing to unpack .../34-libxrender1_1%3a0.9.12-1_s390x.deb ... 185s Unpacking libxrender1:s390x (1:0.9.12-1) ... 185s Selecting previously unselected package libcairo2:s390x. 185s Preparing to unpack .../35-libcairo2_1.18.4-3_s390x.deb ... 185s Unpacking libcairo2:s390x (1.18.4-3) ... 185s Selecting previously unselected package libsharpyuv0:s390x. 185s Preparing to unpack .../36-libsharpyuv0_1.5.0-0.1build1_s390x.deb ... 185s Unpacking libsharpyuv0:s390x (1.5.0-0.1build1) ... 185s Selecting previously unselected package libaom3:s390x. 185s Preparing to unpack .../37-libaom3_3.13.1-2_s390x.deb ... 185s Unpacking libaom3:s390x (3.13.1-2) ... 185s Selecting previously unselected package libheif-plugin-aomdec:s390x. 185s Preparing to unpack .../38-libheif-plugin-aomdec_1.21.2-1_s390x.deb ... 185s Unpacking libheif-plugin-aomdec:s390x (1.21.2-1) ... 185s Selecting previously unselected package libde265-0:s390x. 185s Preparing to unpack .../39-libde265-0_1.0.16-1build1_s390x.deb ... 185s Unpacking libde265-0:s390x (1.0.16-1build1) ... 185s Selecting previously unselected package libheif-plugin-libde265:s390x. 185s Preparing to unpack .../40-libheif-plugin-libde265_1.21.2-1_s390x.deb ... 185s Unpacking libheif-plugin-libde265:s390x (1.21.2-1) ... 185s Selecting previously unselected package libheif1:s390x. 185s Preparing to unpack .../41-libheif1_1.21.2-1_s390x.deb ... 185s Unpacking libheif1:s390x (1.21.2-1) ... 185s Selecting previously unselected package libgomp1:s390x. 185s Preparing to unpack .../42-libgomp1_15.2.0-12ubuntu1_s390x.deb ... 185s Unpacking libgomp1:s390x (15.2.0-12ubuntu1) ... 185s Selecting previously unselected package libimagequant0:s390x. 185s Preparing to unpack .../43-libimagequant0_2.18.0-1build1_s390x.deb ... 185s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 185s Selecting previously unselected package libjpeg-turbo8:s390x. 185s Preparing to unpack .../44-libjpeg-turbo8_2.1.5-4ubuntu2_s390x.deb ... 185s Unpacking libjpeg-turbo8:s390x (2.1.5-4ubuntu2) ... 185s Selecting previously unselected package libjpeg8:s390x. 185s Preparing to unpack .../45-libjpeg8_8c-2ubuntu11_s390x.deb ... 185s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 185s Selecting previously unselected package libdeflate0:s390x. 185s Preparing to unpack .../46-libdeflate0_1.23-2_s390x.deb ... 185s Unpacking libdeflate0:s390x (1.23-2) ... 185s Selecting previously unselected package libjbig0:s390x. 185s Preparing to unpack .../47-libjbig0_2.1-6.1ubuntu3_s390x.deb ... 185s Unpacking libjbig0:s390x (2.1-6.1ubuntu3) ... 185s Selecting previously unselected package libwebp7:s390x. 185s Preparing to unpack .../48-libwebp7_1.5.0-0.1build1_s390x.deb ... 185s Unpacking libwebp7:s390x (1.5.0-0.1build1) ... 185s Selecting previously unselected package libtiff6:s390x. 185s Preparing to unpack .../49-libtiff6_4.7.0-3ubuntu3_s390x.deb ... 185s Unpacking libtiff6:s390x (4.7.0-3ubuntu3) ... 185s Selecting previously unselected package libxpm4:s390x. 185s Preparing to unpack .../50-libxpm4_1%3a3.5.17-1build3_s390x.deb ... 185s Unpacking libxpm4:s390x (1:3.5.17-1build3) ... 185s Selecting previously unselected package libgd3:s390x. 185s Preparing to unpack .../51-libgd3_2.3.3-13ubuntu1_s390x.deb ... 185s Unpacking libgd3:s390x (2.3.3-13ubuntu1) ... 185s Selecting previously unselected package libgvplugin-gd8:s390x. 185s Preparing to unpack .../52-libgvplugin-gd8_14.1.1-2ubuntu2_s390x.deb ... 185s Unpacking libgvplugin-gd8:s390x (14.1.1-2ubuntu2) ... 185s Selecting previously unselected package fontconfig. 185s Preparing to unpack .../53-fontconfig_2.17.1-3ubuntu1_s390x.deb ... 185s Unpacking fontconfig (2.17.1-3ubuntu1) ... 185s Selecting previously unselected package libgraphite2-3:s390x. 185s Preparing to unpack .../54-libgraphite2-3_1.3.14-11ubuntu1_s390x.deb ... 185s Unpacking libgraphite2-3:s390x (1.3.14-11ubuntu1) ... 185s Selecting previously unselected package libharfbuzz0b:s390x. 185s Preparing to unpack .../55-libharfbuzz0b_12.3.1-1_s390x.deb ... 185s Unpacking libharfbuzz0b:s390x (12.3.1-1) ... 185s Selecting previously unselected package libthai-data. 185s Preparing to unpack .../56-libthai-data_0.1.30-1_all.deb ... 185s Unpacking libthai-data (0.1.30-1) ... 185s Selecting previously unselected package libdatrie1:s390x. 185s Preparing to unpack .../57-libdatrie1_0.2.14-1_s390x.deb ... 185s Unpacking libdatrie1:s390x (0.2.14-1) ... 185s Selecting previously unselected package libthai0:s390x. 185s Preparing to unpack .../58-libthai0_0.1.30-1_s390x.deb ... 185s Unpacking libthai0:s390x (0.1.30-1) ... 185s Selecting previously unselected package libpango-1.0-0:s390x. 185s Preparing to unpack .../59-libpango-1.0-0_1.57.0-1_s390x.deb ... 185s Unpacking libpango-1.0-0:s390x (1.57.0-1) ... 185s Selecting previously unselected package libpangoft2-1.0-0:s390x. 185s Preparing to unpack .../60-libpangoft2-1.0-0_1.57.0-1_s390x.deb ... 185s Unpacking libpangoft2-1.0-0:s390x (1.57.0-1) ... 185s Selecting previously unselected package libpangocairo-1.0-0:s390x. 185s Preparing to unpack .../61-libpangocairo-1.0-0_1.57.0-1_s390x.deb ... 185s Unpacking libpangocairo-1.0-0:s390x (1.57.0-1) ... 185s Selecting previously unselected package libgvplugin-pango8:s390x. 185s Preparing to unpack .../62-libgvplugin-pango8_14.1.1-2ubuntu2_s390x.deb ... 185s Unpacking libgvplugin-pango8:s390x (14.1.1-2ubuntu2) ... 185s Selecting previously unselected package graphviz. 185s Preparing to unpack .../63-graphviz_14.1.1-2ubuntu2_s390x.deb ... 185s Unpacking graphviz (14.1.1-2ubuntu2) ... 185s Selecting previously unselected package python3-pydot. 185s Preparing to unpack .../64-python3-pydot_4.0.1-1_all.deb ... 185s Unpacking python3-pydot (4.0.1-1) ... 186s Selecting previously unselected package python3-prov. 186s Preparing to unpack .../65-python3-prov_2.1.1-1_all.deb ... 186s Unpacking python3-prov (2.1.1-1) ... 186s Selecting previously unselected package python3-psutil. 186s Preparing to unpack .../66-python3-psutil_7.1.0-1ubuntu1_s390x.deb ... 186s Unpacking python3-psutil (7.1.0-1ubuntu1) ... 186s Selecting previously unselected package python3-rich-argparse. 186s Preparing to unpack .../67-python3-rich-argparse_1.6.0-2_all.deb ... 186s Unpacking python3-rich-argparse (1.6.0-2) ... 186s Selecting previously unselected package python3-spython. 186s Preparing to unpack .../68-python3-spython_0.3.13-2build1_all.deb ... 186s Unpacking python3-spython (0.3.13-2build1) ... 186s Selecting previously unselected package python3-arcp. 186s Preparing to unpack .../69-python3-arcp_0.2.1-7build1_all.deb ... 186s Unpacking python3-arcp (0.2.1-7build1) ... 186s Selecting previously unselected package cwltool. 186s Preparing to unpack .../70-cwltool_3.1.20251031082601-1_all.deb ... 186s Unpacking cwltool (3.1.20251031082601-1) ... 186s Selecting previously unselected package python3-wcwidth. 186s Preparing to unpack .../71-python3-wcwidth_0.2.14+dfsg1-1build1_all.deb ... 186s Unpacking python3-wcwidth (0.2.14+dfsg1-1build1) ... 186s Selecting previously unselected package python3-blessed. 186s Preparing to unpack .../72-python3-blessed_1.21.0-1_all.deb ... 186s Unpacking python3-blessed (1.21.0-1) ... 186s Selecting previously unselected package python3-configargparse. 186s Preparing to unpack .../73-python3-configargparse_1.7-2_all.deb ... 186s Unpacking python3-configargparse (1.7-2) ... 186s Selecting previously unselected package python3-dill. 186s Preparing to unpack .../74-python3-dill_0.4.0-1_all.deb ... 186s Unpacking python3-dill (0.4.0-1) ... 186s Selecting previously unselected package python3-docker. 186s Preparing to unpack .../75-python3-docker_7.1.0-2ubuntu1_all.deb ... 186s Unpacking python3-docker (7.1.0-2ubuntu1) ... 186s Selecting previously unselected package python3-prefixed. 186s Preparing to unpack .../76-python3-prefixed_0.7.0-1build1_all.deb ... 186s Unpacking python3-prefixed (0.7.0-1build1) ... 186s Selecting previously unselected package python3-enlighten. 186s Preparing to unpack .../77-python3-enlighten_1.11.2-1build1_s390x.deb ... 186s Unpacking python3-enlighten (1.11.2-1build1) ... 186s Selecting previously unselected package python3-prompt-toolkit. 186s Preparing to unpack .../78-python3-prompt-toolkit_3.0.52-2_all.deb ... 186s Unpacking python3-prompt-toolkit (3.0.52-2) ... 186s Selecting previously unselected package python3-pubsub. 186s Preparing to unpack .../79-python3-pubsub_4.0.3-7build1_all.deb ... 186s Unpacking python3-pubsub (4.0.3-7build1) ... 186s Selecting previously unselected package toil. 186s Preparing to unpack .../80-toil_9.1.0-1_all.deb ... 186s Unpacking toil (9.1.0-1) ... 186s Setting up libxdot4:s390x (14.1.1-2ubuntu2) ... 186s Setting up libgraphite2-3:s390x (1.3.14-11ubuntu1) ... 186s Setting up python3-configargparse (1.7-2) ... 186s Setting up python3-arcp (0.2.1-7build1) ... 186s Setting up libcdt6:s390x (14.1.1-2ubuntu2) ... 186s Setting up libpixman-1-0:s390x (0.46.4-1) ... 186s Setting up libsharpyuv0:s390x (1.5.0-0.1build1) ... 186s Setting up libaom3:s390x (3.13.1-2) ... 186s Setting up python3-filelock (3.20.3-1) ... 186s Setting up libxpm4:s390x (1:3.5.17-1build3) ... 186s Setting up libxrender1:s390x (1:0.9.12-1) ... 186s Setting up libdatrie1:s390x (0.2.14-1) ... 186s Setting up libxcb-render0:s390x (1.17.0-2ubuntu1) ... 186s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 186s Setting up python3-mypy-extensions (1.1.0-1) ... 186s Setting up python3-docker (7.1.0-2ubuntu1) ... 187s Setting up python3-ruamel.yaml.clib (0.2.15+ds-1) ... 187s Setting up libdeflate0:s390x (1.23-2) ... 187s Setting up libxcb-shm0:s390x (1.17.0-2ubuntu1) ... 187s Setting up libgomp1:s390x (15.2.0-12ubuntu1) ... 187s Setting up python3-networkx (3.2.1-4ubuntu2) ... 188s Setting up libjbig0:s390x (2.1-6.1ubuntu3) ... 188s Setting up python3-psutil (7.1.0-1ubuntu1) ... 189s Setting up python3-prefixed (0.7.0-1build1) ... 189s Setting up python3-wcwidth (0.2.14+dfsg1-1build1) ... 189s Setting up python3-humanfriendly (10.0-6build1) ... 189s Setting up libfreetype6:s390x (2.14.1+dfsg-2) ... 189s Setting up python3-spython (0.3.13-2build1) ... 190s Setting up libpathplan4:s390x (14.1.1-2ubuntu2) ... 190s Setting up python3-dill (0.4.0-1) ... 190s Setting up libimagequant0:s390x (2.18.0-1build1) ... 190s Setting up fonts-dejavu-mono (2.37-8build1) ... 190s Setting up fonts-dejavu-core (2.37-8build1) ... 190s Setting up libjpeg-turbo8:s390x (2.1.5-4ubuntu2) ... 190s Setting up libltdl7:s390x (2.5.4-9) ... 190s Setting up libcgraph8:s390x (14.1.1-2ubuntu2) ... 190s Setting up libwebp7:s390x (1.5.0-0.1build1) ... 190s Setting up python3-ruamel.yaml (0.18.10+ds-1build1) ... 190s Setting up python3-pubsub (4.0.3-7build1) ... 191s Setting up libgvpr2:s390x (14.1.1-2ubuntu2) ... 191s Setting up python3-rich-argparse (1.6.0-2) ... 191s Setting up python3-rdflib (7.4.0-1) ... 192s Setting up libxslt1.1:s390x (1.1.43-0.3) ... 192s Setting up libharfbuzz0b:s390x (12.3.1-1) ... 192s Setting up libthai-data (0.1.30-1) ... 192s Setting up python3-msgpack (1.1.2-1) ... 192s Setting up python3-cachecontrol (0.14.3-1) ... 192s Setting up libde265-0:s390x (1.0.16-1build1) ... 192s Setting up python3-argcomplete (3.6.3-1) ... 192s Setting up python3-coloredlogs (15.0.1-1build1) ... 193s Setting up python3-mistune (3.1.4-1) ... 193s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 193s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 193s Setting up python3-prompt-toolkit (3.0.52-2) ... 193s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 194s Setting up python3-blessed (1.21.0-1) ... 194s Setting up python3-schema-salad (8.9.20251102115403-1) ... 194s Setting up libthai0:s390x (0.1.30-1) ... 194s Setting up python3-enlighten (1.11.2-1build1) ... 194s Setting up cwl-upgrader (1.2.14-1) ... 195s Setting up libgvc7:s390x (14.1.1-2ubuntu2) ... 195s Setting up python3-lxml:s390x (6.0.2-1) ... 195s Setting up libtiff6:s390x (4.7.0-3ubuntu3) ... 195s Setting up libfontconfig1:s390x (2.17.1-3ubuntu1) ... 195s Setting up fontconfig (2.17.1-3ubuntu1) ... 197s Regenerating fonts cache... done. 197s Setting up libpango-1.0-0:s390x (1.57.0-1) ... 197s Setting up python3-cwl-utils (0.40-1) ... 201s Setting up libcairo2:s390x (1.18.4-3) ... 201s Setting up libpangoft2-1.0-0:s390x (1.57.0-1) ... 201s Setting up libpangocairo-1.0-0:s390x (1.57.0-1) ... 201s Setting up libgvplugin-pango8:s390x (14.1.1-2ubuntu2) ... 201s Setting up libheif-plugin-aomdec:s390x (1.21.2-1) ... 201s Setting up libheif-plugin-libde265:s390x (1.21.2-1) ... 201s Setting up libheif1:s390x (1.21.2-1) ... 201s Setting up libgd3:s390x (2.3.3-13ubuntu1) ... 201s Setting up libgvplugin-gd8:s390x (14.1.1-2ubuntu2) ... 201s Setting up graphviz (14.1.1-2ubuntu2) ... 201s Setting up python3-pydot (4.0.1-1) ... 202s Setting up python3-prov (2.1.1-1) ... 202s Setting up cwltool (3.1.20251031082601-1) ... 202s Setting up toil (9.1.0-1) ... 203s Processing triggers for libc-bin (2.42-2ubuntu4) ... 203s Processing triggers for man-db (2.13.1-1) ... 205s autopkgtest [06:58:19]: test smoke-test: [----------------------- 205s Usage: toil COMMAND ... 205s toil --help 205s toil COMMAND --help 205s 205s Where COMMAND is one of the following: 205s 205s clean - Delete a job store used by a previous Toil workflow invocation. 205s config - Create a config file with all default Toil options. 205s debug-file - Debug tool for copying files contained in a toil jobStore. 205s debug-job - Debug tool for running a toil job locally. 205s destroy-cluster - Terminates the specified cluster and associated resources. 205s kill - Kills rogue toil processes. 205s launch-cluster - Launches a toil leader instance with the specified provisioner. 205s rsync-cluster - Rsyncs into the toil appliance container running on the leader of the cluster. 205s server - CLI entry for the Toil servers. 205s ssh-cluster - SSH into the toil appliance container running on the leader of the cluster. 205s stats - Reports statistical data about a given Toil workflow. 205s status - Tool for reporting on job status. 205s 206s 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: 206s 206s pip install cwltool==3.1.20250110105449 206s 206s usage: toil-cwl-runner [options] WORKFLOW [INFILE] [WF_OPTIONS...] 206s 206s positional arguments: 206s 206s WORKFLOW CWL file to run. 206s 206s INFILE YAML or JSON file of workflow inputs. 206s 206s WF_OPTIONS Additional inputs to the workflow as command-line 206s flags. If CWL workflow takes an input, the name of the 206s input can be used as an option. For example: 206s 206s toil-cwl-runner workflow.cwl --file1 file 206s 206s If an input has the same name as a Toil option, pass 206s '--' before it. 206s 206s options: 206s -h, --help show this help message and exit 206s --not-strict 206s --enable-dev Enable loading and running development versions of CWL 206s --enable-ext Enable loading and running 'cwltool:' extensions to 206s the CWL standards. 206s --quiet 206s --basedir BASEDIR 206s --outdir OUTDIR 206s --version show program's version number and exit 206s --log-dir LOG_DIR Log your tools stdout/stderr to this location outside 206s of container 206s --user-space-docker-cmd USER_SPACE_DOCKER_CMD 206s (Linux/OS X only) Specify a user space docker command 206s (like udocker or dx-docker) that will be used to call 206s 'pull' and 'run' 206s --singularity Use Singularity runtime for running containers. 206s Requires Singularity v2.6.1+ and Linux with kernel 206s version v3.18+ or with overlayfs support backported. 206s --podman Use Podman runtime for running containers. 206s --no-container Do not execute jobs in a Docker container, even when 206s `DockerRequirement` is specified under `hints`. 206s --leave-container Do not delete Docker container used by jobs after they 206s exit 206s --custom-net CUSTOM_NET 206s Specify docker network name to pass to docker run 206s command 206s --no-prepull Do not prepull the container prior to running the 206s workflow 206s --preserve-environment VAR1 VAR2 [VAR1 VAR2 ...] 206s Preserve specified environment variables when running 206s CommandLineTools 206s --preserve-entire-environment 206s Preserve all environment variable when running 206s CommandLineTools. 206s --beta-dependency-resolvers-configuration BETA_DEPENDENCY_RESOLVERS_CONFIGURATION 206s --beta-dependencies-directory BETA_DEPENDENCIES_DIRECTORY 206s --beta-use-biocontainers 206s --beta-conda-dependencies 206s --tmpdir-prefix TMPDIR_PREFIX 206s Path prefix for temporary directories 206s --tmp-outdir-prefix TMP_OUTDIR_PREFIX 206s Path prefix for intermediate output directories 206s --force-docker-pull Pull latest docker image even if it is locally present 206s --no-match-user Disable passing the current uid to `docker run --user` 206s --no-read-only Do not set root directory in the container as read- 206s only 206s --strict-memory-limit 206s When running with software containers and the Docker 206s engine, pass either the calculated memory allocation 206s from ResourceRequirements or the default of 1 gigabyte 206s to Docker's --memory option. 206s --strict-cpu-limit When running with software containers and the Docker 206s engine, pass either the calculated cpu allocation from 206s ResourceRequirements or the default of 1 core to 206s Docker's --cpu option. Requires docker version >= 206s v1.13. 206s --relax-path-checks Relax requirements on path names to permit spaces and 206s hash characters. 206s --default-container DEFAULT_CONTAINER 206s Specify a default docker container that will be used 206s if the workflow fails to specify one. 206s --compute-checksum Compute checksum of contents while collecting outputs 206s --no-compute-checksum 206s Do not compute checksum of contents while collecting 206s outputs 206s --eval-timeout EVAL_TIMEOUT 206s Time to wait for a Javascript expression to evaluate 206s before giving an error, default 20s. 206s --overrides OVERRIDES 206s Read process requirement overrides from file. 206s --mpi-config-file MPI_CONFIG_FILE 206s Platform specific configuration for MPI (parallel 206s launcher, its flag etc). See the cwltool README 206s section 'Running MPI-based tools' for details of the 206s format: https://github.com/common-workflow- 206s language/cwltool#running-mpi-based-tools-that-need-to- 206s be-launched 206s --bypass-file-store Do not use Toil's file store and assume all paths are 206s accessible in place from all nodes. 206s --reference-inputs Do not copy remote inputs into Toil's file store and 206s assume they are accessible in place from all nodes. 206s --disable-streaming Disable file streaming for files that have 206s 'streamable' flag True. 206s --cwl-default-ram Apply CWL specification default ramMin. 206s --no-cwl-default-ram Do not apply CWL specification default ramMin, so that 206s Toil --defaultMemory applies. This can help jobs get 206s to Slurm with no memory limit assigned. 206s --cwl-min-ram CWL_MIN_RAM 206s Specify a minimum memory allocation for all tasks .If 206s --no-cwl-default-ram is passed, this does not apply to 206s tools that do not specify a memory requirement; 206s --defaultMemory is used for those toolsin that case. 206s --destBucket DESTBUCKET 206s Specify a cloud bucket endpoint for output files. 206s --cachedir CACHEDIR Directory to cache intermediate workflow outputs to 206s avoid recomputing steps. Can be very helpful in the 206s development and troubleshooting of CWL documents. This 206s automatically bypasses the file store. Not to be 206s confused with --caching. 206s --runImportsOnWorkers, --run-imports-on-workers 206s Run the file imports on a worker instead of the 206s leader. This is useful if the leader is not optimized 206s for high network performance. If set to true, the 206s argument --importWorkersDisk must also be set. 206s --importWorkersBatchSize, --import-workers-batch-size IMPORT_WORKERS_BATCHSIZE 206s Specify the target total file size for file import 206s batches. As many files as can fit will go into each 206s batch import job. This should be set in conjunction 206s with the argument --runImportsOnWorkers. 206s --importWorkersDisk, --import-workers-disk IMPORT_WORKERS_DISK 206s Specify the disk size each import worker will get. 206s This usually will not need to be set as Toil will 206s attempt to use file streaming when downloading files. 206s If not possible, for example, when downloading from 206s AWS to a GCE job store, this should be set to the 206s largest file size of all files to import. This should 206s be set in conjunction with the arguments 206s --runImportsOnWorkers and --importWorkersBatchSize. 206s 206s --config PATH Get options from a config file. 206s 206s Logging Options: 206s --logCritical Set logging level to Critical. Default: INFO. 206s --logError Set logging level to Error. Default: INFO. 206s --logWarning Set logging level to Warning. Default: INFO. 206s --logInfo Set logging level to Info. Default: INFO. 206s --logDebug Set logging level to Debug. Default: INFO. 206s --logTrace Set logging level to Trace. Default: INFO. 206s --logOff Same as --logCritical. 206s --logLevel {Critical,Error,Warning,Info,Debug,Trace,critical,error,warning,info,debug,trace,CRITICAL,ERROR,WARNING,INFO,DEBUG,TRACE} 206s Set the log level. Default: INFO. Options: 206s ['Critical', 'Error', 'Warning', 'Info', 'Debug', 206s 'Trace', 'critical', 'error', 'warning', 'info', 206s 'debug', 'trace', 'CRITICAL', 'ERROR', 'WARNING', 206s 'INFO', 'DEBUG', 'TRACE']. 206s --logFile LOGFILE File to log in. 206s --rotatingLogging Turn on rotating logging, which prevents log files 206s from getting too big. 206s --logColors BOOL Enable or disable colored logging. Default: True 206s 206s Toil core options: 206s Options to specify the location of the Toil workflow and turn on stats collation about the performance of jobs. 206s 206s --jobstore, --jobStore JOBSTORE 206s The location of the job store for the workflow. A job 206s store holds persistent information about the jobs, 206s stats, and files in a workflow. If the workflow is run 206s with a distributed batch system, the job store must be 206s accessible by all worker nodes. Depending on the 206s desired job store implementation, the location should 206s be formatted according to one of the following 206s schemes: file: where points to a 206s directory on the file system aws:: 206s where is the name of an AWS region like us- 206s west-2 and will be prepended to the names of 206s any top-level AWS resources in use by job store, e.g. 206s S3 buckets. google:: TODO: explain 206s For backwards compatibility, you may also specify 206s ./foo (equivalent to file:./foo or just file:foo) or 206s /bar (equivalent to file:/bar). 206s --workDir PATH Absolute path to directory where temporary files 206s generated during the Toil run should be placed. 206s Standard output and error from batch system jobs 206s (unless --noStdOutErr is set) will be placed in this 206s directory. A cache directory may be placed in this 206s directory. Temp files and folders will be placed in a 206s directory toil- within workDir. The 206s workflowID is generated by Toil and will be reported 206s in the workflow logs. Default is determined by the 206s variables (TMPDIR, TEMP, TMP) via mkdtemp. This 206s directory needs to exist on all machines running jobs; 206s if capturing standard output and error from batch 206s system jobs is desired, it will generally need to be 206s on a shared file system. When sharing a cache between 206s containers on a host, this directory must be shared 206s between the containers. [env var: TOIL_WORKDIR] 206s --coordinationDir PATH 206s Absolute path to directory where Toil will keep state 206s and lock files. When sharing a cache between 206s containers on a host, this directory must be shared 206s between the containers. [env var: 206s TOIL_COORDINATION_DIR] 206s --noStdOutErr Do not capture standard output and error from batch 206s system jobs. 206s --stats Keep statistics about the toil workflow to be used by 206s 'toil stats'. 206s --clean {always,onError,never,onSuccess} 206s Determines the deletion of the jobStore upon 206s completion of the program. Choices: ['always', 206s 'onError', 'never', 'onSuccess']. The --stats option 206s requires information from the jobStore upon completion 206s so the jobStore will never be deleted with that flag. 206s If you wish to be able to restart the run, choose 206s 'never' or 'onSuccess'. Default is 'never' if stats is 206s enabled, and 'onSuccess' otherwise. 206s --cleanWorkDir {always,onError,never,onSuccess} 206s Determines deletion of temporary worker directory upon 206s completion of a job. Choices: ['always', 'onError', 206s 'never', 'onSuccess']. Default = always. WARNING: This 206s option should be changed for debugging only. Running a 206s full pipeline with this option could fill your disk 206s with excessive intermediate data. 206s --clusterStats [OPT_PATH] 206s If enabled, writes out JSON resource usage statistics 206s to a file. The default location for this file is the 206s current working directory, but an absolute path can 206s also be passed to specify where this file should be 206s written. This options only applies when using scalable 206s batch systems. 206s 206s Toil options for restarting an existing workflow: 206s Allows the restart of an existing workflow 206s 206s --restart If --restart is specified then will attempt to restart 206s existing workflow at the location pointed to by the 206s --jobStore option. Will raise an exception if the 206s workflow does not exist 206s 206s Toil options for specifying the batch system: 206s Allows the specification of the batch system. 206s 206s --batchSystem {aws_batch,single_machine,grid_engine,lsf,mesos,slurm,torque,htcondor,kubernetes} 206s The type of batch system to run the job(s) with, 206s currently can be one of aws_batch, single_machine, 206s grid_engine, lsf, mesos, slurm, torque, htcondor, 206s kubernetes. Default = single_machine 206s --disableHotDeployment 206s Hot-deployment was renamed to auto-deployment. Option 206s now redirects to --disableAutoDeployment. Left in for 206s backwards compatibility. 206s --disableAutoDeployment DISABLEAUTODEPLOYMENT 206s Should auto-deployment of Toil Python workflows be 206s deactivated? If True, the workflow's Python code 206s should be present at the same location on all workers. 206s Default = False. 206s --maxJobs MAX_JOBS Specifies the maximum number of jobs to submit to the 206s backing scheduler at once. Not supported on Mesos or 206s AWS Batch. Use 0 for unlimited. Defaults to unlimited. 206s --maxLocalJobs MAX_LOCAL_JOBS 206s Specifies the maximum number of housekeeping jobs to 206s run sumultaneously on the local system. Use 0 for 206s unlimited. Defaults to the number of local cores (4). 206s --manualMemArgs Do not add the default arguments: 'hv=MEMORY' & 206s 'h_vmem=MEMORY' to the qsub call, and instead rely on 206s TOIL_GRIDGENGINE_ARGS to supply alternative arguments. 206s Requires that TOIL_GRIDGENGINE_ARGS be set. 206s --runLocalJobsOnWorkers, --runCwlInternalJobsOnWorkers 206s Whether to run jobs marked as local (e.g. CWLScatter) 206s on the worker nodes instead of the leader node. If 206s false (default), then all such jobs are run on the 206s leader node. Setting this to true can speed up CWL 206s pipelines for very large workflows with many sub- 206s workflows and/or scatters, provided that the worker 206s pool is large enough. 206s --coalesceStatusCalls 206s Ask for job statuses from the batch system in a batch. 206s Deprecated; now always enabled where supported. 206s --statePollingWait STATEPOLLINGWAIT 206s Time, in seconds, to wait before doing a scheduler 206s query for job state. Return cached results if within 206s the waiting period. Only works for grid engine batch 206s systems such as gridengine, htcondor, torque, slurm, 206s and lsf. 206s --statePollingTimeout STATE_POLLING_TIMEOUT 206s Time, in seconds, to retry against a broken scheduler. 206s Only works for grid engine batch systems such as 206s gridengine, htcondor, torque, slurm, and lsf. 206s --batchLogsDir BATCH_LOGS_DIR 206s Directory to tell the backing batch system to log 206s into. Should be available on both the leader and the 206s workers, if the backing batch system writes logs to 206s the worker machines' filesystems, as many HPC 206s schedulers do. If unset, the Toil work directory will 206s be used. Only works for grid engine batch systems such 206s as gridengine, htcondor, torque, slurm, and lsf. [env 206s var: TOIL_BATCH_LOGS_DIR] 206s --memoryIsProduct If the batch system understands requested memory as a 206s product of the requested memory and the numberof 206s cores, set this flag to properly allocate memory. 206s --awsBatchRegion AWS_BATCH_REGION 206s The AWS region containing the AWS Batch queue to 206s submit to. [env var: TOIL_AWS_REGION] 206s --awsBatchQueue AWS_BATCH_QUEUE 206s The name or ARN of the AWS Batch queue to submit to. 206s [env var: TOIL_AWS_BATCH_QUEUE] 206s --awsBatchJobRoleArn AWS_BATCH_JOB_ROLE_ARN 206s The ARN of an IAM role to run AWS Batch jobs as, so 206s they can e.g. access a job store. Must be assumable by 206s ecs-tasks.amazonaws.com. [env var: 206s TOIL_AWS_BATCH_JOB_ROLE_ARN] 206s --scale SCALE A scaling factor to change the value of all submitted 206s tasks's submitted cores. Used in the single_machine 206s batch system. Useful for running workflows on smaller 206s machines than they were designed for, by setting a 206s value less than 1. (default: 1) 206s --slurmAllocateMem SLURM_ALLOCATE_MEM 206s If False, do not use --mem. Used as a workaround for 206s Slurm clusters that reject jobs with memory 206s allocations. [env var: TOIL_SLURM_ALLOCATE_MEM] 206s --slurmDefaultAllMem SLURM_DEFAULT_ALL_MEM 206s If True, assign Toil jobs without their own memory 206s requirements all available memory on a Slurm node (via 206s Slurm --mem=0). [env var: TOIL_SLURM_DEFAULT_ALL_MEM] 206s --slurmTime SLURM_TIME 206s Slurm job time limit, in [DD-]HH:MM:SS format. [env 206s var: TOIL_SLURM_TIME] 206s --slurmPartition SLURM_PARTITION 206s Partition to send Slurm jobs to. [env var: 206s TOIL_SLURM_PARTITION] 206s --slurmGPUPartition SLURM_GPU_PARTITION 206s Partition to send Slurm jobs to if they ask for GPUs. 206s [env var: TOIL_SLURM_GPU_PARTITION] 206s --slurmPE SLURM_PE Special partition to send Slurm jobs to if they ask 206s for more than 1 CPU. [env var: TOIL_SLURM_PE] 206s --slurmArgs SLURM_ARGS 206s Extra arguments to pass to Slurm. [env var: 206s TOIL_SLURM_ARGS] 206s 206s Toil options for configuring storage: 206s Allows configuring Toil's data storage. 206s 206s --symlinkImports BOOL 206s When using a filesystem based job store, CWL input 206s files are by default symlinked in. Setting this option 206s to True instead copies the files into the job store, 206s which may protect them from being modified externally. 206s When set to False, as long as caching is enabled, Toil 206s will protect the file automatically by changing the 206s permissions to read-only. default=True 206s --moveOutputs BOOL When using a filesystem based job store, output files 206s are by default moved to the output directory, and a 206s symlink to the moved exported file is created at the 206s initial location. Setting this option to True instead 206s copies the files into the output directory. Applies to 206s filesystem-based job stores only. default=False 206s --caching BOOL Enable or disable worker level file caching for your 206s workflow, specifying this overrides default from batch 206s system. Does not affect CWL or WDL task caching. 206s --symlinkJobStoreReads BOOL 206s Allow reads and container mounts from a JobStore's 206s shared filesystem directly via symlink. default=True 206s 206s Toil options for autoscaling the cluster of worker nodes: 206s 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. 206s 206s --provisioner, -p {aws,gce,None} 206s The provisioner for cluster auto-scaling. This is the 206s main Toil '--provisioner' option, and defaults to None 206s for running on single machine and non-auto-scaling 206s batch systems. The currently supported choices are 206s ['aws', 'gce', None]. The default is None. 206s --nodeTypes NODETYPES 206s Specifies a list of comma-separated node types, each 206s of which is composed of slash-separated instance 206s types, and an optional spot bid set off by a colon, 206s making the node type preemptible. Instance types may 206s appear in multiple node types, and the same node type 206s may appear as both preemptible and non-preemptible. 206s Valid argument specifying two node types: 206s c5.4xlarge/c5a.4xlarge:0.42,t2.large Node types: 206s c5.4xlarge/c5a.4xlarge:0.42 and t2.large Instance 206s types: c5.4xlarge, c5a.4xlarge, and t2.large 206s Semantics: Bid $0.42/hour for either c5.4xlarge or 206s c5a.4xlarge instances, treated interchangeably, while 206s they are available at that price, and buy t2.large 206s instances at full price. default=[] 206s --maxNodes INT[,INT...] 206s Maximum number of nodes of each type in the cluster, 206s if using autoscaling, provided as a comma-separated 206s list. The first value is used as a default if the list 206s length is less than the number of nodeTypes. 206s default=[10] 206s --minNodes INT[,INT...] 206s Mininum number of nodes of each type in the cluster, 206s if using auto-scaling. This should be provided as a 206s comma-separated list of the same length as the list of 206s node types. default=[0] 206s --targetTime INT Sets how rapidly you aim to complete jobs in seconds. 206s Shorter times mean more aggressive parallelization. 206s The autoscaler attempts to scale up/down so that it 206s expects all queued jobs will complete within 206s targetTime seconds. default=1800 206s --betaInertia FLOAT A smoothing parameter to prevent unnecessary 206s oscillations in the number of provisioned nodes. This 206s controls an exponentially weighted moving average of 206s the estimated number of nodes. A value of 0.0 disables 206s any smoothing, and a value of 0.9 will smooth so much 206s that few changes will ever be made. Must be between 206s 0.0 and 0.9. default=0.1 206s --scaleInterval INT The interval (seconds) between assessing if the scale 206s of the cluster needs to change. default=60 206s --preemptibleCompensation, --preemptableCompensation FLOAT 206s The preference of the autoscaler to replace 206s preemptible nodes with non-preemptible nodes, when 206s preemptible nodes cannot be started for some reason. 206s This value must be between 0.0 and 1.0, inclusive. A 206s value of 0.0 disables such compensation, a value of 206s 0.5 compensates two missing preemptible nodes with a 206s non-preemptible one. A value of 1.0 replaces every 206s missing pre-emptable node with a non-preemptible one. 206s default=0.0 206s --nodeStorage INT Specify the size of the root volume of worker nodes 206s when they are launched in gigabytes. You may want to 206s set this if your jobs require a lot of disk space. 206s (default=50). 206s --nodeStorageOverrides NODETYPE:NODESTORAGE[,NODETYPE:NODESTORAGE...] 206s Comma-separated list of nodeType:nodeStorage that are 206s used to override the default value from --nodeStorage 206s for the specified nodeType(s). This is useful for 206s heterogeneous jobs where some tasks require much more 206s disk than others. 206s --metrics BOOL Enable the prometheus/grafana dashboard for monitoring 206s CPU/RAM usage, queue size, and issued jobs. 206s --assumeZeroOverhead BOOL 206s Ignore scheduler and OS overhead and assume jobs can 206s use every last byte of memory and disk on a node when 206s autoscaling. 206s 206s Toil options for cores/memory requirements: 206s 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. 206s 206s --defaultMemory DEFAULTMEMORY 206s The default amount of memory to request for a job. 206s Only applicable to jobs that do not specify an 206s explicit value for this requirement. Standard suffixes 206s like K, Ki, M, Mi, G or Gi are supported. Default is 206s 2.0 Gi. 206s --defaultCores FLOAT The default amount of cpu to request for a job. Only 206s applicable to jobs that do not specify an explicit 206s value for this requirement. Fractions of a core (for 206s example 0.1) are supported on some batch systems 206s [mesos, single_machine]. Default is 1. 206s --defaultDisk INT The default amount of disk to request for a job. Only 206s applicable to jobs that do not specify an explicit 206s value for this requirement. Standard suffixes like K, 206s Ki, M, Mi, G or Gi are supported. Default is 2.0 Gi. 206s --defaultAccelerators ACCELERATOR[,ACCELERATOR...] 206s The default amount of accelerators to request for a 206s job. Only applicable to jobs that do not specify an 206s explicit value for this requirement. Each accelerator 206s specification can have a type (gpu [default], nvidia, 206s amd, cuda, rocm, opencl, or a specific model like 206s nvidia-tesla-k80), and a count [default: 1]. If both a 206s type and a count are used, they must be separated by a 206s colon. If multiple types of accelerators are used, the 206s specifications are separated by commas. Default is []. 206s --defaultPreemptible, --defaultPreemptable [BOOL] 206s Make all jobs able to run on preemptible (spot) nodes 206s by default. 206s --maxCores INT The max amount of cpu to request for a job. Only 206s applicable to jobs that do not specify an explicit 206s value for this requirement. Fractions of a core (for 206s example 0.1) are supported on some batch systems 206s [mesos, single_machine]. Default is 206s 9223372036854775807. 206s --maxMemory INT The max amount of memory to request for a job. Only 206s applicable to jobs that do not specify an explicit 206s value for this requirement. Standard suffixes like K, 206s Ki, M, Mi, G or Gi are supported. Default is 8.0 Ei. 206s --maxDisk INT The max amount of disk to request for a job. Only 206s applicable to jobs that do not specify an explicit 206s value for this requirement. Standard suffixes like K, 206s Ki, M, Mi, G or Gi are supported. Default is 8.0 Ei. 206s 206s Toil options for rescuing/killing/restarting jobs: 206s The options for jobs that either run too long/fail or get lost (some batch systems have issues!). 206s 206s --retryCount INT Number of times to retry a failing job before giving 206s up and labeling job failed. default=1 206s --stopOnFirstFailure BOOL 206s Stop the workflow at the first complete job failure. 206s --enableUnlimitedPreemptibleRetries, --enableUnlimitedPreemptableRetries BOOL 206s If set, preemptible failures (or any failure due to an 206s instance getting unexpectedly terminated) will not 206s count towards job failures and --retryCount. 206s --doubleMem BOOL If set, batch jobs which die to reaching memory limit 206s on batch schedulers will have their memory doubled and 206s they will be retried. The remaining retry count will 206s be reduced by 1. Currently supported by LSF. 206s --maxJobDuration INT Maximum runtime of a job (in seconds) before we kill 206s it (this is a lower bound, and the actual time before 206s killing the job may be longer). 206s default=9223372036854775807 206s --rescueJobsFrequency INT 206s Period of time to wait (in seconds) between checking 206s for missing/overlong jobs, that is jobs which get lost 206s by the batch system. Expert parameter. default=60 206s --jobStoreTimeout FLOAT 206s Maximum time (in seconds) to wait for a job's update 206s to the job store before declaring it failed. 206s default=30 206s 206s Toil log management options: 206s Options for how Toil should manage its logs. 206s 206s --maxLogFileSize MAXLOGFILESIZE 206s The maximum size of a job log file to keep (in bytes), 206s log files larger than this will be truncated to the 206s last X bytes. Setting this option to zero will prevent 206s any truncation. Setting this option to a negative 206s value will truncate from the beginning. Default=100.0 206s Mi 206s --writeLogs [OPT_PATH] 206s Write worker logs received by the leader into their 206s own files at the specified path. Any non-empty 206s standard output and error from failed batch system 206s jobs will also be written into files at this path. The 206s current working directory will be used if a path is 206s not specified explicitly. Note: By default only the 206s logs of failed jobs are returned to leader. Set log 206s level to 'debug' or enable '--writeLogsFromAllJobs' to 206s get logs back from successful jobs, and adjust 206s 'maxLogFileSize' to control the truncation limit for 206s worker logs. 206s --writeLogsGzip [OPT_PATH] 206s Identical to --writeLogs except the logs files are 206s gzipped on the leader. 206s --writeLogsFromAllJobs BOOL 206s Whether to write logs from all jobs (including the 206s successful ones) without necessarily setting the log 206s level to 'debug'. Ensure that either --writeLogs or 206s --writeLogsGzip is set if enabling this option. 206s --writeMessages PATH File to send messages from the leader's message bus 206s to. 206s --realTimeLogging BOOL 206s Enable real-time logging from workers to leader 206s 206s Toil miscellaneous options: 206s Everything else. 206s 206s --disableChaining BOOL 206s Disables chaining of jobs (chaining uses one job's 206s resource allocation for its successor job if 206s possible). 206s --disableJobStoreChecksumVerification BOOL 206s Disables checksum verification for files transferred 206s to/from the job store. Checksum verification is a 206s safety check to ensure the data is not corrupted 206s during transfer. Currently only supported for non- 206s streaming AWS files. 206s --sseKey PATH Path to file containing 32 character key to be used 206s for server-side encryption on awsJobStore or 206s googleJobStore. SSE will not be used if this flag is 206s not passed. 206s --setEnv, -e NAME=VALUE or NAME 206s Set an environment variable early on in the worker. If 206s VALUE is null, it will be looked up in the current 206s environment. Independently of this option, the worker 206s will try to emulate the leader's environment before 206s running a job, except for some variables known to vary 206s across systems. Using this option, a variable can be 206s injected into the worker process itself before it is 206s started. 206s --servicePollingInterval FLOAT 206s Interval of time service jobs wait between polling for 206s the existence of the keep-alive flag. Default: 60.0 206s --forceDockerAppliance BOOL 206s Disables sanity checking the existence of the docker 206s image specified by TOIL_APPLIANCE_SELF, which Toil 206s uses to provision mesos for autoscaling. 206s --statusWait INT Seconds to wait between reports of running jobs. 206s --disableProgress Disables the progress bar shown when standard error is 206s a terminal. 206s --publishWorkflowMetrics {all,current,no} 206s Whether to publish workflow metrics reports (including 206s unique workflow and task run IDs, job names, and 206s version and Toil feature use information) to Dockstore 206s when a workflow completes. Selecting "current" will 206s publish metrics for the current workflow. Selecting 206s "all" will also publish prior workflow runs from the 206s Toil history database, even if they themselves were 206s run with "no". Note that once published, workflow 206s metrics CANNOT be deleted or un-published; they will 206s stay published forever! 206s 206s Toil debug options: 206s Debug options for finding problems or helping with testing. 206s 206s --debugWorker Experimental no forking mode for local debugging. 206s Specifically, workers are not forked and stderr/stdout 206s are not redirected to the log. 206s --disableWorkerOutputCapture 206s Let worker output go to worker's standard out/error 206s instead of per-job logs. 206s --badWorker FLOAT For testing purposes randomly kill --badWorker 206s proportion of jobs using SIGKILL. default=0.0 206s --badWorkerFailInterval FLOAT 206s When killing the job pick uniformly within the 206s interval from 0.0 to --badWorkerFailInterval seconds 206s after the worker starts. default=0.01 206s 206s Options for recording the Docker container identifier into a file.: 206s --cidfile-dir CIDFILE_DIR 206s Store the Docker container ID into a file in the 206s specified directory. 206s --cidfile-prefix CIDFILE_PREFIX 206s Specify a prefix to the container ID filename. Final 206s file name will be followed by a timestamp. The default 206s is no prefix. 206s 206s Options for recording provenance information of the execution: 206s --provenance PROVENANCE 206s Save provenance to specified folder as a Research 206s Object that captures and aggregates workflow execution 206s and data products. 206s --enable-user-provenance 206s Record user account info as part of provenance. 206s --disable-user-provenance 206s Do not record user account info in provenance. 206s --enable-host-provenance 206s Record host info as part of provenance. 206s --disable-host-provenance 206s Do not record host info in provenance. 206s --orcid ORCID Record user ORCID identifier as part of provenance, 206s e.g. https://orcid.org/0000-0002-1825-0097 or 206s 0000-0002-1825-0097. Alternatively the environment 206s variable ORCID may be set. 206s --full-name CWL_FULL_NAME 206s Record full name of user as part of provenance, e.g. 206s Josiah Carberry. You may need to use shell quotes to 206s preserve spaces. Alternatively the environment 206s variable CWL_FULL_NAME may be set. 206s 206s Args that start with '--' can also be set in a config file 206s (/home/ubuntu/.toil/default.yaml or specified via --config). The config file 206s uses YAML syntax and must represent a YAML 'mapping' (for details, see 206s http://learn.getgrav.org/advanced/yaml). In general, command-line values 206s override environment variables which override config file values which 206s override defaults. 206s autopkgtest [06:58:20]: test smoke-test: -----------------------] 207s smoke-test PASS (superficial) 207s autopkgtest [06:58:21]: test smoke-test: - - - - - - - - - - results - - - - - - - - - - 207s autopkgtest [06:58:21]: test pybuild-autopkgtest: preparing testbed 208s Reading package lists... 208s Building dependency tree... 208s Reading state information... 208s Solving dependencies... 208s The following NEW packages will be installed: 208s autoconf automake autopoint autotools-dev build-essential containerd cpp 208s cpp-15 cpp-15-s390x-linux-gnu cpp-s390x-linux-gnu cwl-utils cwltest 208s cwltool-doc debhelper debugedit dh-autoreconf dh-python 208s dh-strip-nondeterminism docker.io docutils-common dwz fonts-font-awesome 208s fonts-lato g++ g++-15 g++-15-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-15 208s gcc-15-s390x-linux-gnu gcc-s390x-linux-gnu gettext intltool-debian 208s libarchive-zip-perl libasan8 libcc1-0 libdebhelper-perl 208s libfile-stripnondeterminism-perl libgcc-15-dev libisl23 libitm1 libjs-jquery 208s libjs-underscore libjson-perl liblsan0 libmpc3 libpython3.14-minimal 208s libpython3.14-stdlib libstdc++-15-dev libtool libtsan2 libubsan1 m4 208s po-debconf pybuild-plugin-autopkgtest pybuild-plugin-pyproject 208s python3-alabaster python3-all python3-antlr4 python3-astroid python3-build 208s python3-defusedxml python3-doc python3-docutils python3-execnet 208s python3-imagesize python3-iniconfig python3-installer python3-junit.xml 208s python3-pluggy python3-pyproject-hooks python3-pytest 208s python3-pytest-httpserver python3-pytest-timeout python3-pytest-xdist 208s python3-pytz python3-roman-numerals python3-setuptools-scm 208s python3-snowballstemmer python3-sphinx python3-sphinx-autoapi 208s python3-sphinx-autodoc-typehints python3-sphinxcontrib.autoprogram 208s python3-stubserver python3-tz python3-wdlparse python3-werkzeug 208s python3-wheel python3.13-doc python3.14 python3.14-minimal runc sgml-base 208s sphinx-common sphinx-rtd-theme-common xml-core 208s 0 upgraded, 96 newly installed, 0 to remove and 0 not upgraded. 208s Need to get 158 MB of archives. 208s After this operation, 622 MB of additional disk space will be used. 208s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-lato all 2.015-1build1 [2779 kB] 209s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-minimal s390x 3.14.2-1 [917 kB] 209s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-minimal s390x 3.14.2-1 [2510 kB] 209s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x m4 s390x 1.4.20-2 [223 kB] 209s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x autoconf all 2.72-3.1ubuntu1 [384 kB] 209s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x autotools-dev all 20240727.1 [43.4 kB] 209s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x automake all 1:1.18.1-3build1 [582 kB] 209s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x autopoint all 0.23.2-1 [620 kB] 209s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x libisl23 s390x 0.27-1build1 [702 kB] 209s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x libmpc3 s390x 1.3.1-2 [57.4 kB] 209s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15-s390x-linux-gnu s390x 15.2.0-12ubuntu1 [10.2 MB] 209s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15 s390x 15.2.0-12ubuntu1 [1028 B] 209s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [5746 B] 209s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x cpp s390x 4:15.2.0-4ubuntu1 [22.4 kB] 209s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x libcc1-0 s390x 15.2.0-12ubuntu1 [50.0 kB] 209s Get:16 http://ftpmaster.internal/ubuntu resolute/main s390x libitm1 s390x 15.2.0-12ubuntu1 [30.9 kB] 209s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x libasan8 s390x 15.2.0-12ubuntu1 [2968 kB] 209s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x liblsan0 s390x 15.2.0-12ubuntu1 [1354 kB] 209s Get:19 http://ftpmaster.internal/ubuntu resolute/main s390x libtsan2 s390x 15.2.0-12ubuntu1 [2685 kB] 209s Get:20 http://ftpmaster.internal/ubuntu resolute/main s390x libubsan1 s390x 15.2.0-12ubuntu1 [1211 kB] 209s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x libgcc-15-dev s390x 15.2.0-12ubuntu1 [1294 kB] 210s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15-s390x-linux-gnu s390x 15.2.0-12ubuntu1 [19.9 MB] 211s Get:23 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15 s390x 15.2.0-12ubuntu1 [519 kB] 211s Get:24 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [1208 B] 211s Get:25 http://ftpmaster.internal/ubuntu resolute/main s390x gcc s390x 4:15.2.0-4ubuntu1 [5018 B] 211s Get:26 http://ftpmaster.internal/ubuntu resolute/main s390x libstdc++-15-dev s390x 15.2.0-12ubuntu1 [2660 kB] 211s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x g++-15-s390x-linux-gnu s390x 15.2.0-12ubuntu1 [11.7 MB] 211s Get:28 http://ftpmaster.internal/ubuntu resolute/main s390x g++-15 s390x 15.2.0-12ubuntu1 [25.3 kB] 211s Get:29 http://ftpmaster.internal/ubuntu resolute/main s390x g++-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [956 B] 211s Get:30 http://ftpmaster.internal/ubuntu resolute/main s390x g++ s390x 4:15.2.0-4ubuntu1 [1078 B] 211s Get:31 http://ftpmaster.internal/ubuntu resolute/main s390x build-essential s390x 12.12ubuntu2 [5258 B] 211s Get:32 http://ftpmaster.internal/ubuntu resolute/main s390x runc s390x 1.4.0-0ubuntu1 [9248 kB] 212s Get:33 http://ftpmaster.internal/ubuntu resolute/main s390x containerd s390x 2.2.1-0ubuntu1 [26.1 MB] 214s Get:34 http://ftpmaster.internal/ubuntu resolute/universe s390x cwl-utils all 0.40-1 [2578 B] 214s Get:35 http://ftpmaster.internal/ubuntu resolute/main s390x python3-defusedxml all 0.7.1-3build1 [42.4 kB] 214s Get:36 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-junit.xml all 1.9-6 [9062 B] 214s Get:37 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 2.1.0-2 [6962 B] 214s Get:38 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pluggy all 1.6.0-2 [21.1 kB] 214s Get:39 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest all 9.0.2-2 [277 kB] 214s Get:40 http://ftpmaster.internal/ubuntu resolute/universe s390x cwltest all 2.6.20251216093331-1 [29.1 kB] 214s Get:41 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 214s Get:42 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 214s Get:43 http://ftpmaster.internal/ubuntu resolute/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 214s Get:44 http://ftpmaster.internal/ubuntu resolute/universe s390x cwltool-doc all 3.1.20251031082601-1 [332 kB] 214s Get:45 http://ftpmaster.internal/ubuntu resolute/main s390x libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 214s Get:46 http://ftpmaster.internal/ubuntu resolute/main s390x libtool all 2.5.4-9 [169 kB] 214s Get:47 http://ftpmaster.internal/ubuntu resolute/main s390x dh-autoreconf all 21 [12.5 kB] 214s Get:48 http://ftpmaster.internal/ubuntu resolute/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] 214s Get:49 http://ftpmaster.internal/ubuntu resolute/main s390x libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 214s Get:50 http://ftpmaster.internal/ubuntu resolute/main s390x dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 214s Get:51 http://ftpmaster.internal/ubuntu resolute/main s390x debugedit s390x 1:5.2-3 [52.8 kB] 214s Get:52 http://ftpmaster.internal/ubuntu resolute/main s390x dwz s390x 0.16-2 [121 kB] 214s Get:53 http://ftpmaster.internal/ubuntu resolute/main s390x gettext s390x 0.23.2-1 [1062 kB] 214s Get:54 http://ftpmaster.internal/ubuntu resolute/main s390x intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 214s Get:55 http://ftpmaster.internal/ubuntu resolute/main s390x po-debconf all 1.0.22 [215 kB] 214s Get:56 http://ftpmaster.internal/ubuntu resolute/main s390x debhelper all 13.28ubuntu1 [916 kB] 214s Get:57 http://ftpmaster.internal/ubuntu resolute/universe s390x dh-python all 7.20260125 [122 kB] 214s Get:58 http://ftpmaster.internal/ubuntu resolute/universe s390x docker.io s390x 29.1.3-0ubuntu1 [33.2 MB] 217s Get:59 http://ftpmaster.internal/ubuntu resolute/main s390x sgml-base all 1.31+nmu1 [11.0 kB] 217s Get:60 http://ftpmaster.internal/ubuntu resolute/main s390x xml-core all 0.19build1 [20.3 kB] 217s Get:61 http://ftpmaster.internal/ubuntu resolute/main s390x docutils-common all 0.22.4+dfsg-1 [130 kB] 217s Get:62 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-underscore all 1.13.7~dfsg+~1.13.0-1 [86.4 kB] 217s Get:63 http://ftpmaster.internal/ubuntu resolute/main s390x libjson-perl all 4.10000-1 [81.9 kB] 217s Get:64 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-stdlib s390x 3.14.2-1 [2373 kB] 217s Get:65 http://ftpmaster.internal/ubuntu resolute/universe s390x pybuild-plugin-autopkgtest all 7.20260125 [1744 B] 217s Get:66 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 217s Get:67 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-wheel all 0.46.1-2 [22.1 kB] 217s Get:68 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-build all 1.2.2-5 [30.9 kB] 217s Get:69 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 217s Get:70 http://ftpmaster.internal/ubuntu resolute/universe s390x pybuild-plugin-pyproject all 7.20260125 [1712 B] 217s Get:71 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14 s390x 3.14.2-1 [816 kB] 217s Get:72 http://ftpmaster.internal/ubuntu resolute/main s390x python3-all s390x 3.13.9-3 [890 B] 217s Get:73 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-antlr4 all 4.9.2-1build1 [99.1 kB] 217s Get:74 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-astroid all 4.0.2-1ubuntu1 [172 kB] 217s Get:75 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13-doc all 3.13.11-1 [14.3 MB] 218s Get:76 http://ftpmaster.internal/ubuntu resolute/main s390x python3-doc all 3.13.9-3 [11.1 kB] 218s Get:77 http://ftpmaster.internal/ubuntu resolute/main s390x python3-roman-numerals all 4.1.0-1 [8660 B] 218s Get:78 http://ftpmaster.internal/ubuntu resolute/main s390x python3-docutils all 0.22.4+dfsg-1 [439 kB] 218s Get:79 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-execnet all 2.1.1-1build1 [33.5 kB] 218s Get:80 http://ftpmaster.internal/ubuntu resolute/main s390x python3-imagesize all 1.4.1-1build1 [6900 B] 218s Get:81 http://ftpmaster.internal/ubuntu resolute/main s390x python3-werkzeug all 3.1.5-1 [170 kB] 218s Get:82 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest-httpserver all 1.1.3-1 [19.1 kB] 218s Get:83 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest-timeout all 2.4.0-2 [22.5 kB] 218s Get:84 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest-xdist all 3.8.0-4 [34.7 kB] 218s Get:85 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytz all 2025.2-5 [32.4 kB] 218s Get:86 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-setuptools-scm all 8.2.1-4 [32.8 kB] 218s Get:87 http://ftpmaster.internal/ubuntu resolute/main s390x python3-snowballstemmer all 3.0.1-1 [65.9 kB] 218s Get:88 http://ftpmaster.internal/ubuntu resolute/main s390x sphinx-common all 8.2.3-12 [657 kB] 218s Get:89 http://ftpmaster.internal/ubuntu resolute/main s390x python3-alabaster all 0.7.16-0.1build1 [18.6 kB] 218s Get:90 http://ftpmaster.internal/ubuntu resolute/main s390x python3-sphinx all 8.2.3-12 [483 kB] 218s Get:91 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-sphinx-autoapi all 3.6.1-1 [102 kB] 218s Get:92 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-sphinx-autodoc-typehints all 3.5.2-1 [22.7 kB] 218s Get:93 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-sphinxcontrib.autoprogram all 0.1.9-1 [9566 B] 218s Get:94 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-stubserver all 1.1-4build1 [7994 B] 218s Get:95 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-tz all 2025.2-5 [1760 B] 218s Get:96 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-wdlparse all 0.1.0-3build1 [71.0 kB] 219s Preconfiguring packages ... 219s Fetched 158 MB in 10s (15.2 MB/s) 219s Selecting previously unselected package fonts-lato. 219s (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 ... 96062 files and directories currently installed.) 219s Preparing to unpack .../00-fonts-lato_2.015-1build1_all.deb ... 219s Unpacking fonts-lato (2.015-1build1) ... 220s Selecting previously unselected package libpython3.14-minimal:s390x. 220s Preparing to unpack .../01-libpython3.14-minimal_3.14.2-1_s390x.deb ... 220s Unpacking libpython3.14-minimal:s390x (3.14.2-1) ... 220s Selecting previously unselected package python3.14-minimal. 220s Preparing to unpack .../02-python3.14-minimal_3.14.2-1_s390x.deb ... 220s Unpacking python3.14-minimal (3.14.2-1) ... 220s Selecting previously unselected package m4. 220s Preparing to unpack .../03-m4_1.4.20-2_s390x.deb ... 220s Unpacking m4 (1.4.20-2) ... 220s Selecting previously unselected package autoconf. 220s Preparing to unpack .../04-autoconf_2.72-3.1ubuntu1_all.deb ... 220s Unpacking autoconf (2.72-3.1ubuntu1) ... 220s Selecting previously unselected package autotools-dev. 220s Preparing to unpack .../05-autotools-dev_20240727.1_all.deb ... 220s Unpacking autotools-dev (20240727.1) ... 221s Selecting previously unselected package automake. 221s Preparing to unpack .../06-automake_1%3a1.18.1-3build1_all.deb ... 221s Unpacking automake (1:1.18.1-3build1) ... 221s Selecting previously unselected package autopoint. 221s Preparing to unpack .../07-autopoint_0.23.2-1_all.deb ... 221s Unpacking autopoint (0.23.2-1) ... 221s Selecting previously unselected package libisl23:s390x. 221s Preparing to unpack .../08-libisl23_0.27-1build1_s390x.deb ... 221s Unpacking libisl23:s390x (0.27-1build1) ... 221s Selecting previously unselected package libmpc3:s390x. 221s Preparing to unpack .../09-libmpc3_1.3.1-2_s390x.deb ... 221s Unpacking libmpc3:s390x (1.3.1-2) ... 221s Selecting previously unselected package cpp-15-s390x-linux-gnu. 221s Preparing to unpack .../10-cpp-15-s390x-linux-gnu_15.2.0-12ubuntu1_s390x.deb ... 221s Unpacking cpp-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 222s Selecting previously unselected package cpp-15. 222s Preparing to unpack .../11-cpp-15_15.2.0-12ubuntu1_s390x.deb ... 222s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 222s Selecting previously unselected package cpp-s390x-linux-gnu. 222s Preparing to unpack .../12-cpp-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 222s Unpacking cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 222s Selecting previously unselected package cpp. 222s Preparing to unpack .../13-cpp_4%3a15.2.0-4ubuntu1_s390x.deb ... 222s Unpacking cpp (4:15.2.0-4ubuntu1) ... 222s Selecting previously unselected package libcc1-0:s390x. 222s Preparing to unpack .../14-libcc1-0_15.2.0-12ubuntu1_s390x.deb ... 222s Unpacking libcc1-0:s390x (15.2.0-12ubuntu1) ... 222s Selecting previously unselected package libitm1:s390x. 222s Preparing to unpack .../15-libitm1_15.2.0-12ubuntu1_s390x.deb ... 222s Unpacking libitm1:s390x (15.2.0-12ubuntu1) ... 222s Selecting previously unselected package libasan8:s390x. 222s Preparing to unpack .../16-libasan8_15.2.0-12ubuntu1_s390x.deb ... 222s Unpacking libasan8:s390x (15.2.0-12ubuntu1) ... 222s Selecting previously unselected package liblsan0:s390x. 222s Preparing to unpack .../17-liblsan0_15.2.0-12ubuntu1_s390x.deb ... 222s Unpacking liblsan0:s390x (15.2.0-12ubuntu1) ... 222s Selecting previously unselected package libtsan2:s390x. 222s Preparing to unpack .../18-libtsan2_15.2.0-12ubuntu1_s390x.deb ... 222s Unpacking libtsan2:s390x (15.2.0-12ubuntu1) ... 222s Selecting previously unselected package libubsan1:s390x. 222s Preparing to unpack .../19-libubsan1_15.2.0-12ubuntu1_s390x.deb ... 222s Unpacking libubsan1:s390x (15.2.0-12ubuntu1) ... 222s Selecting previously unselected package libgcc-15-dev:s390x. 222s Preparing to unpack .../20-libgcc-15-dev_15.2.0-12ubuntu1_s390x.deb ... 222s Unpacking libgcc-15-dev:s390x (15.2.0-12ubuntu1) ... 222s Selecting previously unselected package gcc-15-s390x-linux-gnu. 222s Preparing to unpack .../21-gcc-15-s390x-linux-gnu_15.2.0-12ubuntu1_s390x.deb ... 222s Unpacking gcc-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 223s Selecting previously unselected package gcc-15. 223s Preparing to unpack .../22-gcc-15_15.2.0-12ubuntu1_s390x.deb ... 223s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 223s Selecting previously unselected package gcc-s390x-linux-gnu. 223s Preparing to unpack .../23-gcc-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 223s Unpacking gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 223s Selecting previously unselected package gcc. 223s 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.../29-g++_4%3a15.2.0-4ubuntu1_s390x.deb ... 224s Unpacking g++ (4:15.2.0-4ubuntu1) ... 224s Selecting previously unselected package build-essential. 224s Preparing to unpack .../30-build-essential_12.12ubuntu2_s390x.deb ... 224s Unpacking build-essential (12.12ubuntu2) ... 224s Selecting previously unselected package runc. 224s Preparing to unpack .../31-runc_1.4.0-0ubuntu1_s390x.deb ... 224s Unpacking runc (1.4.0-0ubuntu1) ... 224s Selecting previously unselected package containerd. 224s Preparing to unpack .../32-containerd_2.2.1-0ubuntu1_s390x.deb ... 224s Unpacking containerd (2.2.1-0ubuntu1) ... 225s Selecting previously unselected package cwl-utils. 225s Preparing to unpack .../33-cwl-utils_0.40-1_all.deb ... 225s Unpacking cwl-utils (0.40-1) ... 225s Selecting previously unselected package python3-defusedxml. 225s Preparing to unpack .../34-python3-defusedxml_0.7.1-3build1_all.deb ... 225s Unpacking python3-defusedxml (0.7.1-3build1) ... 225s Selecting previously unselected package python3-junit.xml. 225s Preparing to unpack .../35-python3-junit.xml_1.9-6_all.deb ... 225s Unpacking python3-junit.xml (1.9-6) ... 225s Selecting previously unselected package python3-iniconfig. 225s Preparing to unpack .../36-python3-iniconfig_2.1.0-2_all.deb ... 225s Unpacking python3-iniconfig (2.1.0-2) ... 225s Selecting previously unselected package python3-pluggy. 225s Preparing to unpack .../37-python3-pluggy_1.6.0-2_all.deb ... 225s Unpacking python3-pluggy (1.6.0-2) ... 225s Selecting previously unselected package python3-pytest. 225s Preparing to unpack .../38-python3-pytest_9.0.2-2_all.deb ... 225s Unpacking python3-pytest (9.0.2-2) ... 225s Selecting previously unselected package cwltest. 225s Preparing to unpack .../39-cwltest_2.6.20251216093331-1_all.deb ... 225s Unpacking cwltest (2.6.20251216093331-1) ... 225s Selecting previously unselected package libjs-jquery. 225s Preparing to unpack .../40-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 225s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 225s Selecting previously unselected package fonts-font-awesome. 225s Preparing to unpack .../41-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1build1_all.deb ... 225s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 225s Selecting previously unselected package sphinx-rtd-theme-common. 225s Preparing to unpack .../42-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 225s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 225s Selecting previously unselected package cwltool-doc. 225s Preparing to unpack .../43-cwltool-doc_3.1.20251031082601-1_all.deb ... 225s Unpacking cwltool-doc (3.1.20251031082601-1) ... 225s Selecting previously unselected package libdebhelper-perl. 225s Preparing to unpack .../44-libdebhelper-perl_13.28ubuntu1_all.deb ... 225s Unpacking libdebhelper-perl (13.28ubuntu1) ... 225s Selecting previously unselected package libtool. 225s Preparing to unpack .../45-libtool_2.5.4-9_all.deb ... 225s Unpacking libtool (2.5.4-9) ... 225s Selecting previously unselected package dh-autoreconf. 225s Preparing to unpack .../46-dh-autoreconf_21_all.deb ... 225s Unpacking dh-autoreconf (21) ... 225s Selecting previously unselected package libarchive-zip-perl. 225s Preparing to unpack .../47-libarchive-zip-perl_1.68-1_all.deb ... 225s Unpacking libarchive-zip-perl (1.68-1) ... 225s Selecting previously unselected package libfile-stripnondeterminism-perl. 225s Preparing to unpack .../48-libfile-stripnondeterminism-perl_1.15.0-1build1_all.deb ... 225s Unpacking libfile-stripnondeterminism-perl (1.15.0-1build1) ... 225s Selecting previously unselected package dh-strip-nondeterminism. 225s Preparing to unpack .../49-dh-strip-nondeterminism_1.15.0-1build1_all.deb ... 225s Unpacking dh-strip-nondeterminism (1.15.0-1build1) ... 225s Selecting previously unselected package debugedit. 225s Preparing to unpack .../50-debugedit_1%3a5.2-3_s390x.deb ... 225s Unpacking debugedit (1:5.2-3) ... 225s Selecting previously unselected package dwz. 225s Preparing to unpack .../51-dwz_0.16-2_s390x.deb ... 225s Unpacking dwz (0.16-2) ... 225s Selecting previously unselected package gettext. 225s Preparing to unpack .../52-gettext_0.23.2-1_s390x.deb ... 225s Unpacking gettext (0.23.2-1) ... 226s Selecting previously unselected package intltool-debian. 226s Preparing to unpack .../53-intltool-debian_0.35.0+20060710.6build1_all.deb ... 226s Unpacking intltool-debian (0.35.0+20060710.6build1) ... 226s Selecting previously unselected package po-debconf. 226s Preparing to unpack .../54-po-debconf_1.0.22_all.deb ... 226s Unpacking po-debconf (1.0.22) ... 226s Selecting previously unselected package debhelper. 226s Preparing to unpack .../55-debhelper_13.28ubuntu1_all.deb ... 226s Unpacking debhelper (13.28ubuntu1) ... 226s Selecting previously unselected package dh-python. 226s Preparing to unpack .../56-dh-python_7.20260125_all.deb ... 226s Unpacking dh-python (7.20260125) ... 226s Selecting previously unselected package docker.io. 226s Preparing to unpack .../57-docker.io_29.1.3-0ubuntu1_s390x.deb ... 226s Unpacking docker.io (29.1.3-0ubuntu1) ... 228s Selecting previously unselected package sgml-base. 228s Preparing to unpack .../58-sgml-base_1.31+nmu1_all.deb ... 228s Unpacking sgml-base (1.31+nmu1) ... 228s Selecting previously unselected package xml-core. 228s Preparing to unpack .../59-xml-core_0.19build1_all.deb ... 228s Unpacking xml-core (0.19build1) ... 228s Selecting previously unselected package docutils-common. 228s Preparing to unpack .../60-docutils-common_0.22.4+dfsg-1_all.deb ... 228s Unpacking docutils-common (0.22.4+dfsg-1) ... 228s Selecting previously unselected package libjs-underscore. 228s Preparing to unpack .../61-libjs-underscore_1.13.7~dfsg+~1.13.0-1_all.deb ... 228s Unpacking libjs-underscore (1.13.7~dfsg+~1.13.0-1) ... 228s Selecting previously unselected package libjson-perl. 228s Preparing to unpack .../62-libjson-perl_4.10000-1_all.deb ... 228s Unpacking libjson-perl (4.10000-1) ... 228s Selecting previously unselected package libpython3.14-stdlib:s390x. 228s Preparing to unpack .../63-libpython3.14-stdlib_3.14.2-1_s390x.deb ... 228s Unpacking libpython3.14-stdlib:s390x (3.14.2-1) ... 228s Selecting previously unselected package pybuild-plugin-autopkgtest. 228s Preparing to unpack .../64-pybuild-plugin-autopkgtest_7.20260125_all.deb ... 228s Unpacking pybuild-plugin-autopkgtest (7.20260125) ... 228s Selecting previously unselected package python3-pyproject-hooks. 228s Preparing to unpack .../65-python3-pyproject-hooks_1.2.0-1_all.deb ... 228s Unpacking python3-pyproject-hooks (1.2.0-1) ... 228s Selecting previously unselected package python3-wheel. 228s Preparing to unpack .../66-python3-wheel_0.46.1-2_all.deb ... 228s Unpacking python3-wheel (0.46.1-2) ... 229s Selecting previously unselected package python3-build. 229s Preparing to unpack .../67-python3-build_1.2.2-5_all.deb ... 229s Unpacking python3-build (1.2.2-5) ... 229s Selecting previously unselected package python3-installer. 229s Preparing to unpack .../68-python3-installer_0.7.0+dfsg1-3_all.deb ... 229s Unpacking python3-installer (0.7.0+dfsg1-3) ... 229s Selecting previously unselected package pybuild-plugin-pyproject. 229s Preparing to unpack .../69-pybuild-plugin-pyproject_7.20260125_all.deb ... 229s Unpacking pybuild-plugin-pyproject (7.20260125) ... 229s Selecting previously unselected package python3.14. 229s Preparing to unpack .../70-python3.14_3.14.2-1_s390x.deb ... 229s Unpacking python3.14 (3.14.2-1) ... 229s Selecting previously unselected package python3-all. 229s Preparing to unpack .../71-python3-all_3.13.9-3_s390x.deb ... 229s Unpacking python3-all (3.13.9-3) ... 229s Selecting previously unselected package python3-antlr4. 229s Preparing to unpack .../72-python3-antlr4_4.9.2-1build1_all.deb ... 229s Unpacking python3-antlr4 (4.9.2-1build1) ... 229s Selecting previously unselected package python3-astroid. 229s Preparing to unpack .../73-python3-astroid_4.0.2-1ubuntu1_all.deb ... 229s Unpacking python3-astroid (4.0.2-1ubuntu1) ... 229s Selecting previously unselected package python3.13-doc. 229s Preparing to unpack .../74-python3.13-doc_3.13.11-1_all.deb ... 229s Unpacking python3.13-doc (3.13.11-1) ... 229s Selecting previously unselected package python3-doc. 229s Preparing to unpack .../75-python3-doc_3.13.9-3_all.deb ... 229s Unpacking python3-doc (3.13.9-3) ... 230s Selecting previously unselected package python3-roman-numerals. 230s Preparing to unpack .../76-python3-roman-numerals_4.1.0-1_all.deb ... 230s Unpacking python3-roman-numerals (4.1.0-1) ... 230s Selecting previously unselected package python3-docutils. 230s Preparing to unpack .../77-python3-docutils_0.22.4+dfsg-1_all.deb ... 230s Unpacking python3-docutils (0.22.4+dfsg-1) ... 230s Selecting previously unselected package python3-execnet. 230s Preparing to unpack .../78-python3-execnet_2.1.1-1build1_all.deb ... 230s Unpacking python3-execnet (2.1.1-1build1) ... 230s Selecting previously unselected package python3-imagesize. 230s Preparing to unpack .../79-python3-imagesize_1.4.1-1build1_all.deb ... 230s Unpacking python3-imagesize (1.4.1-1build1) ... 230s Selecting previously unselected package python3-werkzeug. 230s Preparing to unpack .../80-python3-werkzeug_3.1.5-1_all.deb ... 230s Unpacking python3-werkzeug (3.1.5-1) ... 230s Selecting previously unselected package python3-pytest-httpserver. 230s Preparing to unpack .../81-python3-pytest-httpserver_1.1.3-1_all.deb ... 230s Unpacking python3-pytest-httpserver (1.1.3-1) ... 230s Selecting previously unselected package python3-pytest-timeout. 230s Preparing to unpack .../82-python3-pytest-timeout_2.4.0-2_all.deb ... 230s Unpacking python3-pytest-timeout (2.4.0-2) ... 230s Selecting previously unselected package python3-pytest-xdist. 230s Preparing to unpack .../83-python3-pytest-xdist_3.8.0-4_all.deb ... 230s Unpacking python3-pytest-xdist (3.8.0-4) ... 230s Selecting previously unselected package python3-pytz. 230s Preparing to unpack .../84-python3-pytz_2025.2-5_all.deb ... 230s Unpacking python3-pytz (2025.2-5) ... 230s Selecting previously unselected package python3-setuptools-scm. 230s Preparing to unpack .../85-python3-setuptools-scm_8.2.1-4_all.deb ... 230s Unpacking python3-setuptools-scm (8.2.1-4) ... 230s Selecting previously unselected package python3-snowballstemmer. 230s Preparing to unpack .../86-python3-snowballstemmer_3.0.1-1_all.deb ... 230s Unpacking python3-snowballstemmer (3.0.1-1) ... 230s Selecting previously unselected package sphinx-common. 230s Preparing to unpack .../87-sphinx-common_8.2.3-12_all.deb ... 230s Unpacking sphinx-common (8.2.3-12) ... 230s Selecting previously unselected package python3-alabaster. 230s Preparing to unpack .../88-python3-alabaster_0.7.16-0.1build1_all.deb ... 230s Unpacking python3-alabaster (0.7.16-0.1build1) ... 230s Selecting previously unselected package python3-sphinx. 230s Preparing to unpack .../89-python3-sphinx_8.2.3-12_all.deb ... 230s Unpacking python3-sphinx (8.2.3-12) ... 230s Selecting previously unselected package python3-sphinx-autoapi. 230s Preparing to unpack .../90-python3-sphinx-autoapi_3.6.1-1_all.deb ... 230s Unpacking python3-sphinx-autoapi (3.6.1-1) ... 230s Selecting previously unselected package python3-sphinx-autodoc-typehints. 230s Preparing to unpack .../91-python3-sphinx-autodoc-typehints_3.5.2-1_all.deb ... 230s Unpacking python3-sphinx-autodoc-typehints (3.5.2-1) ... 230s Selecting previously unselected package python3-sphinxcontrib.autoprogram. 230s Preparing to unpack .../92-python3-sphinxcontrib.autoprogram_0.1.9-1_all.deb ... 230s Unpacking python3-sphinxcontrib.autoprogram (0.1.9-1) ... 230s Selecting previously unselected package python3-stubserver. 230s Preparing to unpack .../93-python3-stubserver_1.1-4build1_all.deb ... 230s Unpacking python3-stubserver (1.1-4build1) ... 230s Selecting previously unselected package python3-tz. 230s Preparing to unpack .../94-python3-tz_2025.2-5_all.deb ... 230s Unpacking python3-tz (2025.2-5) ... 230s Selecting previously unselected package python3-wdlparse. 230s Preparing to unpack .../95-python3-wdlparse_0.1.0-3build1_all.deb ... 230s Unpacking python3-wdlparse (0.1.0-3build1) ... 230s Setting up dh-python (7.20260125) ... 231s Setting up python3-iniconfig (2.1.0-2) ... 231s Setting up python3-antlr4 (4.9.2-1build1) ... 232s Setting up gettext (0.23.2-1) ... 232s Setting up fonts-lato (2.015-1build1) ... 232s Setting up python3-defusedxml (0.7.1-3build1) ... 232s Setting up libarchive-zip-perl (1.68-1) ... 232s Setting up python3-alabaster (0.7.16-0.1build1) ... 232s Setting up python3-junit.xml (1.9-6) ... 232s Setting up libdebhelper-perl (13.28ubuntu1) ... 232s Setting up libpython3.14-minimal:s390x (3.14.2-1) ... 232s Setting up m4 (1.4.20-2) ... 232s Setting up python3-pytz (2025.2-5) ... 233s Setting up python3-wheel (0.46.1-2) ... 233s Setting up python3-setuptools-scm (8.2.1-4) ... 233s Setting up python3-tz (2025.2-5) ... 233s Setting up runc (1.4.0-0ubuntu1) ... 233s Setting up intltool-debian (0.35.0+20060710.6build1) ... 233s Setting up python3-stubserver (1.1-4build1) ... 233s Setting up autotools-dev (20240727.1) ... 233s Setting up python3-pyproject-hooks (1.2.0-1) ... 234s Setting up python3-snowballstemmer (3.0.1-1) ... 234s Setting up python3-werkzeug (3.1.5-1) ... 234s Setting up cwl-utils (0.40-1) ... 234s Setting up libmpc3:s390x (1.3.1-2) ... 234s Setting up autopoint (0.23.2-1) ... 234s Setting up python3-installer (0.7.0+dfsg1-3) ... 235s Setting up autoconf (2.72-3.1ubuntu1) ... 235s Setting up python3-pluggy (1.6.0-2) ... 235s Setting up libubsan1:s390x (15.2.0-12ubuntu1) ... 235s Setting up dwz (0.16-2) ... 235s Setting up python3-astroid (4.0.2-1ubuntu1) ... 235s Setting up libasan8:s390x (15.2.0-12ubuntu1) ... 235s Setting up libjson-perl (4.10000-1) ... 235s Setting up python3-pytest-httpserver (1.1.3-1) ... 236s Setting up debugedit (1:5.2-3) ... 236s Setting up python3-roman-numerals (4.1.0-1) ... 236s Setting up sgml-base (1.31+nmu1) ... 236s Setting up libtsan2:s390x (15.2.0-12ubuntu1) ... 236s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 236s Setting up libisl23:s390x (0.27-1build1) ... 236s Setting up python3-build (1.2.2-5) ... 236s Setting up containerd (2.2.1-0ubuntu1) ... 236s Created symlink '/etc/systemd/system/multi-user.target.wants/containerd.service' → '/usr/lib/systemd/system/containerd.service'. 236s Setting up python3-execnet (2.1.1-1build1) ... 237s Setting up python3-wdlparse (0.1.0-3build1) ... 237s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 237s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 237s Setting up python3.14-minimal (3.14.2-1) ... 239s Setting up libcc1-0:s390x (15.2.0-12ubuntu1) ... 239s Setting up liblsan0:s390x (15.2.0-12ubuntu1) ... 239s Setting up libitm1:s390x (15.2.0-12ubuntu1) ... 239s Setting up libjs-underscore (1.13.7~dfsg+~1.13.0-1) ... 239s Setting up python3-imagesize (1.4.1-1build1) ... 239s Setting up automake (1:1.18.1-3build1) ... 239s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 239s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 239s Setting up cwltool-doc (3.1.20251031082601-1) ... 239s Setting up libgcc-15-dev:s390x (15.2.0-12ubuntu1) ... 239s Setting up libpython3.14-stdlib:s390x (3.14.2-1) ... 239s Setting up pybuild-plugin-pyproject (7.20260125) ... 239s Setting up python3-pytest (9.0.2-2) ... 240s Setting up po-debconf (1.0.22) ... 240s Setting up docker.io (29.1.3-0ubuntu1) ... 240s Created symlink '/etc/systemd/system/multi-user.target.wants/docker.service' → '/usr/lib/systemd/system/docker.service'. 240s Created symlink '/etc/systemd/system/sockets.target.wants/docker.socket' → '/usr/lib/systemd/system/docker.socket'. 241s Setting up python3.13-doc (3.13.11-1) ... 241s Setting up libstdc++-15-dev:s390x (15.2.0-12ubuntu1) ... 241s Setting up sphinx-common (8.2.3-12) ... 241s Setting up cwltest (2.6.20251216093331-1) ... 241s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 241s Setting up xml-core (0.19build1) ... 242s Setting up cpp-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 242s Setting up python3.14 (3.14.2-1) ... 244s Setting up gcc-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 244s Setting up python3-doc (3.13.9-3) ... 244s Setting up g++-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 244s Setting up python3-pytest-xdist (3.8.0-4) ... 244s Setting up python3-pytest-timeout (2.4.0-2) ... 244s Setting up cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 244s Setting up python3-all (3.13.9-3) ... 244s Setting up gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 244s Setting up cpp-15 (15.2.0-12ubuntu1) ... 244s Setting up cpp (4:15.2.0-4ubuntu1) ... 244s Setting up g++-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 244s Setting up gcc-15 (15.2.0-12ubuntu1) ... 244s Setting up g++-15 (15.2.0-12ubuntu1) ... 244s Setting up libtool (2.5.4-9) ... 244s Setting up gcc (4:15.2.0-4ubuntu1) ... 244s Setting up dh-autoreconf (21) ... 244s Setting up g++ (4:15.2.0-4ubuntu1) ... 244s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 244s Setting up build-essential (12.12ubuntu2) ... 244s Setting up debhelper (13.28ubuntu1) ... 244s Setting up pybuild-plugin-autopkgtest (7.20260125) ... 244s Processing triggers for install-info (7.2-5) ... 244s Processing triggers for fontconfig (2.17.1-3ubuntu1) ... 244s Processing triggers for libc-bin (2.42-2ubuntu4) ... 244s Processing triggers for systemd (259-1ubuntu2) ... 244s Processing triggers for man-db (2.13.1-1) ... 246s Processing triggers for sgml-base (1.31+nmu1) ... 246s Setting up docutils-common (0.22.4+dfsg-1) ... 246s Processing triggers for sgml-base (1.31+nmu1) ... 246s Setting up python3-docutils (0.22.4+dfsg-1) ... 248s Setting up python3-sphinx (8.2.3-12) ... 249s Setting up python3-sphinx-autodoc-typehints (3.5.2-1) ... 250s Setting up python3-sphinx-autoapi (3.6.1-1) ... 250s Setting up python3-sphinxcontrib.autoprogram (0.1.9-1) ... 251s autopkgtest [06:59:05]: test pybuild-autopkgtest: pybuild-autopkgtest 251s autopkgtest [06:59:05]: test pybuild-autopkgtest: [----------------------- 253s pybuild-autopkgtest 254s I: pybuild base:384: cd /tmp/autopkgtest.cjJpnO/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 268s ============================= test session starts ============================== 268s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.14 268s cachedir: .pytest_cache 268s rootdir: /tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build 268s configfile: setup.cfg 268s plugins: typeguard-4.4.4, xdist-3.8.0, pytest_httpserver-1.1.3, cwltest-2.6.20251216093331, timeout-2.4.0 268s created: 4/4 workers 268s 4 workers [375 items] 268s 268s scheduling tests via LoadScopeScheduling 268s 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 0%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 0%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_default_gpu_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 0%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 1%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 1%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 1%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 1%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 3%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 3%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 3%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 6%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 6%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 7%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 7%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 7%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 8%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 8%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 8%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 8%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 9%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 9%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 9%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw3] [ 9%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw3] [ 10%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw3] [ 10%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw3] [ 10%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw3] [ 10%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw3] [ 11%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 11%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 11%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 12%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 12%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 12%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 12%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 13%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 13%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s [gw0] [ 13%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw3] [ 13%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw3] [ 14%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw3] [ 14%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw3] [ 14%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw3] [ 14%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw3] [ 15%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw3] [ 15%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw0] [ 15%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw0] [ 16%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw0] [ 16%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw0] [ 16%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw0] [ 16%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw0] [ 17%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw0] [ 17%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw0] [ 17%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw0] [ 17%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw0] [ 18%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw0] [ 18%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw0] [ 18%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw3] [ 18%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s docs/scriptsTest.py::ToilDocumentationTest::testArguments <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 268s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 268s [gw0] [ 19%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 269s lib/dockerTest.py::TestDocker::testDockerClean <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 269s [gw1] [ 19%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 269s jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 269s [gw2] [ 19%] PASSED batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_default_gpu_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 269s batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_get_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 269s [gw1] [ 20%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 269s jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 269s [gw2] [ 20%] PASSED batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_get_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 269s batchSystems/test_slurm.py::SlurmTest::test_any_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 269s [gw1] [ 20%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 269s jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 269s [gw2] [ 20%] PASSED batchSystems/test_slurm.py::SlurmTest::test_any_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 269s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 269s [gw1] [ 21%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 269s jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 269s [gw1] [ 21%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 269s jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 269s [gw2] [ 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 269s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_mix_sacct_scontrol <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 269s [gw2] [ 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 270s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 270s [gw1] [ 22%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 270s jobStores/jobStoreTest.py::FileJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 270s [gw2] [ 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 270s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 270s [gw2] [ 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 270s 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 270s [gw2] [ 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 270s 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 270s [gw2] [ 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 270s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_some_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 270s [gw1] [ 23%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 271s jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 271s [gw2] [ 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 271s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_argument_list_too_big <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 271s [gw2] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_argument_list_too_big <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 271s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 271s [gw2] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 271s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 271s [gw1] [ 24%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 271s jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 271s [gw2] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 272s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 272s [gw2] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 272s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 272s [gw2] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 272s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 272s [gw2] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 272s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 272s [gw2] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 272s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 272s [gw2] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 272s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 272s [gw2] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 273s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 273s [gw2] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 273s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 273s [gw2] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 273s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 273s [gw2] [ 27%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 273s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 273s [gw2] [ 27%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 274s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 274s [gw2] [ 27%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 274s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 274s [gw2] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 274s batchSystems/test_slurm.py::SlurmTest::test_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 274s [gw2] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 274s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_export <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 274s [gw2] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_export <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 274s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 274s [gw3] [ 28%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testArguments <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 275s docs/scriptsTest.py::ToilDocumentationTest::testDocker <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 275s [gw2] [ 29%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 275s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_time <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 275s [gw2] [ 29%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_time <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 278s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 278s [gw0] [ 29%] FAILED lib/dockerTest.py::TestDocker::testDockerClean <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 281s lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 281s [gw2] [ 29%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 283s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 283s [gw2] [ 30%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 283s [gw0] [ 30%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 286s lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 286s [gw3] [ 30%] FAILED docs/scriptsTest.py::ToilDocumentationTest::testDocker <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 287s docs/scriptsTest.py::ToilDocumentationTest::testDynamic <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 290s [gw2] [ 30%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 290s [gw0] [ 30%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 294s lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 298s [gw2] [ 30%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 298s [gw0] [ 31%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 301s lib/dockerTest.py::TestDocker::testDockerPipeChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 301s [gw2] [ 31%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 301s [gw1] [ 31%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 302s jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 302s [gw1] [ 31%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw2] [ 31%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 408s [gw0] [ 32%] FAILED lib/dockerTest.py::TestDocker::testDockerPipeChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s [gw2] [ 32%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 408s [gw2] [ 32%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 408s [gw0] [ 32%] FAILED lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s lib/dockerTest.py::TestDocker::testNonCachingDockerChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s [gw2] [ 32%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 408s [gw2] [ 32%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 408s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 408s [gw2] [ 32%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 408s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 408s [gw0] [ 32%] FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s [gw2] [ 33%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 408s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 408s [gw3] [ 33%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testDynamic <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s [gw2] [ 33%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 408s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 408s [gw0] [ 33%] FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s lib/dockerTest.py::TestDocker::testDockerLogs <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s [gw3] [ 34%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s [gw2] [ 34%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 408s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 408s [gw0] [ 34%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s lib/dockerTest.py::TestDocker::testDockerLogs_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s [gw3] [ 34%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s docs/scriptsTest.py::ToilDocumentationTest::testHelloworld <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s [gw3] [ 35%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testHelloworld <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s [gw0] [ 35%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s lib/dockerTest.py::TestDocker::testDockerLogs_Demux <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s [gw3] [ 35%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s [gw3] [ 36%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s docs/scriptsTest.py::ToilDocumentationTest::testJobFunctions <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s [gw0] [ 36%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s [gw3] [ 36%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testJobFunctions <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s docs/scriptsTest.py::ToilDocumentationTest::testManaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s [gw3] [ 36%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testManaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s docs/scriptsTest.py::ToilDocumentationTest::testManaging2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s [gw0] [ 37%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 408s src/dockerCheckTest.py::DockerCheckTest::testApplianceParser <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s [gw0] [ 37%] PASSED src/dockerCheckTest.py::DockerCheckTest::testApplianceParser <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s [gw0] [ 37%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s [gw0] [ 37%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s [gw0] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s [gw0] [ 38%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s [gw0] [ 38%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s [gw0] [ 38%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s [gw3] [ 39%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testManaging2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s docs/scriptsTest.py::ToilDocumentationTest::testPromises <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s [gw0] [ 39%] PASSED src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s [gw0] [ 39%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s [gw0] [ 40%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s [gw0] [ 40%] PASSED src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 408s provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw0] [ 40%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw0] [ 40%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw0] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw0] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw0] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw0] [ 41%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw0] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw0] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw0] [ 42%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw1] [ 42%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw0] [ 43%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 43%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 43%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 44%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 45%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 46%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 47%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 48%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 49%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 50%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s [gw0] [ 51%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 408s provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw0] [ 51%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw1] [ 51%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw1] [ 52%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw0] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw0] [ 52%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw1] [ 52%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw1] [ 53%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw0] [ 53%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw1] [ 53%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw0] [ 53%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw0] [ 54%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw1] [ 54%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw0] [ 54%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s provisioners/clusterScalerTest.py::BinPackingTest::testSorting <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw0] [ 54%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testSorting <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s [gw1] [ 55%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw0] [ 55%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 408s utils/utilsTest.py::TestUtils::test_config_functionality <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 408s [gw1] [ 55%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw1] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw1] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw1] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw1] [ 56%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw1] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_does_not_leak_symlinks <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw1] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_does_not_leak_symlinks <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_init_preserves_symlink_path <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw1] [ 57%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_init_preserves_symlink_path <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_symlink_read_control <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s [gw0] [ 57%] PASSED utils/utilsTest.py::TestUtils::test_config_functionality <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 408s utils/utilsTest.py::TestUtils::testUtilsSort <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 408s [gw1] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_symlink_read_control <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s [gw1] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s [gw1] [ 58%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s [gw3] [ 58%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testPromises <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s docs/scriptsTest.py::ToilDocumentationTest::testPromises2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 408s [gw1] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s [gw1] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s [gw1] [ 59%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s [gw1] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s [gw1] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s [gw1] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s [gw1] [ 60%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s [gw1] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s [gw1] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s [gw1] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s [gw1] [ 61%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 408s src/miscTests.py::TestMisc::testIDStability <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 408s [gw1] [ 62%] PASSED src/miscTests.py::TestMisc::testIDStability <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 408s src/miscTests.py::TestMisc::test_atomic_install <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 408s [gw1] [ 62%] PASSED src/miscTests.py::TestMisc::test_atomic_install <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 408s src/miscTests.py::TestMisc::test_atomic_install_dev <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 408s [gw1] [ 62%] PASSED src/miscTests.py::TestMisc::test_atomic_install_dev <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 408s src/miscTests.py::TestMisc::test_atomic_context_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 408s [gw1] [ 62%] PASSED src/miscTests.py::TestMisc::test_atomic_context_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 408s src/miscTests.py::TestMisc::test_atomic_context_error <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 408s [gw1] [ 63%] PASSED src/miscTests.py::TestMisc::test_atomic_context_error <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 408s src/miscTests.py::TestMisc::test_call_command_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 408s [gw1] [ 63%] PASSED src/miscTests.py::TestMisc::test_call_command_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 408s src/miscTests.py::TestMisc::test_call_command_err <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 408s [gw1] [ 63%] PASSED src/miscTests.py::TestMisc::test_call_command_err <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 408s lib/test_url.py::TestURLAccess::test_get_url_access <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 408s [gw1] [ 64%] PASSED lib/test_url.py::TestURLAccess::test_get_url_access <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 408s lib/test_url.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 408s [gw1] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 408s lib/test_url.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 408s [gw1] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 408s lib/test_url.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 408s [gw1] [ 64%] SKIPPED lib/test_url.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 408s lib/test_url.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 408s [gw1] [ 65%] SKIPPED lib/test_url.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 408s lib/test_url.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 408s [gw1] [ 65%] SKIPPED lib/test_url.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 408s lib/url_plugin_test.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 408s [gw1] [ 65%] PASSED lib/url_plugin_test.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 408s lib/url_plugin_test.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 408s [gw1] [ 65%] PASSED lib/url_plugin_test.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 408s lib/url_plugin_test.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 408s [gw1] [ 66%] PASSED lib/url_plugin_test.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 408s lib/url_plugin_test.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 408s [gw1] [ 66%] PASSED lib/url_plugin_test.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 408s lib/url_plugin_test.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 408s [gw1] [ 66%] PASSED lib/url_plugin_test.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 408s lib/url_plugin_test.py::TestURLAccess::test_url_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 408s [gw1] [ 66%] PASSED lib/url_plugin_test.py::TestURLAccess::test_url_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 408s src/retainTempDirTest.py::TestCleanWorkDir::testNever <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 408s [gw1] [ 67%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testNever <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 408s src/retainTempDirTest.py::TestCleanWorkDir::testAlways <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 408s [gw1] [ 67%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testAlways <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 408s src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 408s [gw1] [ 67%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 408s src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithNoError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 408s [gw1] [ 68%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithNoError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 408s src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 408s [gw1] [ 68%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 408s src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithSuccess <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 408s [gw1] [ 68%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithSuccess <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 408s lib/aws/test_utils.py::TagGenerationTest::test_build_tag <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 408s [gw1] [ 68%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_build_tag <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 408s lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 408s [gw1] [ 69%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 408s lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 408s [gw1] [ 69%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 408s lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 408s [gw1] [ 69%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 408s lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 408s [gw1] [ 69%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 409s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 411s [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 411s [gw3] [ 70%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testPromises2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 412s docs/scriptsTest.py::ToilDocumentationTest::testQuickstart <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 415s [gw1] [ 70%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 415s [gw3] [ 70%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testQuickstart <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 416s docs/scriptsTest.py::ToilDocumentationTest::testRequirements <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 422s [gw1] [ 70%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 426s [gw1] [ 70%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 427s [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 427s [gw3] [ 70%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testRequirements <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 429s docs/scriptsTest.py::ToilDocumentationTest::testStaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 431s [gw1] [ 70%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 431s [gw3] [ 71%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testStaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 433s docs/scriptsTest.py::ToilDocumentationTest::testStats <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 440s [gw1] [ 71%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 440s [gw1] [ 71%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 440s [gw1] [ 71%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 449s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 449s [gw1] [ 71%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s [gw3] [ 71%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testStats <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 460s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s [gw3] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s [gw3] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s [gw3] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s [gw3] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s [gw3] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s [gw3] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s [gw3] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s [gw3] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s [gw3] [ 74%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s [gw3] [ 74%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 460s src/resourceTest.py::TestResource::testStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 460s [gw3] [ 74%] PASSED src/resourceTest.py::TestResource::testStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 460s src/resourceTest.py::TestResource::testPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 460s [gw3] [ 74%] PASSED src/resourceTest.py::TestResource::testPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 460s src/resourceTest.py::TestResource::testStandAloneInPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 460s [gw3] [ 75%] PASSED src/resourceTest.py::TestResource::testStandAloneInPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 460s src/resourceTest.py::TestResource::testBuiltIn <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 460s [gw3] [ 75%] PASSED src/resourceTest.py::TestResource::testBuiltIn <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 466s src/resourceTest.py::TestResource::testNonPyStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 466s [gw3] [ 75%] PASSED src/resourceTest.py::TestResource::testNonPyStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 466s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 466s [gw1] [ 76%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 470s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 470s [gw3] [ 76%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 474s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithClassMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 474s [gw3] [ 76%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithClassMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 475s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithLambda <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 475s [gw1] [ 76%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 477s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 477s [gw3] [ 77%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithLambda <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 478s src/deferredFunctionTest.py::TestDeferredFunction::testBatchSystemCleanupCanHandleWorkerDeaths <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 478s [gw1] [ 77%] SUBPASSED[Testing readwrite file permissions 478s [executable: True] 478s [caching: True] 482s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 482s [gw1] [ 77%] SUBPASSED[Testing readwrite file permissions 482s [executable: True] 482s [caching: False] 482s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 482s [gw3] [ 77%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testBatchSystemCleanupCanHandleWorkerDeaths <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 482s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 482s [gw3] [ 77%] PASSED batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 482s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 482s [gw3] [ 78%] PASSED batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 483s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_still_running <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 483s [gw3] [ 78%] 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 483s lib/test_conversions.py::ConversionTest::test_convert <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 483s [gw3] [ 78%] PASSED lib/test_conversions.py::ConversionTest::test_convert <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 483s lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 483s [gw3] [ 78%] PASSED lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 483s lib/test_conversions.py::ConversionTest::test_human2bytes <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 483s [gw3] [ 79%] PASSED lib/test_conversions.py::ConversionTest::test_human2bytes <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 483s lib/test_history.py::TestHistory::test_history_submittable_detection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 483s [gw3] [ 79%] PASSED lib/test_history.py::TestHistory::test_history_submittable_detection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 484s lib/test_history.py::TestHistory::test_history_deletion <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 484s [gw3] [ 79%] PASSED lib/test_history.py::TestHistory::test_history_deletion <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 487s lib/test_history.py::TestHistory::test_history_size_limit <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 487s [gw1] [ 79%] SUBPASSED[Testing readwrite file permissions 487s [executable: False] 487s [caching: True] 495s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 495s [gw1] [ 79%] SUBPASSED[Testing readwrite file permissions 495s [executable: False] 495s [caching: False] 495s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 495s [gw1] [ 79%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 495s src/miscTests.py::TestPanic::test_panic_by_hand <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 495s [gw1] [ 80%] PASSED src/miscTests.py::TestPanic::test_panic_by_hand <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 495s src/miscTests.py::TestPanic::test_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 495s [gw1] [ 80%] PASSED src/miscTests.py::TestPanic::test_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 495s src/miscTests.py::TestPanic::test_panic_with_secondary <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 495s [gw1] [ 80%] PASSED src/miscTests.py::TestPanic::test_panic_with_secondary <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 495s src/miscTests.py::TestPanic::test_nested_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 495s [gw1] [ 80%] PASSED src/miscTests.py::TestPanic::test_nested_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 495s src/busTest.py::TestMessageBus::test_enum_ints_in_file <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 495s [gw1] [ 81%] PASSED src/busTest.py::TestMessageBus::test_enum_ints_in_file <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 495s src/busTest.py::TestMessageBus::test_cross_thread_messaging <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 495s [gw1] [ 81%] PASSED src/busTest.py::TestMessageBus::test_cross_thread_messaging <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 502s src/busTest.py::TestMessageBus::test_restart_without_bus_path <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 502s [gw3] [ 81%] PASSED lib/test_history.py::TestHistory::test_history_size_limit <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 502s server/serverTest.py::ToilWESServerBenchTest::test_get_service_info <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 502s [gw3] [ 81%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_get_service_info <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 502s server/serverTest.py::ToilWESServerBenchTest::test_health <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 502s [gw3] [ 82%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_health <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 502s server/serverTest.py::ToilWESServerBenchTest::test_home <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 502s [gw3] [ 82%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_home <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 511s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 511s [gw1] [ 82%] PASSED src/busTest.py::TestMessageBus::test_restart_without_bus_path <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 515s src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 515s [gw1] [ 82%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 515s src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 515s [gw3] [ 83%] PASSED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 529s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 529s [gw3] [ 83%] FAILED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 531s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 531s [gw1] [ 83%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 534s src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 534s [gw1] [ 84%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 534s src/promisedRequirementTest.py::TestMesosPromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 534s [gw1] [ 84%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 534s src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 534s [gw1] [ 84%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 534s src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 534s [gw1] [ 84%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 540s utils/toilDebugTest.py::TestDebugJob::test_run_job <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 540s [gw3] [ 85%] FAILED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 542s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 542s [gw1] [ 85%] PASSED utils/toilDebugTest.py::TestDebugJob::test_run_job <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 545s utils/toilDebugTest.py::TestDebugJob::test_print_job_info <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 545s [gw3] [ 85%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 551s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 551s [gw1] [ 85%] PASSED utils/toilDebugTest.py::TestDebugJob::test_print_job_info <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 551s utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 551s [gw1] [ 86%] SKIPPED utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 551s __init__.py::toil.test.make_tests <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 551s [gw1] [ 86%] PASSED __init__.py::toil.test.make_tests <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 556s __init__.py::toil.test.timeLimit <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 556s [gw3] [ 86%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 556s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 556s [gw1] [ 86%] PASSED __init__.py::toil.test.timeLimit <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 556s server/serverTest.py::AWSStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 556s [gw1] [ 87%] SKIPPED server/serverTest.py::AWSStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 556s server/serverTest.py::AWSStateStoreTest::test_state_store_paths <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 556s [gw1] [ 87%] SKIPPED server/serverTest.py::AWSStateStoreTest::test_state_store_paths <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 556s src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 556s [gw1] [ 87%] PASSED src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 556s src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 556s [gw1] [ 88%] PASSED src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 558s src/threadingTest.py::TestThreading::testGlobalMutexOrdering <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 558s [gw3] [ 88%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 559s options/options.py::OptionsTest::test_caching_option_priority <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 559s [gw3] [ 88%] PASSED options/options.py::OptionsTest::test_caching_option_priority <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 559s options/options.py::OptionsTest::test_default_caching_slurm <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 559s [gw3] [ 88%] PASSED options/options.py::OptionsTest::test_default_caching_slurm <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 559s 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 559s [gw3] [ 89%] PASSED batchSystems/test_lsf_helper.py::LSFHelperTest::test_parse_mem_and_cmd_from_output <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_lsf_helper.py 559s jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 559s [gw3] [ 89%] SKIPPED jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 559s lib/test_misc.py::UserNameAvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 559s [gw3] [ 89%] PASSED lib/test_misc.py::UserNameAvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 559s lib/test_misc.py::UserNameUnvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 559s [gw3] [ 89%] PASSED lib/test_misc.py::UserNameUnvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 559s lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 559s [gw3] [ 90%] PASSED lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 559s mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue <- ../../../../usr/lib/python3/dist-packages/toil/test/mesos/MesosDataStructuresTest.py 559s [gw3] [ 90%] PASSED mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue <- ../../../../usr/lib/python3/dist-packages/toil/test/mesos/MesosDataStructuresTest.py 559s provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/provisionerTest.py 559s [gw3] [ 90%] PASSED provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/provisionerTest.py 559s server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 559s [gw3] [ 90%] SKIPPED server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 559s server/serverTest.py::FileStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 559s [gw3] [ 91%] SKIPPED server/serverTest.py::FileStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 559s server/serverTest.py::FileStateStoreURLTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 559s [gw3] [ 91%] SKIPPED server/serverTest.py::FileStateStoreURLTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 566s src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried <- ../../../../usr/lib/python3/dist-packages/toil/test/src/checkpointTest.py 566s [gw0] [ 91%] PASSED utils/utilsTest.py::TestUtils::testUtilsSort <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 571s utils/utilsTest.py::TestUtils::testUnicodeSupport <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 571s [gw0] [ 92%] PASSED utils/utilsTest.py::TestUtils::testUnicodeSupport <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 572s utils/utilsTest.py::TestUtils::testGetPIDStatus <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 572s [gw3] [ 92%] PASSED src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried <- ../../../../usr/lib/python3/dist-packages/toil/test/src/checkpointTest.py 591s src/environmentTest.py::EnvironmentTest::test_environment <- ../../../../usr/lib/python3/dist-packages/toil/test/src/environmentTest.py 591s [gw0] [ 92%] PASSED utils/utilsTest.py::TestUtils::testGetPIDStatus <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 595s utils/utilsTest.py::TestUtils::testGetStatusFailedToilWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 595s [gw2] [ 92%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 601s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 601s [gw3] [ 93%] PASSED src/environmentTest.py::EnvironmentTest::test_environment <- ../../../../usr/lib/python3/dist-packages/toil/test/src/environmentTest.py 605s src/helloWorldTest.py::HelloWorldTest::testHelloWorld <- ../../../../usr/lib/python3/dist-packages/toil/test/src/helloWorldTest.py 605s [gw0] [ 93%] PASSED utils/utilsTest.py::TestUtils::testGetStatusFailedToilWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 618s utils/utilsTest.py::TestUtils::testGetStatusFailedCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 618s [gw2] [ 93%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 621s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 621s [gw3] [ 93%] PASSED src/helloWorldTest.py::HelloWorldTest::testHelloWorld <- ../../../../usr/lib/python3/dist-packages/toil/test/src/helloWorldTest.py 621s src/jobServiceTest.py::TestJobService::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 621s [gw0] [ 94%] PASSED utils/utilsTest.py::TestUtils::testGetStatusFailedCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 637s utils/utilsTest.py::TestUtils::testGetStatusSuccessfulCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 637s [gw2] [ 94%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 642s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 642s [gw0] [ 94%] PASSED utils/utilsTest.py::TestUtils::testGetStatusSuccessfulCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 644s utils/utilsTest.py::TestUtils::testPrintJobLog <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 644s [gw1] [ 94%] PASSED src/threadingTest.py::TestThreading::testGlobalMutexOrdering <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 645s src/threadingTest.py::TestThreading::testLastProcessStanding <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 645s [gw2] [ 95%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 653s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 653s [gw2] [ 95%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 656s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 656s [gw0] [ 95%] PASSED utils/utilsTest.py::TestUtils::testPrintJobLog <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 659s utils/utilsTest.py::TestUtils::testRestartAttribute <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 659s [gw2] [ 96%] SUBPASSED[Testing readwrite file permissions 659s [executable: True] 659s [caching: True] 665s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 665s [gw2] [ 96%] SUBPASSED[Testing readwrite file permissions 665s [executable: True] 665s [caching: False] 672s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 672s [gw2] [ 96%] SUBPASSED[Testing readwrite file permissions 672s [executable: False] 672s [caching: True] 679s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 679s [gw2] [ 96%] SUBPASSED[Testing readwrite file permissions 679s [executable: False] 679s [caching: False] 679s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 679s [gw2] [ 96%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 686s src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger <- ../../../../usr/lib/python3/dist-packages/toil/test/src/realtimeLoggerTest.py 686s [gw2] [ 96%] PASSED src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger <- ../../../../usr/lib/python3/dist-packages/toil/test/src/realtimeLoggerTest.py 698s src/resumabilityTest.py::TestResumability::test_chaining <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resumabilityTest.py 698s [gw3] [ 96%] PASSED src/jobServiceTest.py::TestJobService::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 709s src/jobServiceTest.py::TestPerfectServicet::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 709s [gw2] [ 96%] PASSED src/resumabilityTest.py::TestResumability::test_chaining <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resumabilityTest.py 709s src/workerTest.py::WorkerTests::testNextChainable <- ../../../../usr/lib/python3/dist-packages/toil/test/src/workerTest.py 709s [gw2] [ 97%] PASSED src/workerTest.py::WorkerTests::testNextChainable <- ../../../../usr/lib/python3/dist-packages/toil/test/src/workerTest.py 739s utils/toilDebugTest.py::testFetchJobStoreFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 739s [gw0] [ 97%] PASSED utils/utilsTest.py::TestUtils::testRestartAttribute <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 740s src/promisesTest.py::ChainedIndexedPromisesTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 740s [gw2] [ 97%] PASSED utils/toilDebugTest.py::testFetchJobStoreFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 740s utils/toilKillTest.py::TestToilKillWithAWSJobStore::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 745s [gw2] [ 97%] SKIPPED utils/toilKillTest.py::TestToilKillWithAWSJobStore::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 745s [gw1] [ 98%] PASSED src/threadingTest.py::TestThreading::testLastProcessStanding <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 746s batchSystems/batch_system_plugin_test.py::BatchSystemPluginTest::test_batchsystem_plugin_installable <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batch_system_plugin_test.py 746s [gw1] [ 98%] 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 747s src/promisesTest.py::PathIndexingPromiseTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 747s [gw0] [ 98%] PASSED src/promisesTest.py::ChainedIndexedPromisesTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 750s src/systemTest.py::TestSystem::testAtomicityOfNonEmptyDirectoryRenames <- ../../../../usr/lib/python3/dist-packages/toil/test/src/systemTest.py 756s [gw1] [ 98%] PASSED src/promisesTest.py::PathIndexingPromiseTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 756s [gw3] [ 99%] PASSED src/jobServiceTest.py::TestPerfectServicet::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 766s src/promisesTest.py::CachedUnpicklingJobStoreTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 766s [gw3] [ 99%] PASSED src/promisesTest.py::CachedUnpicklingJobStoreTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 766s utils/toilKillTest.py::TestToilKill::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 1328s [gw3] [ 99%] SKIPPED utils/toilKillTest.py::TestToilKill::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 1330s [gw0] [100%] PASSED src/systemTest.py::TestSystem::testAtomicityOfNonEmptyDirectoryRenames <- ../../../../usr/lib/python3/dist-packages/toil/test/src/systemTest.py 1330s 1330s ==================================== ERRORS ==================================== 1330s _________________ ERROR collecting src/importExportFileTest.py _________________ 1330s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py'. 1330s Hint: make sure your test modules/packages have valid Python names. 1330s Traceback: 1330s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 1330s mod = import_path( 1330s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 1330s importlib.import_module(module_name) 1330s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 1330s return _bootstrap._gcd_import(name[level:], package, level) 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s :1398: in _gcd_import 1330s ??? 1330s :1371: in _find_and_load 1330s ??? 1330s :1342: in _find_and_load_unlocked 1330s ??? 1330s :938: in _load_unlocked 1330s ??? 1330s :759: in exec_module 1330s ??? 1330s :491: in _call_with_frames_removed 1330s ??? 1330s /usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py:30: in 1330s from pytest_subtests import SubTests 1330s E ModuleNotFoundError: No module named 'pytest_subtests' 1330s _________________ ERROR collecting src/jobEncapsulationTest.py _________________ 1330s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py'. 1330s Hint: make sure your test modules/packages have valid Python names. 1330s Traceback: 1330s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 1330s mod = import_path( 1330s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 1330s importlib.import_module(module_name) 1330s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 1330s return _bootstrap._gcd_import(name[level:], package, level) 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s :1398: in _gcd_import 1330s ??? 1330s :1371: in _find_and_load 1330s ??? 1330s :1342: in _find_and_load_unlocked 1330s ??? 1330s :938: in _load_unlocked 1330s ??? 1330s :759: in exec_module 1330s ??? 1330s :491: in _call_with_frames_removed 1330s ??? 1330s /usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py:17: in 1330s from toil.test.src.jobTest import fn1Test 1330s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 1330s from pytest_subtests import SubTests 1330s E ModuleNotFoundError: No module named 'pytest_subtests' 1330s _______________________ ERROR collecting src/jobTest.py ________________________ 1330s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobTest.py'. 1330s Hint: make sure your test modules/packages have valid Python names. 1330s Traceback: 1330s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 1330s mod = import_path( 1330s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 1330s importlib.import_module(module_name) 1330s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 1330s return _bootstrap._gcd_import(name[level:], package, level) 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s :1398: in _gcd_import 1330s ??? 1330s :1371: in _find_and_load 1330s ??? 1330s :1342: in _find_and_load_unlocked 1330s ??? 1330s :938: in _load_unlocked 1330s ??? 1330s :759: in exec_module 1330s ??? 1330s :491: in _call_with_frames_removed 1330s ??? 1330s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 1330s from pytest_subtests import SubTests 1330s E ModuleNotFoundError: No module named 'pytest_subtests' 1330s =================================== FAILURES =================================== 1330s __________________________ TestDocker.testDockerClean __________________________ 1330s [gw0] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 1330s toil.start(A) 1330s ~~~~~~~~~~^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v3 1330s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v3" follows: 1330s =========> 1330s [2026-01-30T07:01:40+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:01:40+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:40+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v1 1330s [2026-01-30T07:01:41+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v1 1330s [2026-01-30T07:01:41+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1330s apiDockerCall( 1330s ~~~~~~~~~~~~~^ 1330s job, 1330s ^^^^ 1330s ...<6 lines>... 1330s privileged=True, 1330s ^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:01:41+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1330s result: TResult | None = func() 1330s ~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1330s lambda: runtest_hook(item=item, **kwds), 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1330s yield 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1330s return result.get_result() 1330s ~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1330s raise exc.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1330s res = yield 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1330s item.runtest() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1330s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1330s result = testfunction(**testargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 1330s file_stats = test_file.stat() 1330s File "/usr/lib/python3.14/pathlib/__init__.py", line 655, in stat 1330s return os.stat(self, follow_symlinks=follow_symlinks) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean0/working/test.txt' 1330s ----------------------------- Captured stderr call ----------------------------- 1330s [2026-01-30T07:01:38+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 0d1f2943-0574-41bc-9c38-901bc2435ada in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean0/jobstore 1330s [2026-01-30T07:01:38+0000] [MainThread] [I] [toil.lib.history] Workflow 0d1f2943-0574-41bc-9c38-901bc2435ada is a run of 1330s [2026-01-30T07:01:38+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:38+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:01:39+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:01:41+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:01:42+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-gw0/testDockerClean0/jobstore kind-_testDockerCleanFn/instance-zoqzwv51. 1330s [2026-01-30T07:01:42+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v1 1330s Exit reason: None 1330s [2026-01-30T07:01:42+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v2 1330s [2026-01-30T07:01:42+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-zoqzwv51" follows: 1330s =========> 1330s [2026-01-30T07:01:40+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:01:40+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:40+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v1 1330s [2026-01-30T07:01:41+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v1 1330s [2026-01-30T07:01:41+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1330s apiDockerCall( 1330s ~~~~~~~~~~~~~^ 1330s job, 1330s ^^^^ 1330s ...<6 lines>... 1330s privileged=True, 1330s ^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:01:41+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:01:42+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v2 with ID kind-_testDockerCleanFn/instance-zoqzwv51 to 0 1330s [2026-01-30T07:01:42+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v3 is completely failed 1330s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1330s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v3 1330s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.lib.history] Workflow 0d1f2943-0574-41bc-9c38-901bc2435ada stopped. Success: False 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean0/jobstore) 1330s ------------------------------ Captured log call ------------------------------- 1330s INFO  toil.lib.history:history.py:369 Recording workflow creation of 0d1f2943-0574-41bc-9c38-901bc2435ada in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean0/jobstore 1330s INFO  toil.lib.history:history.py:399 Workflow 0d1f2943-0574-41bc-9c38-901bc2435ada is a run of 1330s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1330s 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-gw0/testDockerClean0/jobstore kind-_testDockerCleanFn/instance-zoqzwv51. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v1 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v2 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-zoqzwv51" follows: 1330s =========> 1330s [2026-01-30T07:01:40+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:01:40+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:40+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v1 1330s [2026-01-30T07:01:41+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v1 1330s [2026-01-30T07:01:41+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1330s apiDockerCall( 1330s ~~~~~~~~~~~~~^ 1330s job, 1330s ^^^^ 1330s ...<6 lines>... 1330s privileged=True, 1330s ^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:01:41+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v2 with ID kind-_testDockerCleanFn/instance-zoqzwv51 to 0 1330s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v3 is completely failed 1330s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1330s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-zoqzwv51 v3 1330s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1330s INFO  toil.lib.history:history.py:530 Workflow 0d1f2943-0574-41bc-9c38-901bc2435ada stopped. Success: False 1330s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean0/jobstore) 1330s _____________________ TestDocker.testDockerClean_CRx_FORGO _____________________ 1330s [gw0] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 1330s toil.start(A) 1330s ~~~~~~~~~~^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_FORGO0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v3 1330s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v3" follows: 1330s =========> 1330s [2026-01-30T07:01:48+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:01:48+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:48+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v1 1330s [2026-01-30T07:01:48+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v1 1330s [2026-01-30T07:01:48+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1330s apiDockerCall( 1330s ~~~~~~~~~~~~~^ 1330s job, 1330s ^^^^ 1330s ...<6 lines>... 1330s privileged=True, 1330s ^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:01:48+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1330s result: TResult | None = func() 1330s ~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1330s lambda: runtest_hook(item=item, **kwds), 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1330s yield 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1330s return result.get_result() 1330s ~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1330s raise exc.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1330s res = yield 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1330s item.runtest() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1330s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1330s result = testfunction(**testargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 133, in testDockerClean_CRx_FORGO 1330s self.testDockerClean( 1330s ~~~~~~~~~~~~~~~~~~~~^ 1330s tmp_path, caching=False, detached=False, rm=True, deferParam=FORGO 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 1330s file_stats = test_file.stat() 1330s File "/usr/lib/python3.14/pathlib/__init__.py", line 655, in stat 1330s return os.stat(self, follow_symlinks=follow_symlinks) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_FORGO0/working/test.txt' 1330s ----------------------------- Captured stderr call ----------------------------- 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 50caf72b-f128-455b-89cf-1e2fea443085 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_FORGO0/jobstore 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.lib.history] Workflow 50caf72b-f128-455b-89cf-1e2fea443085 is a run of 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:01:48+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-gw0/testDockerClean_CRx_FORGO0/jobstore kind-_testDockerCleanFn/instance-tqjwuj5a. 1330s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v1 1330s Exit reason: None 1330s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v2 1330s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-tqjwuj5a" follows: 1330s =========> 1330s [2026-01-30T07:01:48+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:01:48+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:48+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v1 1330s [2026-01-30T07:01:48+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v1 1330s [2026-01-30T07:01:48+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1330s apiDockerCall( 1330s ~~~~~~~~~~~~~^ 1330s job, 1330s ^^^^ 1330s ...<6 lines>... 1330s privileged=True, 1330s ^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:01:48+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v2 with ID kind-_testDockerCleanFn/instance-tqjwuj5a to 0 1330s [2026-01-30T07:01:48+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v3 is completely failed 1330s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1330s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v3 1330s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:01:52+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:01:52+0000] [MainThread] [I] [toil.lib.history] Workflow 50caf72b-f128-455b-89cf-1e2fea443085 stopped. Success: False 1330s [2026-01-30T07:01:52+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_FORGO0/jobstore) 1330s ------------------------------ Captured log call ------------------------------- 1330s INFO  toil.lib.history:history.py:369 Recording workflow creation of 50caf72b-f128-455b-89cf-1e2fea443085 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_FORGO0/jobstore 1330s INFO  toil.lib.history:history.py:399 Workflow 50caf72b-f128-455b-89cf-1e2fea443085 is a run of 1330s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s 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-gw0/testDockerClean_CRx_FORGO0/jobstore kind-_testDockerCleanFn/instance-tqjwuj5a. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v1 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v2 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-tqjwuj5a" follows: 1330s =========> 1330s [2026-01-30T07:01:48+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:01:48+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:48+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v1 1330s [2026-01-30T07:01:48+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v1 1330s [2026-01-30T07:01:48+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1330s apiDockerCall( 1330s ~~~~~~~~~~~~~^ 1330s job, 1330s ^^^^ 1330s ...<6 lines>... 1330s privileged=True, 1330s ^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:01:48+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v2 with ID kind-_testDockerCleanFn/instance-tqjwuj5a to 0 1330s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 1330s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v3 is completely failed 1330s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1330s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-tqjwuj5a v3 1330s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1330s INFO  toil.lib.history:history.py:530 Workflow 50caf72b-f128-455b-89cf-1e2fea443085 stopped. Success: False 1330s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_FORGO0/jobstore) 1330s _______________________ ToilDocumentationTest.testDocker _______________________ 1330s [gw3] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3.14/unittest/case.py", line 58, in testPartExecutor 1330s yield 1330s File "/usr/lib/python3.14/unittest/case.py", line 669, in run 1330s self._callTestMethod(testMethod) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ 1330s File "/usr/lib/python3.14/unittest/case.py", line 615, in _callTestMethod 1330s result = method() 1330s File "/usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py", line 161, in testDocker 1330s self.checkExitCode("tutorial_docker.py") 1330s ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py", line 50, in checkExitCode 1330s raise RuntimeError(stderr) 1330s RuntimeError: [2026-01-30T07:01:44+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of f2610e60-b924-43fb-a299-a65233bde05f in file:/tmp/tmpv_fc012jtutorial_docker 1330s [2026-01-30T07:01:45+0000] [MainThread] [I] [toil.lib.history] Workflow f2610e60-b924-43fb-a299-a65233bde05f is a run of /usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py 1330s [2026-01-30T07:01:45+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:45+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:01:45+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:01:46+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpv_fc012jtutorial_docker kind-apiDockerCall/instance-af6gzttt. 1330s [2026-01-30T07:01:46+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v1 1330s Exit reason: None 1330s [2026-01-30T07:01:46+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v2 1330s [2026-01-30T07:01:46+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-af6gzttt" follows: 1330s =========> 1330s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v1 1330s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-af6gzttt v1) from description 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v1 1330s [2026-01-30T07:01:46+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:01:46+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:01:46+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v2 with ID kind-apiDockerCall/instance-af6gzttt to 1 1330s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:01:48+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpv_fc012jtutorial_docker kind-apiDockerCall/instance-af6gzttt. 1330s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v3 1330s Exit reason: None 1330s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v5 1330s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-af6gzttt" follows: 1330s =========> 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v4 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-af6gzttt v4) from description 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v4 1330s [2026-01-30T07:01:47+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:01:47+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v5 with ID kind-apiDockerCall/instance-af6gzttt to 0 1330s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.leader] Job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v6 is completely failed 1330s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1330s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v6 1330s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.lib.history] Workflow f2610e60-b924-43fb-a299-a65233bde05f stopped. Success: False 1330s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/tmpv_fc012jtutorial_docker) 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py", line 20, in 1330s toil.start(align) 1330s ~~~~~~~~~~^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/tmpv_fc012jtutorial_docker' contains 1 failed jobs: 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v6 1330s Log from job "'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v6" follows: 1330s =========> 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v4 1330s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-af6gzttt v4) from description 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v4 1330s [2026-01-30T07:01:47+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:01:47+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s 1330s ---------------------------- Captured stdout setup ----------------------------- 1330s 1330s 1330s [TEST] toil.test.docs.scriptsTest.ToilDocumentationTest:testDocker (Jan 29 2026 23:01:43:291745 PST) 1330s 1330s 1330s _____________________ TestDocker.testDockerClean_CRx_STOP ______________________ 1330s [gw0] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 1330s toil.start(A) 1330s ~~~~~~~~~~^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_STOP0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v3 1330s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v3" follows: 1330s =========> 1330s [2026-01-30T07:01:53+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:01:53+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:53+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v1 1330s [2026-01-30T07:01:53+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v1 1330s [2026-01-30T07:01:53+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1330s apiDockerCall( 1330s ~~~~~~~~~~~~~^ 1330s job, 1330s ^^^^ 1330s ...<6 lines>... 1330s privileged=True, 1330s ^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:01:53+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1330s result: TResult | None = func() 1330s ~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1330s lambda: runtest_hook(item=item, **kwds), 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1330s yield 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1330s return result.get_result() 1330s ~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1330s raise exc.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1330s res = yield 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1330s item.runtest() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1330s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1330s result = testfunction(**testargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 138, in testDockerClean_CRx_STOP 1330s self.testDockerClean( 1330s ~~~~~~~~~~~~~~~~~~~~^ 1330s tmp_path, caching=False, detached=False, rm=True, deferParam=STOP 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 1330s file_stats = test_file.stat() 1330s File "/usr/lib/python3.14/pathlib/__init__.py", line 655, in stat 1330s return os.stat(self, follow_symlinks=follow_symlinks) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_STOP0/working/test.txt' 1330s ----------------------------- Captured stderr call ----------------------------- 1330s [2026-01-30T07:01:52+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of ebda0e9c-53b3-4644-aa7b-e45869bb9b37 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_STOP0/jobstore 1330s [2026-01-30T07:01:52+0000] [MainThread] [I] [toil.lib.history] Workflow ebda0e9c-53b3-4644-aa7b-e45869bb9b37 is a run of 1330s [2026-01-30T07:01:52+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:52+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:01:52+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:01:54+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-gw0/testDockerClean_CRx_STOP0/jobstore kind-_testDockerCleanFn/instance-k653mxc1. 1330s [2026-01-30T07:01:54+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v1 1330s Exit reason: None 1330s [2026-01-30T07:01:54+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v2 1330s [2026-01-30T07:01:54+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-k653mxc1" follows: 1330s =========> 1330s [2026-01-30T07:01:53+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:01:53+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:53+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v1 1330s [2026-01-30T07:01:53+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v1 1330s [2026-01-30T07:01:53+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1330s apiDockerCall( 1330s ~~~~~~~~~~~~~^ 1330s job, 1330s ^^^^ 1330s ...<6 lines>... 1330s privileged=True, 1330s ^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:01:53+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:01:54+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v2 with ID kind-_testDockerCleanFn/instance-k653mxc1 to 0 1330s [2026-01-30T07:01:54+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:01:54+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v3 is completely failed 1330s [2026-01-30T07:01:57+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:01:57+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1330s [2026-01-30T07:01:57+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v3 1330s [2026-01-30T07:01:57+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:01:58+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:01:58+0000] [MainThread] [I] [toil.lib.history] Workflow ebda0e9c-53b3-4644-aa7b-e45869bb9b37 stopped. Success: False 1330s [2026-01-30T07:01:58+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_STOP0/jobstore) 1330s ------------------------------ Captured log call ------------------------------- 1330s INFO  toil.lib.history:history.py:369 Recording workflow creation of ebda0e9c-53b3-4644-aa7b-e45869bb9b37 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_STOP0/jobstore 1330s INFO  toil.lib.history:history.py:399 Workflow ebda0e9c-53b3-4644-aa7b-e45869bb9b37 is a run of 1330s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s 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-gw0/testDockerClean_CRx_STOP0/jobstore kind-_testDockerCleanFn/instance-k653mxc1. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v1 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v2 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-k653mxc1" follows: 1330s =========> 1330s [2026-01-30T07:01:53+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:01:53+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:53+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v1 1330s [2026-01-30T07:01:53+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v1 1330s [2026-01-30T07:01:53+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1330s apiDockerCall( 1330s ~~~~~~~~~~~~~^ 1330s job, 1330s ^^^^ 1330s ...<6 lines>... 1330s privileged=True, 1330s ^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:01:53+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v2 with ID kind-_testDockerCleanFn/instance-k653mxc1 to 0 1330s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 1330s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v3 is completely failed 1330s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1330s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-k653mxc1 v3 1330s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1330s INFO  toil.lib.history:history.py:530 Workflow ebda0e9c-53b3-4644-aa7b-e45869bb9b37 stopped. Success: False 1330s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_STOP0/jobstore) 1330s ______________________ TestDocker.testDockerClean_CRx_RM _______________________ 1330s [gw0] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 1330s toil.start(A) 1330s ~~~~~~~~~~^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_RM0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v3 1330s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v3" follows: 1330s =========> 1330s [2026-01-30T07:02:00+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:00+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:00+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v1 1330s [2026-01-30T07:02:01+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v1 1330s [2026-01-30T07:02:01+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1330s apiDockerCall( 1330s ~~~~~~~~~~~~~^ 1330s job, 1330s ^^^^ 1330s ...<6 lines>... 1330s privileged=True, 1330s ^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:01+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1330s result: TResult | None = func() 1330s ~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1330s lambda: runtest_hook(item=item, **kwds), 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1330s yield 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1330s return result.get_result() 1330s ~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1330s raise exc.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1330s res = yield 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1330s item.runtest() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1330s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1330s result = testfunction(**testargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 143, in testDockerClean_CRx_RM 1330s self.testDockerClean( 1330s ~~~~~~~~~~~~~~~~~~~~^ 1330s tmp_path, caching=False, detached=False, rm=True, deferParam=RM 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 1330s file_stats = test_file.stat() 1330s File "/usr/lib/python3.14/pathlib/__init__.py", line 655, in stat 1330s return os.stat(self, follow_symlinks=follow_symlinks) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_RM0/working/test.txt' 1330s ----------------------------- Captured stderr call ----------------------------- 1330s [2026-01-30T07:01:59+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of eb2f77e2-7b97-4a8a-bb4e-ed2577e89e65 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_RM0/jobstore 1330s [2026-01-30T07:01:59+0000] [MainThread] [I] [toil.lib.history] Workflow eb2f77e2-7b97-4a8a-bb4e-ed2577e89e65 is a run of 1330s [2026-01-30T07:01:59+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:01:59+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:01:59+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:01+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:02:02+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-gw0/testDockerClean_CRx_RM0/jobstore kind-_testDockerCleanFn/instance-o5vrabje. 1330s [2026-01-30T07:02:02+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v1 1330s Exit reason: None 1330s [2026-01-30T07:02:02+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v2 1330s [2026-01-30T07:02:02+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-o5vrabje" follows: 1330s =========> 1330s [2026-01-30T07:02:00+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:00+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:00+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v1 1330s [2026-01-30T07:02:01+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v1 1330s [2026-01-30T07:02:01+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1330s apiDockerCall( 1330s ~~~~~~~~~~~~~^ 1330s job, 1330s ^^^^ 1330s ...<6 lines>... 1330s privileged=True, 1330s ^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:01+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:02+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v2 with ID kind-_testDockerCleanFn/instance-o5vrabje to 0 1330s [2026-01-30T07:02:02+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v3 is completely failed 1330s [2026-01-30T07:02:06+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:02:06+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1330s [2026-01-30T07:02:06+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v3 1330s [2026-01-30T07:02:06+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:02:06+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:02:06+0000] [MainThread] [I] [toil.lib.history] Workflow eb2f77e2-7b97-4a8a-bb4e-ed2577e89e65 stopped. Success: False 1330s [2026-01-30T07:02:06+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_RM0/jobstore) 1330s ------------------------------ Captured log call ------------------------------- 1330s INFO  toil.lib.history:history.py:369 Recording workflow creation of eb2f77e2-7b97-4a8a-bb4e-ed2577e89e65 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_RM0/jobstore 1330s INFO  toil.lib.history:history.py:399 Workflow eb2f77e2-7b97-4a8a-bb4e-ed2577e89e65 is a run of 1330s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1330s 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-gw0/testDockerClean_CRx_RM0/jobstore kind-_testDockerCleanFn/instance-o5vrabje. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v1 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v2 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-o5vrabje" follows: 1330s =========> 1330s [2026-01-30T07:02:00+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:00+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:00+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v1 1330s [2026-01-30T07:02:01+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v1 1330s [2026-01-30T07:02:01+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1330s apiDockerCall( 1330s ~~~~~~~~~~~~~^ 1330s job, 1330s ^^^^ 1330s ...<6 lines>... 1330s privileged=True, 1330s ^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:01+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v2 with ID kind-_testDockerCleanFn/instance-o5vrabje to 0 1330s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v3 is completely failed 1330s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1330s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-o5vrabje v3 1330s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1330s INFO  toil.lib.history:history.py:530 Workflow eb2f77e2-7b97-4a8a-bb4e-ed2577e89e65 stopped. Success: False 1330s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_RM0/jobstore) 1330s ________________________ TestDocker.testDockerPipeChain ________________________ 1330s [gw0] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1330s result: TResult | None = func() 1330s ~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1330s lambda: runtest_hook(item=item, **kwds), 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1330s yield 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1330s return result.get_result() 1330s ~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1330s raise exc.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1330s res = yield 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1330s item.runtest() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1330s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1330s result = testfunction(**testargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 310, in testDockerPipeChain 1330s rv = Job.Runner.startToil(A, options) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1330s return toil.start(job) 1330s ~~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerPipeChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v6 1330s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v6" follows: 1330s =========> 1330s [2026-01-30T07:02:12+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:12+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:12+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v4 1330s [2026-01-30T07:02:13+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v4 1330s [2026-01-30T07:02:13+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1330s return apiDockerCall( 1330s job, 1330s ...<2 lines>... 1330s privileged=True, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:13+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s ----------------------------- Captured stderr call ----------------------------- 1330s [2026-01-30T07:02:07+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of f9fc3405-dbad-492e-a7d1-41b8b64e8310 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerPipeChain0/jobstore 1330s [2026-01-30T07:02:07+0000] [MainThread] [I] [toil.lib.history] Workflow f9fc3405-dbad-492e-a7d1-41b8b64e8310 is a run of 1330s [2026-01-30T07:02:08+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:08+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:02:08+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:10+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:02:11+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-gw0/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-2zr83ctl. 1330s [2026-01-30T07:02:11+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v1 1330s Exit reason: None 1330s [2026-01-30T07:02:11+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v2 1330s [2026-01-30T07:02:11+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-2zr83ctl" follows: 1330s =========> 1330s [2026-01-30T07:02:09+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:09+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:09+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v1 1330s [2026-01-30T07:02:09+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v1 1330s [2026-01-30T07:02:09+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1330s return apiDockerCall( 1330s job, 1330s ...<2 lines>... 1330s privileged=True, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:09+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:11+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v2 with ID kind-_testDockerPipeChainFn/instance-2zr83ctl to 1 1330s [2026-01-30T07:02:11+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:13+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-gw0/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-2zr83ctl. 1330s [2026-01-30T07:02:13+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v3 1330s Exit reason: None 1330s [2026-01-30T07:02:13+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v5 1330s [2026-01-30T07:02:13+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-2zr83ctl" follows: 1330s =========> 1330s [2026-01-30T07:02:12+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:12+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:12+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v4 1330s [2026-01-30T07:02:13+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v4 1330s [2026-01-30T07:02:13+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1330s return apiDockerCall( 1330s job, 1330s ...<2 lines>... 1330s privileged=True, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:13+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:13+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v5 with ID kind-_testDockerPipeChainFn/instance-2zr83ctl to 0 1330s [2026-01-30T07:02:13+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v6 is completely failed 1330s [2026-01-30T07:02:17+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:02:17+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1330s [2026-01-30T07:02:17+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v6 1330s [2026-01-30T07:02:17+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:02:17+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:02:17+0000] [MainThread] [I] [toil.lib.history] Workflow f9fc3405-dbad-492e-a7d1-41b8b64e8310 stopped. Success: False 1330s [2026-01-30T07:02:17+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerPipeChain0/jobstore) 1330s ------------------------------ Captured log call ------------------------------- 1330s INFO  toil.lib.history:history.py:369 Recording workflow creation of f9fc3405-dbad-492e-a7d1-41b8b64e8310 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerPipeChain0/jobstore 1330s INFO  toil.lib.history:history.py:399 Workflow f9fc3405-dbad-492e-a7d1-41b8b64e8310 is a run of 1330s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1330s 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-gw0/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-2zr83ctl. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v1 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v2 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-2zr83ctl" follows: 1330s =========> 1330s [2026-01-30T07:02:09+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:09+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:09+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v1 1330s [2026-01-30T07:02:09+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v1 1330s [2026-01-30T07:02:09+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1330s return apiDockerCall( 1330s job, 1330s ...<2 lines>... 1330s privileged=True, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:09+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v2 with ID kind-_testDockerPipeChainFn/instance-2zr83ctl to 1 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s 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-gw0/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-2zr83ctl. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v3 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v5 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-2zr83ctl" follows: 1330s =========> 1330s [2026-01-30T07:02:12+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:12+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:12+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v4 1330s [2026-01-30T07:02:13+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v4 1330s [2026-01-30T07:02:13+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1330s return apiDockerCall( 1330s job, 1330s ...<2 lines>... 1330s privileged=True, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:13+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v5 with ID kind-_testDockerPipeChainFn/instance-2zr83ctl to 0 1330s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v6 is completely failed 1330s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1330s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v6 1330s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1330s INFO  toil.lib.history:history.py:530 Workflow f9fc3405-dbad-492e-a7d1-41b8b64e8310 stopped. Success: False 1330s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerPipeChain0/jobstore) 1330s _________________ TestDocker.testDockerPipeChainErrorDetection _________________ 1330s [gw0] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1330s result: TResult | None = func() 1330s ~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1330s lambda: runtest_hook(item=item, **kwds), 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1330s yield 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1330s return result.get_result() 1330s ~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1330s raise exc.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1330s res = yield 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1330s item.runtest() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1330s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1330s result = testfunction(**testargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 332, in testDockerPipeChainErrorDetection 1330s rv = Job.Runner.startToil(A, options) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1330s return toil.start(job) 1330s ~~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerPipeChainErrorDetect0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v6 1330s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v6" follows: 1330s =========> 1330s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v4 1330s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v4 1330s [2026-01-30T07:02:23+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1330s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1330s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:23+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s ----------------------------- Captured stderr call ----------------------------- 1330s [2026-01-30T07:02:18+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 1020adcf-fd49-485f-a63e-727a5a43cb86 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerPipeChainErrorDetect0/jobstore 1330s [2026-01-30T07:02:18+0000] [MainThread] [I] [toil.lib.history] Workflow 1020adcf-fd49-485f-a63e-727a5a43cb86 is a run of 1330s [2026-01-30T07:02:18+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:18+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:02:18+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:20+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:02:21+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-gw0/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-stk221sm. 1330s [2026-01-30T07:02:21+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v1 1330s Exit reason: None 1330s [2026-01-30T07:02:21+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v2 1330s [2026-01-30T07:02:21+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-stk221sm" follows: 1330s =========> 1330s [2026-01-30T07:02:19+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:19+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v1 1330s [2026-01-30T07:02:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v1 1330s [2026-01-30T07:02:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1330s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1330s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:21+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v2 with ID kind-_testDockerPipeChainErrorFn/instance-stk221sm to 1 1330s [2026-01-30T07:02:21+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:23+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-gw0/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-stk221sm. 1330s [2026-01-30T07:02:23+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v3 1330s Exit reason: None 1330s [2026-01-30T07:02:23+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v5 1330s [2026-01-30T07:02:23+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-stk221sm" follows: 1330s =========> 1330s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v4 1330s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v4 1330s [2026-01-30T07:02:23+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1330s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1330s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:23+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:23+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v5 with ID kind-_testDockerPipeChainErrorFn/instance-stk221sm to 0 1330s [2026-01-30T07:02:23+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v6 is completely failed 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v6 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.lib.history] Workflow 1020adcf-fd49-485f-a63e-727a5a43cb86 stopped. Success: False 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerPipeChainErrorDetect0/jobstore) 1330s ------------------------------ Captured log call ------------------------------- 1330s INFO  toil.lib.history:history.py:369 Recording workflow creation of 1020adcf-fd49-485f-a63e-727a5a43cb86 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerPipeChainErrorDetect0/jobstore 1330s INFO  toil.lib.history:history.py:399 Workflow 1020adcf-fd49-485f-a63e-727a5a43cb86 is a run of 1330s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1330s 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-gw0/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-stk221sm. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v1 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v2 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-stk221sm" follows: 1330s =========> 1330s [2026-01-30T07:02:19+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:19+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v1 1330s [2026-01-30T07:02:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v1 1330s [2026-01-30T07:02:20+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1330s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1330s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:20+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v2 with ID kind-_testDockerPipeChainErrorFn/instance-stk221sm to 1 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s 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-gw0/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-stk221sm. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v3 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v5 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-stk221sm" follows: 1330s =========> 1330s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v4 1330s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v4 1330s [2026-01-30T07:02:23+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1330s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1330s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:23+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v5 with ID kind-_testDockerPipeChainErrorFn/instance-stk221sm to 0 1330s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v6 is completely failed 1330s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1330s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v6 1330s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1330s INFO  toil.lib.history:history.py:530 Workflow 1020adcf-fd49-485f-a63e-727a5a43cb86 stopped. Success: False 1330s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerPipeChainErrorDetect0/jobstore) 1330s _____________________ TestDocker.testNonCachingDockerChain _____________________ 1330s [gw0] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1330s result: TResult | None = func() 1330s ~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1330s lambda: runtest_hook(item=item, **kwds), 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1330s yield 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1330s return result.get_result() 1330s ~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1330s raise exc.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1330s res = yield 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1330s item.runtest() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1330s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1330s result = testfunction(**testargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 336, in testNonCachingDockerChain 1330s self.testDockerPipeChain(tmp_path, caching=True) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 310, in testDockerPipeChain 1330s rv = Job.Runner.startToil(A, options) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1330s return toil.start(job) 1330s ~~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testNonCachingDockerChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v6 1330s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v6" follows: 1330s =========> 1330s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4 1330s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4 1330s [2026-01-30T07:02:28+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4 used 1.00x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:02:28+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1330s return apiDockerCall( 1330s job, 1330s ...<2 lines>... 1330s privileged=True, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:28+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s ----------------------------- Captured stderr call ----------------------------- 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 07157293-8314-4b9c-8e6e-6dbfaf4826d2 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testNonCachingDockerChain0/jobstore 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.lib.history] Workflow 07157293-8314-4b9c-8e6e-6dbfaf4826d2 is a run of 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:27+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-gw0/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-6ztzu3qa. 1330s [2026-01-30T07:02:27+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v1 1330s Exit reason: None 1330s [2026-01-30T07:02:27+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v2 1330s [2026-01-30T07:02:27+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-6ztzu3qa" follows: 1330s =========> 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v1 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v1 1330s [2026-01-30T07:02:27+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v1 used 1.14x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:02:27+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1330s return apiDockerCall( 1330s job, 1330s ...<2 lines>... 1330s privileged=True, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:27+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:27+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v2 with ID kind-_testDockerPipeChainFn/instance-6ztzu3qa to 1 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:28+0000] [Thread-29 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:02:28: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v1 used 1.14x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:02:28+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-gw0/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-6ztzu3qa. 1330s [2026-01-30T07:02:28+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v3 1330s Exit reason: None 1330s [2026-01-30T07:02:28+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v5 1330s [2026-01-30T07:02:28+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-6ztzu3qa" follows: 1330s =========> 1330s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4 1330s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4 1330s [2026-01-30T07:02:28+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4 used 1.00x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:02:28+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1330s return apiDockerCall( 1330s job, 1330s ...<2 lines>... 1330s privileged=True, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:28+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:28+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v5 with ID kind-_testDockerPipeChainFn/instance-6ztzu3qa to 0 1330s [2026-01-30T07:02:28+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v6 is completely failed 1330s [2026-01-30T07:02:28+0000] [Thread-29 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:02:28: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4 used 1.00x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:02:32+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:02:32+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1330s [2026-01-30T07:02:32+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v6 1330s [2026-01-30T07:02:32+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil.lib.history] Workflow 07157293-8314-4b9c-8e6e-6dbfaf4826d2 stopped. Success: False 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testNonCachingDockerChain0/jobstore) 1330s ------------------------------ Captured log call ------------------------------- 1330s INFO  toil.lib.history:history.py:369 Recording workflow creation of 07157293-8314-4b9c-8e6e-6dbfaf4826d2 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testNonCachingDockerChain0/jobstore 1330s INFO  toil.lib.history:history.py:399 Workflow 07157293-8314-4b9c-8e6e-6dbfaf4826d2 is a run of 1330s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s 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-gw0/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-6ztzu3qa. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v1 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v2 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-6ztzu3qa" follows: 1330s =========> 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v1 1330s [2026-01-30T07:02:27+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v1 1330s [2026-01-30T07:02:27+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v1 used 1.14x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:02:27+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1330s return apiDockerCall( 1330s job, 1330s ...<2 lines>... 1330s privileged=True, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:27+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v2 with ID kind-_testDockerPipeChainFn/instance-6ztzu3qa to 1 1330s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:02:28: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v1 used 1.14x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s 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-gw0/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-6ztzu3qa. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v3 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v5 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-6ztzu3qa" follows: 1330s =========> 1330s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4 1330s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4 1330s [2026-01-30T07:02:28+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4 used 1.00x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:02:28+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1330s return apiDockerCall( 1330s job, 1330s ...<2 lines>... 1330s privileged=True, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:28+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v5 with ID kind-_testDockerPipeChainFn/instance-6ztzu3qa to 0 1330s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v6 is completely failed 1330s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:02:28: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4 used 1.00x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1330s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v6 1330s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1330s INFO  toil.lib.history:history.py:530 Workflow 07157293-8314-4b9c-8e6e-6dbfaf4826d2 stopped. Success: False 1330s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testNonCachingDockerChain0/jobstore) 1330s ______________ TestDocker.testNonCachingDockerChainErrorDetection ______________ 1330s [gw0] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1330s result: TResult | None = func() 1330s ~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1330s lambda: runtest_hook(item=item, **kwds), 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1330s yield 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1330s return result.get_result() 1330s ~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1330s raise exc.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1330s res = yield 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1330s item.runtest() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1330s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1330s result = testfunction(**testargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 339, in testNonCachingDockerChainErrorDetection 1330s self.testDockerPipeChainErrorDetection(tmp_path, caching=True) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 332, in testDockerPipeChainErrorDetection 1330s rv = Job.Runner.startToil(A, options) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1330s return toil.start(job) 1330s ~~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testNonCachingDockerChainError0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v6 1330s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v6" follows: 1330s =========> 1330s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v4 1330s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v4 1330s [2026-01-30T07:02:34+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 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. 1330s [2026-01-30T07:02:34+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1330s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1330s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:34+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s ----------------------------- Captured stderr call ----------------------------- 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of fac25d36-990a-48aa-b3dd-2db142b075ca in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testNonCachingDockerChainError0/jobstore 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil.lib.history] Workflow fac25d36-990a-48aa-b3dd-2db142b075ca is a run of 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:34+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-gw0/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-kanj6ak1. 1330s [2026-01-30T07:02:34+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v1 1330s Exit reason: None 1330s [2026-01-30T07:02:34+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v2 1330s [2026-01-30T07:02:34+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-kanj6ak1" follows: 1330s =========> 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v1 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v1 1330s [2026-01-30T07:02:33+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v1 used 1.15x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:02:33+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1330s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1330s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:33+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:34+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v2 with ID kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 to 1 1330s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:34+0000] [Thread-33 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:02:34: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v1 used 1.15x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:02:34+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-gw0/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-kanj6ak1. 1330s [2026-01-30T07:02:34+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v3 1330s Exit reason: None 1330s [2026-01-30T07:02:34+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v5 1330s [2026-01-30T07:02:34+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-kanj6ak1" follows: 1330s =========> 1330s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v4 1330s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v4 1330s [2026-01-30T07:02:34+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 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. 1330s [2026-01-30T07:02:34+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1330s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1330s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:34+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:34+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v5 with ID kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 to 0 1330s [2026-01-30T07:02:34+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v6 is completely failed 1330s [2026-01-30T07:02:35+0000] [Thread-33 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:02:34: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 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. 1330s [2026-01-30T07:02:38+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:02:38+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1330s [2026-01-30T07:02:38+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v6 1330s [2026-01-30T07:02:38+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil.lib.history] Workflow fac25d36-990a-48aa-b3dd-2db142b075ca stopped. Success: False 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testNonCachingDockerChainError0/jobstore) 1330s ------------------------------ Captured log call ------------------------------- 1330s INFO  toil.lib.history:history.py:369 Recording workflow creation of fac25d36-990a-48aa-b3dd-2db142b075ca in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testNonCachingDockerChainError0/jobstore 1330s INFO  toil.lib.history:history.py:399 Workflow fac25d36-990a-48aa-b3dd-2db142b075ca is a run of 1330s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s 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-gw0/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-kanj6ak1. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v1 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v2 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-kanj6ak1" follows: 1330s =========> 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v1 1330s [2026-01-30T07:02:33+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v1 1330s [2026-01-30T07:02:33+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v1 used 1.15x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:02:33+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1330s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1330s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:33+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v2 with ID kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 to 1 1330s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:02:34: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v1 used 1.15x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s 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-gw0/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-kanj6ak1. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v3 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v5 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-kanj6ak1" follows: 1330s =========> 1330s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v4 1330s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v4 1330s [2026-01-30T07:02:34+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 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. 1330s [2026-01-30T07:02:34+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1330s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1330s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:34+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v5 with ID kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 to 0 1330s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v6 is completely failed 1330s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:02:34: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 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. 1330s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1330s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v6 1330s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1330s INFO  toil.lib.history:history.py:530 Workflow fac25d36-990a-48aa-b3dd-2db142b075ca stopped. Success: False 1330s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testNonCachingDockerChainError0/jobstore) 1330s __________________________ TestDocker.testDockerLogs ___________________________ 1330s [gw0] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1330s result: TResult | None = func() 1330s ~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1330s lambda: runtest_hook(item=item, **kwds), 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1330s yield 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1330s return result.get_result() 1330s ~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1330s raise exc.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1330s res = yield 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1330s item.runtest() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1330s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1330s result = testfunction(**testargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 1330s rv = Job.Runner.startToil(A, options) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1330s return toil.start(job) 1330s ~~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v6 1330s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v6" follows: 1330s =========> 1330s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v4 1330s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v4 1330s [2026-01-30T07:02:40+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:40+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s ----------------------------- Captured stderr call ----------------------------- 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of c4eb55f0-09a7-4028-be7b-7cddd93b9977 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs0/jobstore 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil.lib.history] Workflow c4eb55f0-09a7-4028-be7b-7cddd93b9977 is a run of 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:40+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-gw0/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-40spkqys. 1330s [2026-01-30T07:02:40+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v1 1330s Exit reason: None 1330s [2026-01-30T07:02:40+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v2 1330s [2026-01-30T07:02:40+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-40spkqys" follows: 1330s =========> 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v1 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v1 1330s [2026-01-30T07:02:39+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:39+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:40+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v2 with ID kind-_testDockerLogsFn/instance-40spkqys to 1 1330s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:40+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-gw0/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-40spkqys. 1330s [2026-01-30T07:02:40+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v3 1330s Exit reason: None 1330s [2026-01-30T07:02:40+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v5 1330s [2026-01-30T07:02:40+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-40spkqys" follows: 1330s =========> 1330s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v4 1330s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v4 1330s [2026-01-30T07:02:40+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:40+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:40+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v5 with ID kind-_testDockerLogsFn/instance-40spkqys to 0 1330s [2026-01-30T07:02:40+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v6 is completely failed 1330s [2026-01-30T07:02:44+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:02:44+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1330s [2026-01-30T07:02:44+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v6 1330s [2026-01-30T07:02:44+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:02:45+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:02:45+0000] [MainThread] [I] [toil.lib.history] Workflow c4eb55f0-09a7-4028-be7b-7cddd93b9977 stopped. Success: False 1330s [2026-01-30T07:02:45+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs0/jobstore) 1330s ------------------------------ Captured log call ------------------------------- 1330s INFO  toil.lib.history:history.py:369 Recording workflow creation of c4eb55f0-09a7-4028-be7b-7cddd93b9977 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs0/jobstore 1330s INFO  toil.lib.history:history.py:399 Workflow c4eb55f0-09a7-4028-be7b-7cddd93b9977 is a run of 1330s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s 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-gw0/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-40spkqys. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v1 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v2 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-40spkqys" follows: 1330s =========> 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v1 1330s [2026-01-30T07:02:39+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v1 1330s [2026-01-30T07:02:39+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:39+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v2 with ID kind-_testDockerLogsFn/instance-40spkqys to 1 1330s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s 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-gw0/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-40spkqys. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v3 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v5 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-40spkqys" follows: 1330s =========> 1330s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v4 1330s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v4 1330s [2026-01-30T07:02:40+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:40+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v5 with ID kind-_testDockerLogsFn/instance-40spkqys to 0 1330s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v6 is completely failed 1330s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1330s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v6 1330s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1330s INFO  toil.lib.history:history.py:530 Workflow c4eb55f0-09a7-4028-be7b-7cddd93b9977 stopped. Success: False 1330s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs0/jobstore) 1330s _______________________ TestDocker.testDockerLogs_Stream _______________________ 1330s [gw0] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1330s result: TResult | None = func() 1330s ~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1330s lambda: runtest_hook(item=item, **kwds), 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1330s yield 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1330s return result.get_result() 1330s ~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1330s raise exc.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1330s res = yield 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1330s item.runtest() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1330s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1330s result = testfunction(**testargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 366, in testDockerLogs_Stream 1330s self.testDockerLogs(tmp_path, stream=True, demux=False) 1330s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 1330s rv = Job.Runner.startToil(A, options) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1330s return toil.start(job) 1330s ~~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v6 1330s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v6" follows: 1330s =========> 1330s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v4 1330s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v4 1330s [2026-01-30T07:02:50+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:50+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s ----------------------------- Captured stderr call ----------------------------- 1330s [2026-01-30T07:02:45+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 24803836-efff-4f9a-8d29-4dc5913b91a7 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Stream0/jobstore 1330s [2026-01-30T07:02:45+0000] [MainThread] [I] [toil.lib.history] Workflow 24803836-efff-4f9a-8d29-4dc5913b91a7 is a run of 1330s [2026-01-30T07:02:46+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:46+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:02:46+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:48+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:02:49+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-gw0/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-sxbjohmq. 1330s [2026-01-30T07:02:49+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v1 1330s Exit reason: None 1330s [2026-01-30T07:02:49+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v2 1330s [2026-01-30T07:02:49+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-sxbjohmq" follows: 1330s =========> 1330s [2026-01-30T07:02:48+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:48+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:48+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v1 1330s [2026-01-30T07:02:49+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v1 1330s [2026-01-30T07:02:49+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:49+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:49+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v2 with ID kind-_testDockerLogsFn/instance-sxbjohmq to 1 1330s [2026-01-30T07:02:49+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:50+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-gw0/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-sxbjohmq. 1330s [2026-01-30T07:02:50+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v3 1330s Exit reason: None 1330s [2026-01-30T07:02:50+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v5 1330s [2026-01-30T07:02:50+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-sxbjohmq" follows: 1330s =========> 1330s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v4 1330s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v4 1330s [2026-01-30T07:02:50+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:50+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:50+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v5 with ID kind-_testDockerLogsFn/instance-sxbjohmq to 0 1330s [2026-01-30T07:02:50+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v6 is completely failed 1330s [2026-01-30T07:02:54+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:02:54+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1330s [2026-01-30T07:02:54+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v6 1330s [2026-01-30T07:02:54+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:02:54+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:02:54+0000] [MainThread] [I] [toil.lib.history] Workflow 24803836-efff-4f9a-8d29-4dc5913b91a7 stopped. Success: False 1330s [2026-01-30T07:02:54+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Stream0/jobstore) 1330s ------------------------------ Captured log call ------------------------------- 1330s INFO  toil.lib.history:history.py:369 Recording workflow creation of 24803836-efff-4f9a-8d29-4dc5913b91a7 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Stream0/jobstore 1330s INFO  toil.lib.history:history.py:399 Workflow 24803836-efff-4f9a-8d29-4dc5913b91a7 is a run of 1330s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1330s 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-gw0/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-sxbjohmq. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v1 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v2 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-sxbjohmq" follows: 1330s =========> 1330s [2026-01-30T07:02:48+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:48+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:48+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v1 1330s [2026-01-30T07:02:49+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v1 1330s [2026-01-30T07:02:49+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:49+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v2 with ID kind-_testDockerLogsFn/instance-sxbjohmq to 1 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s 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-gw0/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-sxbjohmq. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v3 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v5 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-sxbjohmq" follows: 1330s =========> 1330s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v4 1330s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v4 1330s [2026-01-30T07:02:50+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:50+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v5 with ID kind-_testDockerLogsFn/instance-sxbjohmq to 0 1330s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v6 is completely failed 1330s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1330s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v6 1330s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1330s INFO  toil.lib.history:history.py:530 Workflow 24803836-efff-4f9a-8d29-4dc5913b91a7 stopped. Success: False 1330s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Stream0/jobstore) 1330s _______________________ TestDocker.testDockerLogs_Demux ________________________ 1330s [gw0] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1330s result: TResult | None = func() 1330s ~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1330s lambda: runtest_hook(item=item, **kwds), 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1330s yield 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1330s return result.get_result() 1330s ~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1330s raise exc.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1330s res = yield 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1330s item.runtest() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1330s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1330s result = testfunction(**testargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 369, in testDockerLogs_Demux 1330s self.testDockerLogs(tmp_path, stream=False, demux=True) 1330s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 1330s rv = Job.Runner.startToil(A, options) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1330s return toil.start(job) 1330s ~~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Demux0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v6 1330s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v6" follows: 1330s =========> 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v4 1330s [2026-01-30T07:02:56+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v4 1330s [2026-01-30T07:02:56+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:56+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s ----------------------------- Captured stderr call ----------------------------- 1330s [2026-01-30T07:02:54+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 9ab07141-53a2-45af-8484-80d1f049282c in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Demux0/jobstore 1330s [2026-01-30T07:02:54+0000] [MainThread] [I] [toil.lib.history] Workflow 9ab07141-53a2-45af-8484-80d1f049282c is a run of 1330s [2026-01-30T07:02:54+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:54+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:02:54+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:55+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-gw0/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-o3abbidv. 1330s [2026-01-30T07:02:55+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v1 1330s Exit reason: None 1330s [2026-01-30T07:02:55+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v2 1330s [2026-01-30T07:02:55+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-o3abbidv" follows: 1330s =========> 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v1 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v1 1330s [2026-01-30T07:02:55+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:55+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:55+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v2 with ID kind-_testDockerLogsFn/instance-o3abbidv to 1 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:02:56+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-gw0/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-o3abbidv. 1330s [2026-01-30T07:02:56+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v3 1330s Exit reason: None 1330s [2026-01-30T07:02:56+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v5 1330s [2026-01-30T07:02:56+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-o3abbidv" follows: 1330s =========> 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v4 1330s [2026-01-30T07:02:56+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v4 1330s [2026-01-30T07:02:56+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:56+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:02:56+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v5 with ID kind-_testDockerLogsFn/instance-o3abbidv to 0 1330s [2026-01-30T07:02:56+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v6 is completely failed 1330s [2026-01-30T07:02:59+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:02:59+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1330s [2026-01-30T07:02:59+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v6 1330s [2026-01-30T07:02:59+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:03:00+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:03:00+0000] [MainThread] [I] [toil.lib.history] Workflow 9ab07141-53a2-45af-8484-80d1f049282c stopped. Success: False 1330s [2026-01-30T07:03:00+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Demux0/jobstore) 1330s ------------------------------ Captured log call ------------------------------- 1330s INFO  toil.lib.history:history.py:369 Recording workflow creation of 9ab07141-53a2-45af-8484-80d1f049282c in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Demux0/jobstore 1330s INFO  toil.lib.history:history.py:399 Workflow 9ab07141-53a2-45af-8484-80d1f049282c is a run of 1330s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s 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-gw0/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-o3abbidv. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v1 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v2 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-o3abbidv" follows: 1330s =========> 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v1 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v1 1330s [2026-01-30T07:02:55+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:55+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v2 with ID kind-_testDockerLogsFn/instance-o3abbidv to 1 1330s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s 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-gw0/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-o3abbidv. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v3 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v5 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-o3abbidv" follows: 1330s =========> 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v4 1330s [2026-01-30T07:02:56+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v4 1330s [2026-01-30T07:02:56+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:02:56+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v5 with ID kind-_testDockerLogsFn/instance-o3abbidv to 0 1330s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v6 is completely failed 1330s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1330s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v6 1330s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1330s INFO  toil.lib.history:history.py:530 Workflow 9ab07141-53a2-45af-8484-80d1f049282c stopped. Success: False 1330s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Demux0/jobstore) 1330s ____________________ TestDocker.testDockerLogs_Demux_Stream ____________________ 1330s [gw0] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1330s result: TResult | None = func() 1330s ~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1330s lambda: runtest_hook(item=item, **kwds), 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1330s yield 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1330s return result.get_result() 1330s ~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1330s raise exc.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1330s res = yield 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1330s item.runtest() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1330s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1330s result = testfunction(**testargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 372, in testDockerLogs_Demux_Stream 1330s self.testDockerLogs(tmp_path, stream=True, demux=True) 1330s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 1330s rv = Job.Runner.startToil(A, options) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1330s return toil.start(job) 1330s ~~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Demux_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v6 1330s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v6" follows: 1330s =========> 1330s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v4 1330s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v4 1330s [2026-01-30T07:03:02+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:03:02+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s ----------------------------- Captured stderr call ----------------------------- 1330s [2026-01-30T07:03:00+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of ea8c3465-f32d-41cd-bcae-b3ffa9041e66 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Demux_Stream0/jobstore 1330s [2026-01-30T07:03:00+0000] [MainThread] [I] [toil.lib.history] Workflow ea8c3465-f32d-41cd-bcae-b3ffa9041e66 is a run of 1330s [2026-01-30T07:03:00+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:03:00+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:03:00+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:03:02+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-gw0/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-m1zzytz9. 1330s [2026-01-30T07:03:02+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v1 1330s Exit reason: None 1330s [2026-01-30T07:03:02+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v2 1330s [2026-01-30T07:03:02+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-m1zzytz9" follows: 1330s =========> 1330s [2026-01-30T07:03:00+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:03:00+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:03:00+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v1 1330s [2026-01-30T07:03:01+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v1 1330s [2026-01-30T07:03:01+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:03:01+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:03:02+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v2 with ID kind-_testDockerLogsFn/instance-m1zzytz9 to 1 1330s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s [2026-01-30T07:03:02+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-gw0/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-m1zzytz9. 1330s [2026-01-30T07:03:02+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v3 1330s Exit reason: None 1330s [2026-01-30T07:03:02+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v5 1330s [2026-01-30T07:03:02+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-m1zzytz9" follows: 1330s =========> 1330s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v4 1330s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v4 1330s [2026-01-30T07:03:02+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:03:02+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s [2026-01-30T07:03:02+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v5 with ID kind-_testDockerLogsFn/instance-m1zzytz9 to 0 1330s [2026-01-30T07:03:02+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v6 is completely failed 1330s [2026-01-30T07:03:06+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:03:06+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1330s [2026-01-30T07:03:06+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v6 1330s [2026-01-30T07:03:06+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:03:06+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:03:06+0000] [MainThread] [I] [toil.lib.history] Workflow ea8c3465-f32d-41cd-bcae-b3ffa9041e66 stopped. Success: False 1330s [2026-01-30T07:03:07+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Demux_Stream0/jobstore) 1330s ------------------------------ Captured log call ------------------------------- 1330s INFO  toil.lib.history:history.py:369 Recording workflow creation of ea8c3465-f32d-41cd-bcae-b3ffa9041e66 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Demux_Stream0/jobstore 1330s INFO  toil.lib.history:history.py:399 Workflow ea8c3465-f32d-41cd-bcae-b3ffa9041e66 is a run of 1330s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s 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-gw0/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-m1zzytz9. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v1 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v2 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-m1zzytz9" follows: 1330s =========> 1330s [2026-01-30T07:03:00+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:03:00+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:03:00+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v1 1330s [2026-01-30T07:03:01+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v1 1330s [2026-01-30T07:03:01+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:03:01+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v2 with ID kind-_testDockerLogsFn/instance-m1zzytz9 to 1 1330s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 1330s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1330s 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-gw0/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-m1zzytz9. 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v3 1330s Exit reason: None 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v5 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-m1zzytz9" follows: 1330s =========> 1330s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v4 1330s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v4 1330s [2026-01-30T07:03:02+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s PermissionError: [Errno 13] Permission denied 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1330s resp = conn.urlopen( 1330s method=request.method, 1330s ...<9 lines>... 1330s chunked=chunked, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1330s retries = retries.increment( 1330s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1330s raise reraise(type(error), error, _stacktrace) 1330s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1330s raise value.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1330s response = self._make_request( 1330s conn, 1330s ...<10 lines>... 1330s **response_kw, 1330s ) 1330s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1330s conn.request( 1330s ~~~~~~~~~~~~^ 1330s method, 1330s ^^^^^^^ 1330s ...<6 lines>... 1330s enforce_content_length=enforce_content_length, 1330s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1330s self.endheaders() 1330s ~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1330s self._send_output(message_body, encode_chunked=encode_chunked) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1330s self.send(msg) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1330s self.connect() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1330s sock.connect(self.unix_socket) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1330s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s During handling of the above exception, another exception occurred: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1330s return self.version(api_version=False)["ApiVersion"] 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1330s return self._result(self._get(url), json=True) 1330s ~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1330s return f(self, *args, **kwargs) 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1330s return self.get(url, **self._set_request_timeout(kwargs)) 1330s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1330s return self.request("GET", url, **kwargs) 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1330s resp = self.send(prep, **send_kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1330s r = adapter.send(request, **kwargs) 1330s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1330s raise ConnectionError(err, request=request) 1330s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s The above exception was the direct cause of the following exception: 1330s 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1330s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1330s out = apiDockerCall( 1330s job, 1330s ...<8 lines>... 1330s demux=demux, 1330s ) 1330s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1330s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1330s return cls( 1330s timeout=timeout, 1330s ...<3 lines>... 1330s **kwargs_from_env(**kwargs) 1330s ) 1330s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1330s self.api = APIClient(*args, **kwargs) 1330s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1330s self._version = self._retrieve_server_version() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1330s raise DockerException( 1330s f'Error while fetching server API version: {e}' 1330s ) from e 1330s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1330s 1330s [2026-01-30T07:03:02+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v5 with ID kind-_testDockerLogsFn/instance-m1zzytz9 to 0 1330s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v6 is completely failed 1330s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1330s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v6 1330s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1330s INFO  toil.lib.history:history.py:530 Workflow ea8c3465-f32d-41cd-bcae-b3ffa9041e66 stopped. Success: False 1330s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Demux_Stream0/jobstore) 1330s __ TestSingleMachinePromisedRequirements.testPromisesWithJobStoreFileObjects ___ 1330s [gw3] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1330s result: TResult | None = func() 1330s ~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1330s lambda: runtest_hook(item=item, **kwds), 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1330s yield 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1330s return result.get_result() 1330s ~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1330s raise exc.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1330s res = yield 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1330s item.runtest() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1330s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1330s result = testfunction(**testargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py", line 145, in testPromisesWithJobStoreFileObjects 1330s Job.Runner.startToil(F1, self.getOptions(tmp_path, caching=caching)) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1330s return toil.start(job) 1330s ~~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore' contains 2 failed jobs: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8, '_writer' kind-_writer/instance-0jjweo4g v4 1330s Log from job "'_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8" follows: 1330s =========> 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'ddb3944d-bb71-491a-8af0-2530f6b8aa01', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpibd3pj3m', '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} 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/funcnzj665b2 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.worker] Parsed job description 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1330s [2026-01-30T07:05:49+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:49+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:49+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. 1330s [2026-01-30T07:05:50+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:50+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:50+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. 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore'. 1330s [2026-01-30T07:05:50+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6) from description '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6) with ID (kind-EncapsulatedJob/instance-zzj5b9s8). 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6) with ID (kind-EncapsulatedJob/instance-zzj5b9s8) which wants 2147483648 of our 100589039616 bytes. 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 100589039616 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 100589039616 bytes 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:50+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 used 4.50x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:05:50+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 1330s self.evaluatePromisedRequirements() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 1330s ].getValue() 1330s ~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 1330s return func(*self._args) 1330s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 1330s 1330s [2026-01-30T07:05:50+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [pydot] pydot initializing 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [pydot] pydot 4.0.1 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1330s <========= 1330s ----------------------------- Captured stderr call ----------------------------- 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.common] Initialized default configuration: {"config_version": 1.0} 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.batchSystems.options] Add options for aws_batch batch system 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.batchSystems.options] Add options for single_machine batch system 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.batchSystems.options] Add options for grid_engine batch system 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.batchSystems.options] Add options for lsf batch system 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.batchSystems.options] Add options for slurm batch system 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.batchSystems.options] Add options for torque batch system 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'urllib3', 'salad', 'asyncio', 'requests', 'rdflib', 'concurrent', 'boto3', 'humanfriendly', 'debugWorkflow', 'dill', 'test', 'cwltest', 'boto', 'bcdocs', 'cachecontrol', 'docker', 'botocore'} 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.statsAndLogging] Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'urllib3', 'salad', 'asyncio', 'requests', 'rdflib', 'concurrent', 'boto3', 'humanfriendly', 'debugWorkflow', 'dill', 'test', 'cwltest', 'boto', 'bcdocs', 'cachecontrol', 'docker', 'botocore'} 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.statsAndLogging] Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.common] Initialized default configuration: {"config_version": 1.0} 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.batchSystems.options] Add options for aws_batch batch system 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.batchSystems.options] Add options for single_machine batch system 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.batchSystems.options] Add options for grid_engine batch system 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.batchSystems.options] Add options for lsf batch system 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.batchSystems.options] Add options for slurm batch system 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.batchSystems.options] Add options for torque batch system 1330s [2026-01-30T07:05:44+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-gw3/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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} 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore'. 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.jobStores.abstractJobStore] The workflow ID is: 'ddb3944d-bb71-491a-8af0-2530f6b8aa01' 1330s [2026-01-30T07:05:44+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of ddb3944d-bb71-491a-8af0-2530f6b8aa01 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore 1330s [2026-01-30T07:05:44+0000] [MainThread] [I] [toil.lib.history] Workflow ddb3944d-bb71-491a-8af0-2530f6b8aa01 is a run of 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.common] Using the single machine batch system 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.common] Created the workflow directory for this machine at /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 1330s [2026-01-30T07:05:44+0000] [Thread-33 (daddy)] [D] [toil.batchSystems.singleMachine] Started daddy thread for batch system 4395914683376. 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Started batch system 4395914683376 in normal mode. 1330s [2026-01-30T07:05:44+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. 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.common] No user script to auto-deploy. 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.common] Written the environment for the jobs to the environment file 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.common] Caching all jobs in job store 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.common] 0 jobs downloaded. 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-4cb64118db38401f9718009df6664b46/stream for result of '_writer' TemporaryID(06bf9a78-b31e-4a1e-9a10-beb2873d214f) v0 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.job] Saving graph of 5 jobs, 5 non-service, 5 new 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.job] Processing job 'Job' kind-Job/instance-udha0fwb v0 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.job] Processing job '_follower' kind-_follower/instance-b2nm9dsr v0 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-d87f34bfc397446da8408462ffd3809c/stream for result of '_writer' kind-_writer/instance-0jjweo4g v0 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-3754b37b5f454ddca89a8dd48252222d/stream for result of '_writer' kind-_writer/instance-1i_cf2_k v0 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v0 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-1i_cf2_k v0 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-0jjweo4g v0 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.job] New job version: 'Job' kind-Job/instance-udha0fwb v1 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-_follower/instance-b2nm9dsr v1 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-1i_cf2_k v1 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-0jjweo4g v1 1330s [2026-01-30T07:05:44+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'ddb3944d-bb71-491a-8af0-2530f6b8aa01', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpibd3pj3m', '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} 1330s [2026-01-30T07:05:44+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.bus] Listening for message topic: toil.bus.JobUpdatedMessage 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.toilState] Found job to run: kind-_writer/instance-0jjweo4g, with body: True, with checkpoint: False, with services: False, with no next successors: False 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-0jjweo4g', result_status=0) 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.leader] Found 1 jobs to start and 0 jobs with successors to run 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.leader] Checked batch system has no running jobs and no updated jobs 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.serviceManager] Initializing service manager 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-0jjweo4g v1 with result status: 0 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-_writer/instance-0jjweo4g with disk: 2.0 Gi, memory: 2.0 Gi, cores: 2.0, accelerators: [], preemptible: False 1330s [2026-01-30T07:05:44+0000] [MainThread] [I] [toil.leader] Issued job '_writer' kind-_writer/instance-0jjweo4g v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 2, accelerators: [], preemptible: False 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_writer', job_id='kind-_writer/instance-0jjweo4g', toil_batch_id=1) 1330s [2026-01-30T07:05:44+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 1330s [2026-01-30T07:05:44+0000] [Thread-33 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-_writer/instance-0jjweo4g 1330s [2026-01-30T07:05:44+0000] [Thread-33 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 1 as child 9757 1330s [2026-01-30T07:05:45+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'requests', 'concurrent', 'botocore', 'boto', 'dill', 'boto3', 'asyncio', 'docker', 'urllib3'} 1330s [2026-01-30T07:05:45+0000] [MainThread] [D] [toil.worker] Worker started for job _writer... 1330s [2026-01-30T07:05:45+0000] [MainThread] [D] [toil.common] Obtained node ID 6fa530d97284404a9688ce299e64170e from file /var/lib/dbus/machine-id 1330s [2026-01-30T07:05:45+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:45+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/1296/worker_log.txt 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/funczrgbjge3 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=1, external_batch_id='9757', batch_system='SingleMachineBatchSystem') 1330s [2026-01-30T07:05:46+0000] [Thread-33 (daddy)] [D] [toil.batchSystems.singleMachine] Child 9757 for job 1 succeeded 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 1 with exit value: 0 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.leader] Job ended: '_writer' kind-_writer/instance-0jjweo4g v1 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_writer', job_id='kind-_writer/instance-0jjweo4g', exit_code=0) 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.leader] Job '_writer' kind-_writer/instance-0jjweo4g v1 continues to exist (i.e. has more to do) 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-0jjweo4g', result_status=0) 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.leader] Added job: '_writer' kind-_writer/instance-0jjweo4g v4 to updated jobs 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-0jjweo4g v4 with result status: 0 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.leader] Job: kind-_writer/instance-0jjweo4g has 1 successors to schedule 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.toilState] Successors: 1 more for kind-_writer/instance-0jjweo4g, now have 1 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.leader] Added job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 as coming after job '_writer' kind-_writer/instance-0jjweo4g v4 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-zzj5b9s8 with disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.leader] Issued job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 with job batch system ID: 2 and disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-zzj5b9s8', toil_batch_id=2) 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 1330s [2026-01-30T07:05:46+0000] [Thread-33 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-zzj5b9s8 1330s [2026-01-30T07:05:46+0000] [Thread-33 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 2 as child 9782 1330s [2026-01-30T07:05:46+0000] [Thread-36 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:05:46: Job '_writer' kind-_writer/instance-0jjweo4g v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:46+0000] [Thread-36 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:05:46: Job '_writer' kind-_writer/instance-0jjweo4g v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:46+0000] [Thread-36 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Received Toil worker log. Disable debug level logging to hide this output 1330s [2026-01-30T07:05:46+0000] [Thread-36 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Log from job "JobFunctionWrappingJob" follows: 1330s =========> 1330s [2026-01-30T07:05:45+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:05:45+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:05:45+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'ddb3944d-bb71-491a-8af0-2530f6b8aa01', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpibd3pj3m', '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} 1330s [2026-01-30T07:05:45+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/funczrgbjge3 1330s [2026-01-30T07:05:45+0000] [MainThread] [D] [toil.worker] Parsed job description 1330s [2026-01-30T07:05:45+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-0jjweo4g v1 1330s [2026-01-30T07:05:45+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:46+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. 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:46+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. 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-0jjweo4g v1) from description '_writer' kind-_writer/instance-0jjweo4g v1 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-0jjweo4g v1) with ID (kind-_writer/instance-0jjweo4g). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_writer' kind-_writer/instance-0jjweo4g v1) with ID (kind-_writer/instance-0jjweo4g) which wants 2147483648 of our 100589039616 bytes. 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 100589039616 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 0 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 100589039616 bytes 1330s [2026-01-30T07:05:46+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). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Hardlinked file /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/1296/job/tmpesj6yvnn.tmp into cache at /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/cache-ddb3944d-bb71-491a-8af0-2530f6b8aa01/tmpl8x6feclda0630cdd8595f613377f1fad1daee7b7dbaf609; deferring write to job store 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-4cb64118db38401f9718009df6664b46/stream from Job('_writer' kind-_writer/instance-0jjweo4g v1) with a 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-d87f34bfc397446da8408462ffd3809c/stream from Job('_writer' kind-_writer/instance-0jjweo4g v1) with a 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-0jjweo4g v1 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-0jjweo4g v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-0jjweo4g v1 forked from '_writer' kind-_writer/instance-0jjweo4g v1 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-0jjweo4g v2 1330s [2026-01-30T07:05:46+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-0jjweo4g v2 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-0jjweo4g v2 would chain to ID kind-_writer/instance-1i_cf2_k 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Chaining from '_writer' kind-_writer/instance-0jjweo4g v2 to '_writer' kind-_writer/instance-1i_cf2_k v1 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] '_writer' kind-_writer/instance-1i_cf2_k v1 is adopting successor phases from '_writer' kind-_writer/instance-0jjweo4g v2 of: [] 1330s [2026-01-30T07:05:46+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Actually executing upload for file files/for-job/kind-_writer/instance-0jjweo4g/file-f08195e477964ca3b9d190067081f43b/tmpesj6yvnn.tmp 1330s [2026-01-30T07:05:46+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-0jjweo4g v1 1330s [2026-01-30T07:05:46+0000] [Thread-2 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-0jjweo4g v2 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-0jjweo4g v2) with ID (kind-_writer/instance-0jjweo4g). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-0jjweo4g v2 forked from '_writer' kind-_writer/instance-0jjweo4g v2 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-0jjweo4g v3 1330s [2026-01-30T07:05:46+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.worker] Starting the next job 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-0jjweo4g v3 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-0jjweo4g v3) from description '_writer' kind-_writer/instance-0jjweo4g v3 1330s [2026-01-30T07:05:46+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-0jjweo4g v2 1330s [2026-01-30T07:05:46+0000] [Thread-3 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-0jjweo4g v3 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-0jjweo4g v3) with ID (kind-_writer/instance-0jjweo4g). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_writer' kind-_writer/instance-0jjweo4g v3) with ID (kind-_writer/instance-0jjweo4g) which wants 2147483648 of our 100589039616 bytes. 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 100589039616 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1024 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 100589039616 bytes 1330s [2026-01-30T07:05:46+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). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Hardlinked file /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/1296/job/tmplqgi8qqp.tmp into cache at /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/cache-ddb3944d-bb71-491a-8af0-2530f6b8aa01/tmp9dms7hhkb86046da5a3e24aaf2eb4072247caadc090aa206; deferring write to job store 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-3754b37b5f454ddca89a8dd48252222d/stream from Job('_writer' kind-_writer/instance-0jjweo4g v3) with a 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-0jjweo4g v3 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-0jjweo4g v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-0jjweo4g v3 forked from '_writer' kind-_writer/instance-0jjweo4g v3 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-0jjweo4g v4 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-0jjweo4g v4 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-0jjweo4g v4 would chain to ID kind-EncapsulatedJob/instance-zzj5b9s8 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.worker] Preemptibility is different for the next job, returning to the leader 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Not chaining from job '_writer' kind-_writer/instance-0jjweo4g v4 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/1296. Set --cleanWorkDir to retain this log 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 0.835001 seconds 1330s [2026-01-30T07:05:46+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 1330s [2026-01-30T07:05:46+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Actually executing upload for file files/for-job/kind-_writer/instance-0jjweo4g/file-27f897b31daa46cd8a7da991b0f8e28f/tmplqgi8qqp.tmp 1330s [2026-01-30T07:05:46+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-0jjweo4g v3 1330s [2026-01-30T07:05:46+0000] [Thread-4 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-0jjweo4g v4 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [pydot] pydot initializing 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [pydot] pydot 4.0.1 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1330s <========= 1330s [2026-01-30T07:05:47+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'asyncio', 'docker', 'requests', 'dill', 'urllib3', 'boto3', 'concurrent', 'botocore', 'boto'} 1330s [2026-01-30T07:05:47+0000] [MainThread] [D] [toil.worker] Worker started for job EncapsulatedJob... 1330s [2026-01-30T07:05:47+0000] [MainThread] [D] [toil.common] Obtained node ID 6fa530d97284404a9688ce299e64170e from file /var/lib/dbus/machine-id 1330s [2026-01-30T07:05:47+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:47+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/dda3/worker_log.txt 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v4 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/functvnm0r2c 1330s [2026-01-30T07:05:48+0000] [Thread-33 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-zzj5b9s8. 1330s [2026-01-30T07:05:48+0000] [Thread-33 (daddy)] [D] [toil.batchSystems.singleMachine] Child 9782 for job 2 succeeded 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 2 with exit value: 1 1330s [2026-01-30T07:05:48+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 1330s Exit reason: None 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-zzj5b9s8', exit_code=1) 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=2, external_batch_id='9782', batch_system='SingleMachineBatchSystem') 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.leader] Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 continues to exist (i.e. has more to do) 1330s [2026-01-30T07:05:48+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v4 1330s [2026-01-30T07:05:48+0000] [MainThread] [W] [toil.leader] Log from job "kind-EncapsulatedJob/instance-zzj5b9s8" follows: 1330s =========> 1330s [2026-01-30T07:05:47+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:05:47+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:05:47+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'ddb3944d-bb71-491a-8af0-2530f6b8aa01', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpibd3pj3m', '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} 1330s [2026-01-30T07:05:47+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/functvnm0r2c 1330s [2026-01-30T07:05:47+0000] [MainThread] [D] [toil.worker] Parsed job description 1330s [2026-01-30T07:05:47+0000] [MainThread] [I] [toil.worker] Working on job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 1330s [2026-01-30T07:05:47+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:48+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. 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:48+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. 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] Loaded body Job('EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1) from description 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1) with ID (kind-EncapsulatedJob/instance-zzj5b9s8). 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1) with ID (kind-EncapsulatedJob/instance-zzj5b9s8) which wants 1000000 of our 100589039616 bytes. 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 100589039616 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 1000000 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 100589039616 bytes 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 forked from 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] Skip ahead to job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 1330s [2026-01-30T07:05:48+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 1330s [2026-01-30T07:05:48+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 used 11.38x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] Completed body for 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.worker] 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 would chain to ID kind-_follower/instance-b2nm9dsr 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] Chaining from 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 to '_follower' kind-_follower/instance-b2nm9dsr v1 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] '_follower' kind-_follower/instance-b2nm9dsr v1 is adopting successor phases from 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 of: [{'kind-Job/instance-udha0fwb'}] 1330s [2026-01-30T07:05:48+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 1330s [2026-01-30T07:05:48+0000] [Thread-2 (startCommitThread)] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v2) with ID (kind-EncapsulatedJob/instance-zzj5b9s8). 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v2 forked from '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v2 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 1330s [2026-01-30T07:05:48+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.worker] Starting the next job 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore'. 1330s [2026-01-30T07:05:48+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v2 1330s [2026-01-30T07:05:48+0000] [Thread-3 (startCommitThread)] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3) from description '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3) with ID (kind-EncapsulatedJob/instance-zzj5b9s8). 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3) with ID (kind-EncapsulatedJob/instance-zzj5b9s8) which wants 1000000 of our 100589039616 bytes. 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 100589039616 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 1000000 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 100589039616 bytes 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:48+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 used 10.31x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:05:48+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 1330s self.evaluatePromisedRequirements() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 1330s ].getValue() 1330s ~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 1330s return func(*self._args) 1330s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 1330s 1330s [2026-01-30T07:05:48+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [pydot] pydot initializing 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [pydot] pydot 4.0.1 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1330s <========= 1330s [2026-01-30T07:05:48+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v4 with ID kind-EncapsulatedJob/instance-zzj5b9s8 to 1 1330s [2026-01-30T07:05:48+0000] [MainThread] [W] [toil.job] We have increased the default memory of the failed job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v4 to 2147483648 bytes 1330s [2026-01-30T07:05:48+0000] [MainThread] [W] [toil.job] We have increased the disk of the failed job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v4 to the default of 2147483648 bytes 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v5 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-zzj5b9s8', result_status=1) 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.leader] Added job: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v5 to updated jobs 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.leader] Updating status of job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v5 with result status: 1 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-zzj5b9s8 with disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.leader] Issued job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v5 with job batch system ID: 3 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-zzj5b9s8', toil_batch_id=3) 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 1330s [2026-01-30T07:05:48+0000] [Thread-33 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-zzj5b9s8 1330s [2026-01-30T07:05:48+0000] [Thread-33 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 3 as child 9815 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'boto', 'docker', 'asyncio', 'urllib3', 'concurrent', 'botocore', 'dill', 'requests', 'boto3'} 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.worker] Worker started for job _follower... 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.common] Obtained node ID 6fa530d97284404a9688ce299e64170e from file /var/lib/dbus/machine-id 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/7bd9/worker_log.txt 1330s [2026-01-30T07:05:48+0000] [Thread-36 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:05:48: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1330s [2026-01-30T07:05:48+0000] [Thread-36 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:05:48: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 used 11.38x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:05:48+0000] [Thread-36 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:05:48: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1330s [2026-01-30T07:05:48+0000] [Thread-36 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:05:48: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 used 10.31x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=3, external_batch_id='9815', batch_system='SingleMachineBatchSystem') 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v7 1330s [2026-01-30T07:05:50+0000] [Thread-36 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:05:50: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:50+0000] [Thread-36 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:05:50: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 used 4.50x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/funcnzj665b2 1330s [2026-01-30T07:05:50+0000] [Thread-33 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-zzj5b9s8. 1330s [2026-01-30T07:05:50+0000] [Thread-33 (daddy)] [D] [toil.batchSystems.singleMachine] Child 9815 for job 3 succeeded 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 3 with exit value: 1 1330s [2026-01-30T07:05:50+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v5 1330s Exit reason: None 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-zzj5b9s8', exit_code=1) 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.leader] Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v5 continues to exist (i.e. has more to do) 1330s [2026-01-30T07:05:50+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v7 1330s [2026-01-30T07:05:50+0000] [MainThread] [W] [toil.leader] Log from job "kind-EncapsulatedJob/instance-zzj5b9s8" follows: 1330s =========> 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'ddb3944d-bb71-491a-8af0-2530f6b8aa01', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpibd3pj3m', '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} 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/funcnzj665b2 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.worker] Parsed job description 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1330s [2026-01-30T07:05:49+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:49+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:49+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. 1330s [2026-01-30T07:05:50+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:50+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:50+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. 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore'. 1330s [2026-01-30T07:05:50+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6) from description '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6) with ID (kind-EncapsulatedJob/instance-zzj5b9s8). 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6) with ID (kind-EncapsulatedJob/instance-zzj5b9s8) which wants 2147483648 of our 100589039616 bytes. 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 100589039616 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 100589039616 bytes 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:50+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 used 4.50x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:05:50+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 1330s self.evaluatePromisedRequirements() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 1330s ].getValue() 1330s ~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 1330s return func(*self._args) 1330s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 1330s 1330s [2026-01-30T07:05:50+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [pydot] pydot initializing 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [pydot] pydot 4.0.1 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1330s <========= 1330s [2026-01-30T07:05:50+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v7 with ID kind-EncapsulatedJob/instance-zzj5b9s8 to 0 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-zzj5b9s8', result_status=1) 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.leader] Added job: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8 to updated jobs 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.leader] Updating status of job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8 with result status: 1 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-zzj5b9s8') 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.leader] Found new failed successors: kind-Job/instance-udha0fwb of job: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.leader] Totally failed job: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8 is marking direct predecessor: '_writer' kind-_writer/instance-0jjweo4g v4 as having failed jobs 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.leader] Cleaning the predecessors of kind-EncapsulatedJob/instance-zzj5b9s8 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.toilState] Successors: one fewer for kind-_writer/instance-0jjweo4g, now have 0 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-0jjweo4g', result_status=0) 1330s [2026-01-30T07:05:50+0000] [MainThread] [W] [toil.leader] Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8 is completely failed 1330s [2026-01-30T07:05:52+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s [2026-01-30T07:05:52+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-0jjweo4g v4 with result status: 0 1330s [2026-01-30T07:05:52+0000] [MainThread] [D] [toil.leader] Job kind-_writer/instance-0jjweo4g is being processed as completely failed 1330s [2026-01-30T07:05:52+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_writer', job_id='kind-_writer/instance-0jjweo4g') 1330s [2026-01-30T07:05:52+0000] [MainThread] [D] [toil.leader] Found new failed successors: of job: '_writer' kind-_writer/instance-0jjweo4g v4 1330s [2026-01-30T07:05:54+0000] [MainThread] [D] [toil.leader] Finished the main loop: no jobs left to run. 1330s [2026-01-30T07:05:54+0000] [MainThread] [D] [toil.serviceManager] Waiting for service manager thread to finish ... 1330s [2026-01-30T07:05:55+0000] [Thread-35 (__start_services)] [D] [toil.serviceManager] Received signal to quit starting services. 1330s [2026-01-30T07:05:56+0000] [MainThread] [D] [toil.serviceManager] ... finished shutting down the service manager. Took 1.7446215152740479 seconds 1330s [2026-01-30T07:05:56+0000] [MainThread] [D] [toil.statsAndLogging] Waiting for stats and logging collator thread to finish ... 1330s [2026-01-30T07:05:56+0000] [MainThread] [D] [toil.statsAndLogging] ... finished collating stats and logs. Took 0.15448403358459473 seconds 1330s [2026-01-30T07:05:56+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:05:56+0000] [MainThread] [I] [toil.leader] Finished toil run with 2 failed jobs. 1330s [2026-01-30T07:05:56+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8 '_writer' kind-_writer/instance-0jjweo4g v4 1330s [2026-01-30T07:05:56+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:05:57+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.common] Shutting down batch system ... 1330s [2026-01-30T07:05:57+0000] [Thread-33 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread cleaning up 0 remaining children for batch system 4395914683376... 1330s [2026-01-30T07:05:57+0000] [Thread-33 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread for batch system 4395914683376 finishing because no children should now exist 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Attempting worker cleanup 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.deferred] Cleaning up deferred functions system 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/func05te4q11 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/func05te4q11 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Connecting to latest caching database cache-0.db for cleanup 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting workflow directory /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting coordination directory /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.common] ... finished shutting down the batch system in 0.06792092323303223 seconds. 1330s [2026-01-30T07:05:57+0000] [MainThread] [I] [toil.lib.history] Workflow ddb3944d-bb71-491a-8af0-2530f6b8aa01 stopped. Success: False 1330s ------------------------------ Captured log call ------------------------------- 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.common:common.py:796 Initialized default configuration: {"config_version": 1.0} 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for aws_batch batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for single_machine batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for grid_engine batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for lsf batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for slurm batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for torque batch system 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:488 Suppressing the following loggers: {'urllib3', 'salad', 'asyncio', 'requests', 'rdflib', 'concurrent', 'boto3', 'humanfriendly', 'debugWorkflow', 'dill', 'test', 'cwltest', 'boto', 'bcdocs', 'cachecontrol', 'docker', 'botocore'} 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:447 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:488 Suppressing the following loggers: {'urllib3', 'salad', 'asyncio', 'requests', 'rdflib', 'concurrent', 'boto3', 'humanfriendly', 'debugWorkflow', 'dill', 'test', 'cwltest', 'boto', 'bcdocs', 'cachecontrol', 'docker', 'botocore'} 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:447 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 1330s DEBUG  toil.common:common.py:796 Initialized default configuration: {"config_version": 1.0} 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for aws_batch batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for single_machine batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for grid_engine batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for lsf batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for slurm batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for torque batch system 1330s 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-gw3/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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} 1330s DEBUG  toil.jobStores.fileJobStore:fileJobStore.py:93 Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore'. 1330s DEBUG  toil.jobStores.abstractJobStore:abstractJobStore.py:212 The workflow ID is: 'ddb3944d-bb71-491a-8af0-2530f6b8aa01' 1330s INFO  toil.lib.history:history.py:369 Recording workflow creation of ddb3944d-bb71-491a-8af0-2530f6b8aa01 in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore 1330s INFO  toil.lib.history:history.py:399 Workflow ddb3944d-bb71-491a-8af0-2530f6b8aa01 is a run of 1330s DEBUG  toil.common:common.py:1346 Using the single machine batch system 1330s DEBUG  toil.common:common.py:1723 Created the workflow directory for this machine at /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:247 Started daddy thread for batch system 4395914683376. 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:229 Started batch system 4395914683376 in normal mode. 1330s 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. 1330s DEBUG  toil.common:common.py:1409 No user script to auto-deploy. 1330s DEBUG  toil.common:common.py:1576 Written the environment for the jobs to the environment file 1330s DEBUG  toil.common:common.py:1580 Caching all jobs in job store 1330s DEBUG  toil.common:common.py:1584 0 jobs downloaded. 1330s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-4cb64118db38401f9718009df6664b46/stream for result of '_writer' TemporaryID(06bf9a78-b31e-4a1e-9a10-beb2873d214f) v0 1330s DEBUG  toil.job:job.py:3000 Saving graph of 5 jobs, 5 non-service, 5 new 1330s DEBUG  toil.job:job.py:3023 Processing job 'Job' kind-Job/instance-udha0fwb v0 1330s DEBUG  toil.job:job.py:3023 Processing job '_follower' kind-_follower/instance-b2nm9dsr v0 1330s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-d87f34bfc397446da8408462ffd3809c/stream for result of '_writer' kind-_writer/instance-0jjweo4g v0 1330s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-3754b37b5f454ddca89a8dd48252222d/stream for result of '_writer' kind-_writer/instance-1i_cf2_k v0 1330s DEBUG  toil.job:job.py:3023 Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v0 1330s DEBUG  toil.job:job.py:3023 Processing job '_writer' kind-_writer/instance-1i_cf2_k v0 1330s DEBUG  toil.job:job.py:3023 Processing job '_writer' kind-_writer/instance-0jjweo4g v0 1330s DEBUG  toil.job:job.py:1507 New job version: 'Job' kind-Job/instance-udha0fwb v1 1330s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-_follower/instance-b2nm9dsr v1 1330s DEBUG  toil.job:job.py:1507 New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 1330s DEBUG  toil.job:job.py:1507 New job version: '_writer' kind-_writer/instance-1i_cf2_k v1 1330s DEBUG  toil.job:job.py:1507 New job version: '_writer' kind-_writer/instance-0jjweo4g v1 1330s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s DEBUG  toil:__init__.py:481 Configuration: {'cwl': False, 'workflowID': 'ddb3944d-bb71-491a-8af0-2530f6b8aa01', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpibd3pj3m', '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} 1330s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1330s DEBUG  toil.bus:bus.py:403 Listening for message topic: toil.bus.JobUpdatedMessage 1330s DEBUG  toil.toilState:toilState.py:322 Found job to run: kind-_writer/instance-0jjweo4g, with body: True, with checkpoint: False, with services: False, with no next successors: False 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-0jjweo4g', result_status=0) 1330s DEBUG  toil.leader:leader.py:145 Found 1 jobs to start and 0 jobs with successors to run 1330s DEBUG  toil.leader:leader.py:157 Checked batch system has no running jobs and no updated jobs 1330s DEBUG  toil.serviceManager:serviceManager.py:35 Initializing service manager 1330s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-0jjweo4g v1 with result status: 0 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-_writer/instance-0jjweo4g with disk: 2.0 Gi, memory: 2.0 Gi, cores: 2.0, accelerators: [], preemptible: False 1330s INFO  toil.leader:leader.py:1132 Issued job '_writer' kind-_writer/instance-0jjweo4g v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 2, accelerators: [], preemptible: False 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_writer', job_id='kind-_writer/instance-0jjweo4g', toil_batch_id=1) 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-_writer/instance-0jjweo4g 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 1 as child 9757 1330s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=1, external_batch_id='9757', batch_system='SingleMachineBatchSystem') 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 9757 for job 1 succeeded 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 1 with exit value: 0 1330s DEBUG  toil.leader:leader.py:846 Job ended: '_writer' kind-_writer/instance-0jjweo4g v1 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_writer', job_id='kind-_writer/instance-0jjweo4g', exit_code=0) 1330s DEBUG  toil.leader:leader.py:1455 Job '_writer' kind-_writer/instance-0jjweo4g v1 continues to exist (i.e. has more to do) 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-0jjweo4g', result_status=0) 1330s DEBUG  toil.leader:leader.py:1620 Added job: '_writer' kind-_writer/instance-0jjweo4g v4 to updated jobs 1330s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-0jjweo4g v4 with result status: 0 1330s DEBUG  toil.leader:leader.py:506 Job: kind-_writer/instance-0jjweo4g has 1 successors to schedule 1330s DEBUG  toil.toilState:toilState.py:264 Successors: 1 more for kind-_writer/instance-0jjweo4g, now have 1 1330s DEBUG  toil.leader:leader.py:476 Added job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 as coming after job '_writer' kind-_writer/instance-0jjweo4g v4 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-zzj5b9s8 with disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 1330s INFO  toil.leader:leader.py:1132 Issued job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 with job batch system ID: 2 and disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-zzj5b9s8', toil_batch_id=2) 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-zzj5b9s8 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 2 as child 9782 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:05:46: Job '_writer' kind-_writer/instance-0jjweo4g v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:05:46: Job '_writer' kind-_writer/instance-0jjweo4g v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:98 Received Toil worker log. Disable debug level logging to hide this output 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:101 Log from job "JobFunctionWrappingJob" follows: 1330s =========> 1330s [2026-01-30T07:05:45+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:05:45+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:05:45+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'ddb3944d-bb71-491a-8af0-2530f6b8aa01', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpibd3pj3m', '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} 1330s [2026-01-30T07:05:45+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/funczrgbjge3 1330s [2026-01-30T07:05:45+0000] [MainThread] [D] [toil.worker] Parsed job description 1330s [2026-01-30T07:05:45+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-0jjweo4g v1 1330s [2026-01-30T07:05:45+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:46+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. 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:46+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. 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-0jjweo4g v1) from description '_writer' kind-_writer/instance-0jjweo4g v1 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-0jjweo4g v1) with ID (kind-_writer/instance-0jjweo4g). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_writer' kind-_writer/instance-0jjweo4g v1) with ID (kind-_writer/instance-0jjweo4g) which wants 2147483648 of our 100589039616 bytes. 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 100589039616 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 0 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 100589039616 bytes 1330s [2026-01-30T07:05:46+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). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Hardlinked file /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/1296/job/tmpesj6yvnn.tmp into cache at /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/cache-ddb3944d-bb71-491a-8af0-2530f6b8aa01/tmpl8x6feclda0630cdd8595f613377f1fad1daee7b7dbaf609; deferring write to job store 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-4cb64118db38401f9718009df6664b46/stream from Job('_writer' kind-_writer/instance-0jjweo4g v1) with a 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-d87f34bfc397446da8408462ffd3809c/stream from Job('_writer' kind-_writer/instance-0jjweo4g v1) with a 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-0jjweo4g v1 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-0jjweo4g v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-0jjweo4g v1 forked from '_writer' kind-_writer/instance-0jjweo4g v1 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-0jjweo4g v2 1330s [2026-01-30T07:05:46+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-0jjweo4g v2 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-0jjweo4g v2 would chain to ID kind-_writer/instance-1i_cf2_k 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Chaining from '_writer' kind-_writer/instance-0jjweo4g v2 to '_writer' kind-_writer/instance-1i_cf2_k v1 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] '_writer' kind-_writer/instance-1i_cf2_k v1 is adopting successor phases from '_writer' kind-_writer/instance-0jjweo4g v2 of: [] 1330s [2026-01-30T07:05:46+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Actually executing upload for file files/for-job/kind-_writer/instance-0jjweo4g/file-f08195e477964ca3b9d190067081f43b/tmpesj6yvnn.tmp 1330s [2026-01-30T07:05:46+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-0jjweo4g v1 1330s [2026-01-30T07:05:46+0000] [Thread-2 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-0jjweo4g v2 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-0jjweo4g v2) with ID (kind-_writer/instance-0jjweo4g). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-0jjweo4g v2 forked from '_writer' kind-_writer/instance-0jjweo4g v2 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-0jjweo4g v3 1330s [2026-01-30T07:05:46+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.worker] Starting the next job 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-0jjweo4g v3 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-0jjweo4g v3) from description '_writer' kind-_writer/instance-0jjweo4g v3 1330s [2026-01-30T07:05:46+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-0jjweo4g v2 1330s [2026-01-30T07:05:46+0000] [Thread-3 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-0jjweo4g v3 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_writer' kind-_writer/instance-0jjweo4g v3) with ID (kind-_writer/instance-0jjweo4g). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_writer' kind-_writer/instance-0jjweo4g v3) with ID (kind-_writer/instance-0jjweo4g) which wants 2147483648 of our 100589039616 bytes. 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 100589039616 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1024 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 100589039616 bytes 1330s [2026-01-30T07:05:46+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). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Hardlinked file /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/1296/job/tmplqgi8qqp.tmp into cache at /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/cache-ddb3944d-bb71-491a-8af0-2530f6b8aa01/tmp9dms7hhkb86046da5a3e24aaf2eb4072247caadc090aa206; deferring write to job store 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-3754b37b5f454ddca89a8dd48252222d/stream from Job('_writer' kind-_writer/instance-0jjweo4g v3) with a 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-0jjweo4g v3 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-0jjweo4g v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_writer' kind-_writer/instance-0jjweo4g v3 forked from '_writer' kind-_writer/instance-0jjweo4g v3 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_writer' kind-_writer/instance-0jjweo4g v4 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-0jjweo4g v4 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-0jjweo4g v4 would chain to ID kind-EncapsulatedJob/instance-zzj5b9s8 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [toil.worker] Preemptibility is different for the next job, returning to the leader 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Not chaining from job '_writer' kind-_writer/instance-0jjweo4g v4 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/1296. Set --cleanWorkDir to retain this log 1330s [2026-01-30T07:05:46+0000] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 0.835001 seconds 1330s [2026-01-30T07:05:46+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 1330s [2026-01-30T07:05:46+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Actually executing upload for file files/for-job/kind-_writer/instance-0jjweo4g/file-27f897b31daa46cd8a7da991b0f8e28f/tmplqgi8qqp.tmp 1330s [2026-01-30T07:05:46+0000] [Thread-4 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_writer' kind-_writer/instance-0jjweo4g v3 1330s [2026-01-30T07:05:46+0000] [Thread-4 (startCommitThread)] [D] [toil.job] New job version: '_writer' kind-_writer/instance-0jjweo4g v4 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [pydot] pydot initializing 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [pydot] pydot 4.0.1 1330s [2026-01-30T07:05:46+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1330s <========= 1330s 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-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-zzj5b9s8. 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 9782 for job 2 succeeded 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 2 with exit value: 1 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 1330s Exit reason: None 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-zzj5b9s8', exit_code=1) 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=2, external_batch_id='9782', batch_system='SingleMachineBatchSystem') 1330s DEBUG  toil.leader:leader.py:1455 Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 continues to exist (i.e. has more to do) 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v4 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-EncapsulatedJob/instance-zzj5b9s8" follows: 1330s =========> 1330s [2026-01-30T07:05:47+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:05:47+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:05:47+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'ddb3944d-bb71-491a-8af0-2530f6b8aa01', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpibd3pj3m', '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} 1330s [2026-01-30T07:05:47+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/functvnm0r2c 1330s [2026-01-30T07:05:47+0000] [MainThread] [D] [toil.worker] Parsed job description 1330s [2026-01-30T07:05:47+0000] [MainThread] [I] [toil.worker] Working on job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 1330s [2026-01-30T07:05:47+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:48+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. 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:48+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. 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] Loaded body Job('EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1) from description 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1) with ID (kind-EncapsulatedJob/instance-zzj5b9s8). 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1) with ID (kind-EncapsulatedJob/instance-zzj5b9s8) which wants 1000000 of our 100589039616 bytes. 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 100589039616 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 1000000 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 100589039616 bytes 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 forked from 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] Skip ahead to job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 1330s [2026-01-30T07:05:48+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 1330s [2026-01-30T07:05:48+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 used 11.38x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] Completed body for 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.worker] 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 would chain to ID kind-_follower/instance-b2nm9dsr 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] Chaining from 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 to '_follower' kind-_follower/instance-b2nm9dsr v1 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] '_follower' kind-_follower/instance-b2nm9dsr v1 is adopting successor phases from 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 of: [{'kind-Job/instance-udha0fwb'}] 1330s [2026-01-30T07:05:48+0000] [Thread-2 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 1330s [2026-01-30T07:05:48+0000] [Thread-2 (startCommitThread)] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v2) with ID (kind-EncapsulatedJob/instance-zzj5b9s8). 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting commit of '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v2 forked from '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v2 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] Skip ahead to job version: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 1330s [2026-01-30T07:05:48+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file uploads asynchronously 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.worker] Starting the next job 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore'. 1330s [2026-01-30T07:05:48+0000] [Thread-3 (startCommitThread)] [D] [toil.fileStores.cachingFileStore] Committing file deletes and job state changes asynchronously from '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v2 1330s [2026-01-30T07:05:48+0000] [Thread-3 (startCommitThread)] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3) from description '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3) with ID (kind-EncapsulatedJob/instance-zzj5b9s8). 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3) with ID (kind-EncapsulatedJob/instance-zzj5b9s8) which wants 1000000 of our 100589039616 bytes. 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 100589039616 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 1000000 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 100589039616 bytes 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:48+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 used 10.31x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:05:48+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 1330s self.evaluatePromisedRequirements() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 1330s ].getValue() 1330s ~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 1330s return func(*self._args) 1330s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 1330s 1330s [2026-01-30T07:05:48+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [pydot] pydot initializing 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [pydot] pydot 4.0.1 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v4 with ID kind-EncapsulatedJob/instance-zzj5b9s8 to 1 1330s WARNING  toil.job:job.py:1413 We have increased the default memory of the failed job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v4 to 2147483648 bytes 1330s WARNING  toil.job:job.py:1421 We have increased the disk of the failed job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v4 to the default of 2147483648 bytes 1330s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v5 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-zzj5b9s8', result_status=1) 1330s DEBUG  toil.leader:leader.py:1620 Added job: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v5 to updated jobs 1330s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s DEBUG  toil.leader:leader.py:606 Updating status of job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v5 with result status: 1 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-zzj5b9s8 with disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 1330s INFO  toil.leader:leader.py:1132 Issued job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v5 with job batch system ID: 3 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-zzj5b9s8', toil_batch_id=3) 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-zzj5b9s8 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 3 as child 9815 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:05:48: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1330s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:05:48: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-zzj5b9s8 v2 used 11.38x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:05:48: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1330s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:05:48: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v3 used 10.31x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=3, external_batch_id='9815', batch_system='SingleMachineBatchSystem') 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:05:50: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 1330s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:05:50: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 used 4.50x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s 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-gw3/testPromisesWithJobStoreFileOb0/jobstore kind-EncapsulatedJob/instance-zzj5b9s8. 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 9815 for job 3 succeeded 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 3 with exit value: 1 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v5 1330s Exit reason: None 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-zzj5b9s8', exit_code=1) 1330s DEBUG  toil.leader:leader.py:1455 Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v5 continues to exist (i.e. has more to do) 1330s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v7 1330s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-EncapsulatedJob/instance-zzj5b9s8" follows: 1330s =========> 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'ddb3944d-bb71-491a-8af0-2530f6b8aa01', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpibd3pj3m', '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} 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/funcnzj665b2 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.worker] Parsed job description 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 1330s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 1330s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1330s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1330s [2026-01-30T07:05:49+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:49+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:49+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. 1330s [2026-01-30T07:05:50+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:50+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:50+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. 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore'. 1330s [2026-01-30T07:05:50+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6) from description '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6) with ID (kind-EncapsulatedJob/instance-zzj5b9s8). 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6) with ID (kind-EncapsulatedJob/instance-zzj5b9s8) which wants 2147483648 of our 100589039616 bytes. 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 100589039616 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 100589039616 bytes 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:50+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 used 4.50x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:05:50+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 1330s self.evaluatePromisedRequirements() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 1330s ].getValue() 1330s ~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 1330s return func(*self._args) 1330s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 1330s 1330s [2026-01-30T07:05:50+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [pydot] pydot initializing 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [pydot] pydot 4.0.1 1330s [2026-01-30T07:05:50+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1330s <========= 1330s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v7 with ID kind-EncapsulatedJob/instance-zzj5b9s8 to 0 1330s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-zzj5b9s8', result_status=1) 1330s DEBUG  toil.leader:leader.py:1620 Added job: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8 to updated jobs 1330s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s DEBUG  toil.leader:leader.py:606 Updating status of job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8 with result status: 1 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-zzj5b9s8') 1330s DEBUG  toil.leader:leader.py:1735 Found new failed successors: kind-Job/instance-udha0fwb of job: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8 1330s DEBUG  toil.leader:leader.py:1779 Totally failed job: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8 is marking direct predecessor: '_writer' kind-_writer/instance-0jjweo4g v4 as having failed jobs 1330s DEBUG  toil.leader:leader.py:1846 Cleaning the predecessors of kind-EncapsulatedJob/instance-zzj5b9s8 1330s DEBUG  toil.toilState:toilState.py:283 Successors: one fewer for kind-_writer/instance-0jjweo4g, now have 0 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-0jjweo4g', result_status=0) 1330s WARNING  toil.leader:leader.py:643 Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8 is completely failed 1330s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-0jjweo4g v4 with result status: 0 1330s DEBUG  toil.leader:leader.py:597 Job kind-_writer/instance-0jjweo4g is being processed as completely failed 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_writer', job_id='kind-_writer/instance-0jjweo4g') 1330s DEBUG  toil.leader:leader.py:1735 Found new failed successors: of job: '_writer' kind-_writer/instance-0jjweo4g v4 1330s DEBUG  toil.leader:leader.py:969 Finished the main loop: no jobs left to run. 1330s DEBUG  toil.serviceManager:serviceManager.py:236 Waiting for service manager thread to finish ... 1330s DEBUG  toil.serviceManager:serviceManager.py:261 Received signal to quit starting services. 1330s DEBUG  toil.serviceManager:serviceManager.py:243 ... finished shutting down the service manager. Took 1.7446215152740479 seconds 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:296 Waiting for stats and logging collator thread to finish ... 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:300 ... finished collating stats and logs. Took 0.15448403358459473 seconds 1330s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s INFO  toil.leader:leader.py:317 Finished toil run with 2 failed jobs. 1330s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8 '_writer' kind-_writer/instance-0jjweo4g v4 1330s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1330s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1330s DEBUG  toil.common:common.py:1800 Shutting down batch system ... 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:317 Daddy thread cleaning up 0 remaining children for batch system 4395914683376... 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:325 Daddy thread for batch system 4395914683376 finishing because no children should now exist 1330s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:503 Attempting worker cleanup 1330s DEBUG  toil.lib.threading:threading.py:109 Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s DEBUG  toil.deferred:deferred.py:215 Cleaning up deferred functions system 1330s DEBUG  toil.deferred:deferred.py:159 Opened with own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/func05te4q11 1330s DEBUG  toil.deferred:deferred.py:291 Running orphaned deferred functions 1330s DEBUG  toil.deferred:deferred.py:369 Ran orphaned deferred functions from 0 abandoned state files 1330s DEBUG  toil.deferred:deferred.py:167 Removing own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/func05te4q11 1330s DEBUG  toil.lib.threading:threading.py:109 Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1330s DEBUG  toil.fileStores.cachingFileStore:cachingFileStore.py:2402 Connecting to latest caching database cache-0.db for cleanup 1330s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:517 Deleting workflow directory /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/workdir/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 1330s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:521 Deleting coordination directory /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 1330s DEBUG  toil.common:common.py:1802 ... finished shutting down the batch system in 0.06792092323303223 seconds. 1330s INFO  toil.lib.history:history.py:530 Workflow ddb3944d-bb71-491a-8af0-2530f6b8aa01 stopped. Success: False 1330s __ TestSingleMachinePromisedRequirements.testPromisesWithNonCachingFileStore ___ 1330s [gw3] linux -- Python 3.14.2 /usr/bin/python3.14 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1330s result: TResult | None = func() 1330s ~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1330s lambda: runtest_hook(item=item, **kwds), 1330s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1330s yield 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1330s return result.get_result() 1330s ~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1330s raise exc.with_traceback(tb) 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1330s res = yield 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1330s teardown.throw(exception) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1330s return (yield) 1330s ^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1330s item.runtest() 1330s ~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1330s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1330s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1330s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1330s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1330s raise exception 1330s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1330s res = hook_impl.function(*args) 1330s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1330s result = testfunction(**testargs) 1330s File "/usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py", line 148, in testPromisesWithNonCachingFileStore 1330s self.testPromisesWithJobStoreFileObjects(tmp_path, caching=False) 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py", line 145, in testPromisesWithJobStoreFileObjects 1330s Job.Runner.startToil(F1, self.getOptions(tmp_path, caching=caching)) 1330s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1330s return toil.start(job) 1330s ~~~~~~~~~~^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1330s return self._runMainLoop(rootJobDescription) 1330s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1330s ).run() 1330s ~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1330s raise FailedJobsException( 1330s ...<3 lines>... 1330s ) 1330s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore' contains 2 failed jobs: '_writer' kind-_writer/instance-icv7qr07 v4, '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 1330s Log from job "'_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8" follows: 1330s =========> 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '9758239f-8230-4707-9a89-f88f4814da8c', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpzhq9eyr4', '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} 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funcgb66nmmu 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.worker] Parsed job description 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:06:01+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. 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:06:01+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. 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore'. 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6) from description '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:06:01+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 used 6.03x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:06:01+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 1330s self.evaluatePromisedRequirements() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 1330s ].getValue() 1330s ~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 1330s return func(*self._args) 1330s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 1330s 1330s [2026-01-30T07:06:01+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [pydot] pydot initializing 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [pydot] pydot 4.0.1 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1330s <========= 1330s ----------------------------- Captured stderr call ----------------------------- 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.common] Initialized default configuration: {"config_version": 1.0} 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.options] Add options for aws_batch batch system 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.options] Add options for single_machine batch system 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.options] Add options for grid_engine batch system 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.options] Add options for lsf batch system 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.options] Add options for slurm batch system 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.options] Add options for torque batch system 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'urllib3', 'salad', 'asyncio', 'requests', 'rdflib', 'concurrent', 'boto3', 'humanfriendly', 'debugWorkflow', 'dill', 'test', 'cwltest', 'boto', 'bcdocs', 'cachecontrol', 'docker', 'botocore'} 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.statsAndLogging] Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'urllib3', 'salad', 'asyncio', 'requests', 'rdflib', 'concurrent', 'boto3', 'humanfriendly', 'debugWorkflow', 'dill', 'test', 'cwltest', 'boto', 'bcdocs', 'cachecontrol', 'docker', 'botocore'} 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.statsAndLogging] Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.common] Initialized default configuration: {"config_version": 1.0} 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.options] Add options for aws_batch batch system 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.options] Add options for single_machine batch system 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.options] Add options for grid_engine batch system 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.options] Add options for lsf batch system 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.options] Add options for slurm batch system 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.options] Add options for torque batch system 1330s [2026-01-30T07:05:57+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-gw3/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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} 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore'. 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.jobStores.abstractJobStore] The workflow ID is: '9758239f-8230-4707-9a89-f88f4814da8c' 1330s [2026-01-30T07:05:57+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 9758239f-8230-4707-9a89-f88f4814da8c in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore 1330s [2026-01-30T07:05:57+0000] [MainThread] [I] [toil.lib.history] Workflow 9758239f-8230-4707-9a89-f88f4814da8c is a run of 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.common] Using the single machine batch system 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.common] Created the workflow directory for this machine at /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/workdir/toilwf-687cdbabed03577e875959feb6b5cc2e 1330s [2026-01-30T07:05:57+0000] [Thread-37 (daddy)] [D] [toil.batchSystems.singleMachine] Started daddy thread for batch system 4395914682160. 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Started batch system 4395914682160 in normal mode. 1330s [2026-01-30T07:05:57+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. 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.common] No user script to auto-deploy. 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.common] Written the environment for the jobs to the environment file 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.common] Caching all jobs in job store 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.common] 0 jobs downloaded. 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-7a5ec3163cbb43da86b6609c3085e792/stream for result of '_writer' TemporaryID(eb6efaac-ee59-4b5c-a7cb-6a97420c4615) v0 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.job] Saving graph of 5 jobs, 5 non-service, 5 new 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.job] Processing job 'Job' kind-Job/instance-67qr9tq8 v0 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.job] Processing job '_follower' kind-_follower/instance-i9covkiz v0 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-0ee48f0c3f4647cebd9570c11d0c73be/stream for result of '_writer' kind-_writer/instance-icv7qr07 v0 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-0e825c8da25b4eb38fee2032fafa83da/stream for result of '_writer' kind-_writer/instance-_k_tg9sb v0 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v0 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-_k_tg9sb v0 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-icv7qr07 v0 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.job] New job version: 'Job' kind-Job/instance-67qr9tq8 v1 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-_follower/instance-i9covkiz v1 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-_k_tg9sb v1 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-icv7qr07 v1 1330s [2026-01-30T07:05:57+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '9758239f-8230-4707-9a89-f88f4814da8c', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpzhq9eyr4', '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} 1330s [2026-01-30T07:05:57+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.bus] Listening for message topic: toil.bus.JobUpdatedMessage 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.toilState] Found job to run: kind-_writer/instance-icv7qr07, with body: True, with checkpoint: False, with services: False, with no next successors: False 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-icv7qr07', result_status=0) 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.leader] Found 1 jobs to start and 0 jobs with successors to run 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.leader] Checked batch system has no running jobs and no updated jobs 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.serviceManager] Initializing service manager 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-icv7qr07 v1 with result status: 0 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore kind-_writer/instance-icv7qr07 with disk: 2.0 Gi, memory: 2.0 Gi, cores: 2.0, accelerators: [], preemptible: False 1330s [2026-01-30T07:05:57+0000] [MainThread] [I] [toil.leader] Issued job '_writer' kind-_writer/instance-icv7qr07 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 2, accelerators: [], preemptible: False 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_writer', job_id='kind-_writer/instance-icv7qr07', toil_batch_id=1) 1330s [2026-01-30T07:05:57+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 1330s [2026-01-30T07:05:57+0000] [Thread-37 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore kind-_writer/instance-icv7qr07 1330s [2026-01-30T07:05:57+0000] [Thread-37 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 1 as child 10047 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'boto', 'docker', 'botocore', 'requests', 'asyncio', 'boto3', 'concurrent', 'urllib3', 'dill'} 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.worker] Worker started for job _writer... 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.common] Obtained node ID 6fa530d97284404a9688ce299e64170e from file /var/lib/dbus/machine-id 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/workdir/toilwf-687cdbabed03577e875959feb6b5cc2e/96e5/worker_log.txt 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funccmbc6weg 1330s [2026-01-30T07:05:58+0000] [Thread-37 (daddy)] [D] [toil.batchSystems.singleMachine] Child 10047 for job 1 succeeded 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 1 with exit value: 0 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.leader] Job ended: '_writer' kind-_writer/instance-icv7qr07 v1 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_writer', job_id='kind-_writer/instance-icv7qr07', exit_code=0) 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=1, external_batch_id='10047', batch_system='SingleMachineBatchSystem') 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.leader] Job '_writer' kind-_writer/instance-icv7qr07 v1 continues to exist (i.e. has more to do) 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-icv7qr07', result_status=0) 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.leader] Added job: '_writer' kind-_writer/instance-icv7qr07 v4 to updated jobs 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-icv7qr07 v4 with result status: 0 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.leader] Job: kind-_writer/instance-icv7qr07 has 1 successors to schedule 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.toilState] Successors: 1 more for kind-_writer/instance-icv7qr07, now have 1 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.leader] Added job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 as coming after job '_writer' kind-_writer/instance-icv7qr07 v4 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-bpvbpt4v with disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.leader] Issued job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 with job batch system ID: 2 and disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-bpvbpt4v', toil_batch_id=2) 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 1330s [2026-01-30T07:05:58+0000] [Thread-40 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:05:58: Job '_writer' kind-_writer/instance-icv7qr07 v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:58+0000] [Thread-40 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:05:58: Job '_writer' kind-_writer/instance-icv7qr07 v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:58+0000] [Thread-40 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Received Toil worker log. Disable debug level logging to hide this output 1330s [2026-01-30T07:05:58+0000] [Thread-40 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Log from job "JobFunctionWrappingJob" follows: 1330s =========> 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '9758239f-8230-4707-9a89-f88f4814da8c', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpzhq9eyr4', '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} 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funccmbc6weg 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.worker] Parsed job description 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-icv7qr07 v1 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:58+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. 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:58+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. 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-icv7qr07 v1) from description '_writer' kind-_writer/instance-icv7qr07 v1 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:58+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). 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-7a5ec3163cbb43da86b6609c3085e792/stream from Job('_writer' kind-_writer/instance-icv7qr07 v1) with a 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-0ee48f0c3f4647cebd9570c11d0c73be/stream from Job('_writer' kind-_writer/instance-icv7qr07 v1) with a 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-icv7qr07 v1 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-icv7qr07 v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-icv7qr07 v2 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-icv7qr07 v2 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-icv7qr07 v2 would chain to ID kind-_writer/instance-_k_tg9sb 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Chaining from '_writer' kind-_writer/instance-icv7qr07 v2 to '_writer' kind-_writer/instance-_k_tg9sb v1 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] '_writer' kind-_writer/instance-_k_tg9sb v1 is adopting successor phases from '_writer' kind-_writer/instance-icv7qr07 v2 of: [] 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-icv7qr07 v3 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.worker] Starting the next job 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-icv7qr07 v3 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-icv7qr07 v3) from description '_writer' kind-_writer/instance-icv7qr07 v3 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:58+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). 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-0e825c8da25b4eb38fee2032fafa83da/stream from Job('_writer' kind-_writer/instance-icv7qr07 v3) with a 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-icv7qr07 v3 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-icv7qr07 v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-icv7qr07 v4 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-icv7qr07 v4 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-icv7qr07 v4 would chain to ID kind-EncapsulatedJob/instance-bpvbpt4v 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.worker] Preemptibility is different for the next job, returning to the leader 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Not chaining from job '_writer' kind-_writer/instance-icv7qr07 v4 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/workdir/toilwf-687cdbabed03577e875959feb6b5cc2e/96e5. Set --cleanWorkDir to retain this log 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 0.339904 seconds 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [pydot] pydot initializing 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [pydot] pydot 4.0.1 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1330s <========= 1330s [2026-01-30T07:05:58+0000] [Thread-37 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-bpvbpt4v 1330s [2026-01-30T07:05:58+0000] [Thread-37 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 2 as child 10074 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'requests', 'asyncio', 'boto', 'botocore', 'docker', 'urllib3', 'dill', 'boto3', 'concurrent'} 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.worker] Worker started for job EncapsulatedJob... 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.common] Obtained node ID 6fa530d97284404a9688ce299e64170e from file /var/lib/dbus/machine-id 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/workdir/toilwf-687cdbabed03577e875959feb6b5cc2e/7d6e/worker_log.txt 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v4 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funcmdawh8e5 1330s [2026-01-30T07:06:00+0000] [Thread-40 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:06:00: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1330s [2026-01-30T07:06:00+0000] [Thread-40 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:06:00: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v2 used 7.95x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:06:00+0000] [Thread-40 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:06:00: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1330s [2026-01-30T07:06:00+0000] [Thread-40 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:06:00: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3 used 11.14x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:06:00+0000] [Thread-37 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-bpvbpt4v. 1330s [2026-01-30T07:06:00+0000] [Thread-37 (daddy)] [D] [toil.batchSystems.singleMachine] Child 10074 for job 2 succeeded 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 2 with exit value: 1 1330s [2026-01-30T07:06:00+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 1330s Exit reason: None 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-bpvbpt4v', exit_code=1) 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=2, external_batch_id='10074', batch_system='SingleMachineBatchSystem') 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.leader] Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 continues to exist (i.e. has more to do) 1330s [2026-01-30T07:06:00+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v4 1330s [2026-01-30T07:06:00+0000] [MainThread] [W] [toil.leader] Log from job "kind-EncapsulatedJob/instance-bpvbpt4v" follows: 1330s =========> 1330s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '9758239f-8230-4707-9a89-f88f4814da8c', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpzhq9eyr4', '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} 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funcmdawh8e5 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.worker] Parsed job description 1330s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil.worker] Working on job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1330s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:59+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. 1330s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:59+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. 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil.worker] Loaded body Job('EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1) from description 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v2 1330s [2026-01-30T07:05:59+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v2 used 7.95x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil.worker] Completed body for 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v2 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.worker] 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v2 would chain to ID kind-_follower/instance-i9covkiz 1330s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil.worker] Chaining from 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v2 to '_follower' kind-_follower/instance-i9covkiz v1 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.job] '_follower' kind-_follower/instance-i9covkiz v1 is adopting successor phases from 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v2 of: [{'kind-Job/instance-67qr9tq8'}] 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.worker] Starting the next job 1330s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore'. 1330s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3) from description '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:59+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3 used 11.14x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:05:59+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 1330s self.evaluatePromisedRequirements() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 1330s ].getValue() 1330s ~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 1330s return func(*self._args) 1330s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 1330s 1330s [2026-01-30T07:05:59+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [pydot] pydot initializing 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [pydot] pydot 4.0.1 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1330s <========= 1330s [2026-01-30T07:06:00+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v4 with ID kind-EncapsulatedJob/instance-bpvbpt4v to 1 1330s [2026-01-30T07:06:00+0000] [MainThread] [W] [toil.job] We have increased the default memory of the failed job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v4 to 2147483648 bytes 1330s [2026-01-30T07:06:00+0000] [MainThread] [W] [toil.job] We have increased the disk of the failed job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v4 to the default of 2147483648 bytes 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v5 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-bpvbpt4v', result_status=1) 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.leader] Added job: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v5 to updated jobs 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.leader] Updating status of job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v5 with result status: 1 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Issuing the command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-bpvbpt4v with disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 1330s [2026-01-30T07:06:00+0000] [MainThread] [I] [toil.leader] Issued job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v5 with job batch system ID: 3 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-bpvbpt4v', toil_batch_id=3) 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 1330s [2026-01-30T07:06:00+0000] [Thread-37 (daddy)] [D] [toil.batchSystems.singleMachine] Attempting to run job command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-bpvbpt4v 1330s [2026-01-30T07:06:00+0000] [Thread-37 (daddy)] [D] [toil.batchSystems.singleMachine] Launched job 3 as child 10127 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'concurrent', 'urllib3', 'boto3', 'dill', 'asyncio', 'boto', 'docker', 'requests', 'botocore'} 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.worker] Worker started for job _follower... 1330s [2026-01-30T07:06:00+0000] [MainThread] [D] [toil.common] Obtained node ID 6fa530d97284404a9688ce299e64170e from file /var/lib/dbus/machine-id 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.worker] Redirecting logging to /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/workdir/toilwf-687cdbabed03577e875959feb6b5cc2e/8431/worker_log.txt 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v7 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funcgb66nmmu 1330s [2026-01-30T07:06:02+0000] [Thread-37 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-bpvbpt4v. 1330s [2026-01-30T07:06:02+0000] [Thread-37 (daddy)] [D] [toil.batchSystems.singleMachine] Child 10127 for job 3 succeeded 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.batchSystems.singleMachine] Ran jobID: 3 with exit value: 1 1330s [2026-01-30T07:06:02+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v5 1330s Exit reason: None 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-bpvbpt4v', exit_code=1) 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=3, external_batch_id='10127', batch_system='SingleMachineBatchSystem') 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.leader] Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v5 continues to exist (i.e. has more to do) 1330s [2026-01-30T07:06:02+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v7 1330s [2026-01-30T07:06:02+0000] [MainThread] [W] [toil.leader] Log from job "kind-EncapsulatedJob/instance-bpvbpt4v" follows: 1330s =========> 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '9758239f-8230-4707-9a89-f88f4814da8c', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpzhq9eyr4', '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} 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funcgb66nmmu 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.worker] Parsed job description 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:06:01+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. 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:06:01+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. 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore'. 1330s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6) from description '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:06:01+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 used 6.03x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:06:01+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1330s Traceback (most recent call last): 1330s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1330s job._runner( 1330s ~~~~~~~~~~~^ 1330s jobGraph=None, 1330s ^^^^^^^^^^^^^^ 1330s ...<2 lines>... 1330s defer=defer, 1330s ^^^^^^^^^^^^ 1330s ) 1330s ^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1330s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1330s return self.run(fileStore) 1330s ~~~~~~~~^^^^^^^^^^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 1330s self.evaluatePromisedRequirements() 1330s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 1330s ].getValue() 1330s ~~~~~~~~^^ 1330s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 1330s return func(*self._args) 1330s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 1330s 1330s [2026-01-30T07:06:01+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [pydot] pydot initializing 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [pydot] pydot 4.0.1 1330s [2026-01-30T07:06:01+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1330s <========= 1330s [2026-01-30T07:06:02+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v7 with ID kind-EncapsulatedJob/instance-bpvbpt4v to 0 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-bpvbpt4v', result_status=1) 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.leader] Added job: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 to updated jobs 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.leader] Updating status of job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 with result status: 1 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-bpvbpt4v') 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.leader] Found new failed successors: kind-Job/instance-67qr9tq8 of job: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.leader] Totally failed job: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 is marking direct predecessor: '_writer' kind-_writer/instance-icv7qr07 v4 as having failed jobs 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.leader] Cleaning the predecessors of kind-EncapsulatedJob/instance-bpvbpt4v 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.toilState] Successors: one fewer for kind-_writer/instance-icv7qr07, now have 0 1330s [2026-01-30T07:06:02+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-icv7qr07', result_status=0) 1330s [2026-01-30T07:06:02+0000] [MainThread] [W] [toil.leader] Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 is completely failed 1330s [2026-01-30T07:06:02+0000] [Thread-40 (statsAndLoggingAggregator)] [D] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:06:02: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:06:02+0000] [Thread-40 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:06:02: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 used 6.03x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s [2026-01-30T07:06:04+0000] [MainThread] [D] [toil.leader] Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s [2026-01-30T07:06:04+0000] [MainThread] [D] [toil.leader] Updating status of job '_writer' kind-_writer/instance-icv7qr07 v4 with result status: 0 1330s [2026-01-30T07:06:04+0000] [MainThread] [D] [toil.leader] Job kind-_writer/instance-icv7qr07 is being processed as completely failed 1330s [2026-01-30T07:06:04+0000] [MainThread] [D] [toil.bus] Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_writer', job_id='kind-_writer/instance-icv7qr07') 1330s [2026-01-30T07:06:04+0000] [MainThread] [D] [toil.leader] Found new failed successors: of job: '_writer' kind-_writer/instance-icv7qr07 v4 1330s [2026-01-30T07:06:06+0000] [MainThread] [D] [toil.leader] Finished the main loop: no jobs left to run. 1330s [2026-01-30T07:06:06+0000] [MainThread] [D] [toil.serviceManager] Waiting for service manager thread to finish ... 1330s [2026-01-30T07:06:06+0000] [Thread-39 (__start_services)] [D] [toil.serviceManager] Received signal to quit starting services. 1330s [2026-01-30T07:06:07+0000] [MainThread] [D] [toil.serviceManager] ... finished shutting down the service manager. Took 1.683164358139038 seconds 1330s [2026-01-30T07:06:07+0000] [MainThread] [D] [toil.statsAndLogging] Waiting for stats and logging collator thread to finish ... 1330s [2026-01-30T07:06:08+0000] [MainThread] [D] [toil.statsAndLogging] ... finished collating stats and logs. Took 0.6425068378448486 seconds 1330s [2026-01-30T07:06:08+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1330s [2026-01-30T07:06:08+0000] [MainThread] [I] [toil.leader] Finished toil run with 2 failed jobs. 1330s [2026-01-30T07:06:08+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_writer' kind-_writer/instance-icv7qr07 v4 '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 1330s [2026-01-30T07:06:08+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1330s [2026-01-30T07:06:08+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1330s [2026-01-30T07:06:08+0000] [MainThread] [D] [toil.common] Shutting down batch system ... 1330s [2026-01-30T07:06:09+0000] [Thread-37 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread cleaning up 0 remaining children for batch system 4395914682160... 1330s [2026-01-30T07:06:09+0000] [Thread-37 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread for batch system 4395914682160 finishing because no children should now exist 1330s [2026-01-30T07:06:09+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Attempting worker cleanup 1330s [2026-01-30T07:06:09+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:06:09+0000] [MainThread] [D] [toil.deferred] Cleaning up deferred functions system 1330s [2026-01-30T07:06:09+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funcv08fz0_j 1330s [2026-01-30T07:06:09+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:06:09+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:06:09+0000] [MainThread] [D] [toil.deferred] Removing own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funcv08fz0_j 1330s [2026-01-30T07:06:09+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:06:09+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting workflow directory /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/workdir/toilwf-687cdbabed03577e875959feb6b5cc2e 1330s [2026-01-30T07:06:09+0000] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting coordination directory /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e 1330s [2026-01-30T07:06:09+0000] [MainThread] [D] [toil.common] ... finished shutting down the batch system in 0.20757818222045898 seconds. 1330s [2026-01-30T07:06:09+0000] [MainThread] [I] [toil.lib.history] Workflow 9758239f-8230-4707-9a89-f88f4814da8c stopped. Success: False 1330s ------------------------------ Captured log call ------------------------------- 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.resource:resource.py:458 Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1330s DEBUG  toil.common:common.py:796 Initialized default configuration: {"config_version": 1.0} 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for aws_batch batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for single_machine batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for grid_engine batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for lsf batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for slurm batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for torque batch system 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:488 Suppressing the following loggers: {'urllib3', 'salad', 'asyncio', 'requests', 'rdflib', 'concurrent', 'boto3', 'humanfriendly', 'debugWorkflow', 'dill', 'test', 'cwltest', 'boto', 'bcdocs', 'cachecontrol', 'docker', 'botocore'} 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:447 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:488 Suppressing the following loggers: {'urllib3', 'salad', 'asyncio', 'requests', 'rdflib', 'concurrent', 'boto3', 'humanfriendly', 'debugWorkflow', 'dill', 'test', 'cwltest', 'boto', 'bcdocs', 'cachecontrol', 'docker', 'botocore'} 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:447 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. 1330s DEBUG  toil.common:common.py:796 Initialized default configuration: {"config_version": 1.0} 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for aws_batch batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for single_machine batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for grid_engine batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for lsf batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for slurm batch system 1330s DEBUG  toil.batchSystems.options:options.py:207 Add options for torque batch system 1330s 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-gw3/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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} 1330s DEBUG  toil.jobStores.fileJobStore:fileJobStore.py:93 Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore'. 1330s DEBUG  toil.jobStores.abstractJobStore:abstractJobStore.py:212 The workflow ID is: '9758239f-8230-4707-9a89-f88f4814da8c' 1330s INFO  toil.lib.history:history.py:369 Recording workflow creation of 9758239f-8230-4707-9a89-f88f4814da8c in file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore 1330s INFO  toil.lib.history:history.py:399 Workflow 9758239f-8230-4707-9a89-f88f4814da8c is a run of 1330s DEBUG  toil.common:common.py:1346 Using the single machine batch system 1330s DEBUG  toil.common:common.py:1723 Created the workflow directory for this machine at /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/workdir/toilwf-687cdbabed03577e875959feb6b5cc2e 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:247 Started daddy thread for batch system 4395914682160. 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:229 Started batch system 4395914682160 in normal mode. 1330s 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. 1330s DEBUG  toil.common:common.py:1409 No user script to auto-deploy. 1330s DEBUG  toil.common:common.py:1576 Written the environment for the jobs to the environment file 1330s DEBUG  toil.common:common.py:1580 Caching all jobs in job store 1330s DEBUG  toil.common:common.py:1584 0 jobs downloaded. 1330s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-7a5ec3163cbb43da86b6609c3085e792/stream for result of '_writer' TemporaryID(eb6efaac-ee59-4b5c-a7cb-6a97420c4615) v0 1330s DEBUG  toil.job:job.py:3000 Saving graph of 5 jobs, 5 non-service, 5 new 1330s DEBUG  toil.job:job.py:3023 Processing job 'Job' kind-Job/instance-67qr9tq8 v0 1330s DEBUG  toil.job:job.py:3023 Processing job '_follower' kind-_follower/instance-i9covkiz v0 1330s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-0ee48f0c3f4647cebd9570c11d0c73be/stream for result of '_writer' kind-_writer/instance-icv7qr07 v0 1330s DEBUG  toil.job:job.py:2226 Issuing promise files/no-job/file-0e825c8da25b4eb38fee2032fafa83da/stream for result of '_writer' kind-_writer/instance-_k_tg9sb v0 1330s DEBUG  toil.job:job.py:3023 Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v0 1330s DEBUG  toil.job:job.py:3023 Processing job '_writer' kind-_writer/instance-_k_tg9sb v0 1330s DEBUG  toil.job:job.py:3023 Processing job '_writer' kind-_writer/instance-icv7qr07 v0 1330s DEBUG  toil.job:job.py:1507 New job version: 'Job' kind-Job/instance-67qr9tq8 v1 1330s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-_follower/instance-i9covkiz v1 1330s DEBUG  toil.job:job.py:1507 New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 1330s DEBUG  toil.job:job.py:1507 New job version: '_writer' kind-_writer/instance-_k_tg9sb v1 1330s DEBUG  toil.job:job.py:1507 New job version: '_writer' kind-_writer/instance-icv7qr07 v1 1330s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s DEBUG  toil:__init__.py:481 Configuration: {'cwl': False, 'workflowID': '9758239f-8230-4707-9a89-f88f4814da8c', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpzhq9eyr4', '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} 1330s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1330s DEBUG  toil.bus:bus.py:403 Listening for message topic: toil.bus.JobUpdatedMessage 1330s DEBUG  toil.toilState:toilState.py:322 Found job to run: kind-_writer/instance-icv7qr07, with body: True, with checkpoint: False, with services: False, with no next successors: False 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-icv7qr07', result_status=0) 1330s DEBUG  toil.leader:leader.py:145 Found 1 jobs to start and 0 jobs with successors to run 1330s DEBUG  toil.leader:leader.py:157 Checked batch system has no running jobs and no updated jobs 1330s DEBUG  toil.serviceManager:serviceManager.py:35 Initializing service manager 1330s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-icv7qr07 v1 with result status: 0 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore kind-_writer/instance-icv7qr07 with disk: 2.0 Gi, memory: 2.0 Gi, cores: 2.0, accelerators: [], preemptible: False 1330s INFO  toil.leader:leader.py:1132 Issued job '_writer' kind-_writer/instance-icv7qr07 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 2, accelerators: [], preemptible: False 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_writer', job_id='kind-_writer/instance-icv7qr07', toil_batch_id=1) 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker _writer file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore kind-_writer/instance-icv7qr07 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 1 as child 10047 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 10047 for job 1 succeeded 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 1 with exit value: 0 1330s DEBUG  toil.leader:leader.py:846 Job ended: '_writer' kind-_writer/instance-icv7qr07 v1 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_writer', job_id='kind-_writer/instance-icv7qr07', exit_code=0) 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=1, external_batch_id='10047', batch_system='SingleMachineBatchSystem') 1330s DEBUG  toil.leader:leader.py:1455 Job '_writer' kind-_writer/instance-icv7qr07 v1 continues to exist (i.e. has more to do) 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-icv7qr07', result_status=0) 1330s DEBUG  toil.leader:leader.py:1620 Added job: '_writer' kind-_writer/instance-icv7qr07 v4 to updated jobs 1330s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 1330s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1330s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-icv7qr07 v4 with result status: 0 1330s DEBUG  toil.leader:leader.py:506 Job: kind-_writer/instance-icv7qr07 has 1 successors to schedule 1330s DEBUG  toil.toilState:toilState.py:264 Successors: 1 more for kind-_writer/instance-icv7qr07, now have 1 1330s DEBUG  toil.leader:leader.py:476 Added job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 as coming after job '_writer' kind-_writer/instance-icv7qr07 v4 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-bpvbpt4v with disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 1330s INFO  toil.leader:leader.py:1132 Issued job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 with job batch system ID: 2 and disk: 976.6 Ki, memory: 30.5 Mi, cores: 0.1, accelerators: [], preemptible: True 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-bpvbpt4v', toil_batch_id=2) 1330s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:05:58: Job '_writer' kind-_writer/instance-icv7qr07 v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:05:58: Job '_writer' kind-_writer/instance-icv7qr07 v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:98 Received Toil worker log. Disable debug level logging to hide this output 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:101 Log from job "JobFunctionWrappingJob" follows: 1330s =========> 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '9758239f-8230-4707-9a89-f88f4814da8c', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpzhq9eyr4', '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} 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funccmbc6weg 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.worker] Parsed job description 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-icv7qr07 v1 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:58+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. 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1330s [2026-01-30T07:05:58+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. 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-icv7qr07 v1) from description '_writer' kind-_writer/instance-icv7qr07 v1 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:58+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). 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-7a5ec3163cbb43da86b6609c3085e792/stream from Job('_writer' kind-_writer/instance-icv7qr07 v1) with a 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-0ee48f0c3f4647cebd9570c11d0c73be/stream from Job('_writer' kind-_writer/instance-icv7qr07 v1) with a 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-icv7qr07 v1 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-icv7qr07 v1 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-icv7qr07 v2 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-icv7qr07 v2 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-icv7qr07 v2 would chain to ID kind-_writer/instance-_k_tg9sb 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Chaining from '_writer' kind-_writer/instance-icv7qr07 v2 to '_writer' kind-_writer/instance-_k_tg9sb v1 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] '_writer' kind-_writer/instance-_k_tg9sb v1 is adopting successor phases from '_writer' kind-_writer/instance-icv7qr07 v2 of: [] 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-icv7qr07 v3 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.worker] Starting the next job 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Working on job '_writer' kind-_writer/instance-icv7qr07 v3 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Loaded body Job('_writer' kind-_writer/instance-icv7qr07 v3) from description '_writer' kind-_writer/instance-icv7qr07 v3 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running job 1330s [2026-01-30T07:05:58+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). 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Resolve promise files/no-job/file-0e825c8da25b4eb38fee2032fafa83da/stream from Job('_writer' kind-_writer/instance-icv7qr07 v3) with a 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] Processing job '_writer' kind-_writer/instance-icv7qr07 v3 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_writer' kind-_writer/instance-icv7qr07 v3 used 0.00% disk (8.0 KiB [8192B] used, 2.0 GiB [2147483648B] requested). 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.job] New job version: '_writer' kind-_writer/instance-icv7qr07 v4 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Completed body for '_writer' kind-_writer/instance-icv7qr07 v4 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.worker] '_writer' kind-_writer/instance-icv7qr07 v4 would chain to ID kind-EncapsulatedJob/instance-bpvbpt4v 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [toil.worker] Preemptibility is different for the next job, returning to the leader 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Not chaining from job '_writer' kind-_writer/instance-icv7qr07 v4 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/workdir/toilwf-687cdbabed03577e875959feb6b5cc2e/96e5. Set --cleanWorkDir to retain this log 1330s [2026-01-30T07:05:58+0000] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 0.339904 seconds 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [pydot] pydot initializing 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [pydot] pydot 4.0.1 1330s [2026-01-30T07:05:58+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1330s <========= 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker EncapsulatedJob file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-bpvbpt4v 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 2 as child 10074 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:06:00: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1330s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:06:00: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v2 used 7.95x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:06:00: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1330s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:06:00: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3 used 11.14x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1330s 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-gw3/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-bpvbpt4v. 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 10074 for job 2 succeeded 1330s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 2 with exit value: 1 1330s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 1331s Exit reason: None 1331s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='EncapsulatedJob', job_id='kind-EncapsulatedJob/instance-bpvbpt4v', exit_code=1) 1331s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=2, external_batch_id='10074', batch_system='SingleMachineBatchSystem') 1331s DEBUG  toil.leader:leader.py:1455 Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 continues to exist (i.e. has more to do) 1331s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v4 1331s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-EncapsulatedJob/instance-bpvbpt4v" follows: 1331s =========> 1331s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '9758239f-8230-4707-9a89-f88f4814da8c', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpzhq9eyr4', '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} 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funcmdawh8e5 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.worker] Parsed job description 1331s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil.worker] Working on job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1331s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1331s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1331s [2026-01-30T07:05:59+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. 1331s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1331s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1331s [2026-01-30T07:05:59+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. 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.resource] Module dir is /usr/lib/python3/dist-packages, our prefix is /usr, virtualenv: False 1331s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil.worker] Loaded body Job('EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1) from description 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running job 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 0 new 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.job] Processing job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v1 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.job] New job version: 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v2 1331s [2026-01-30T07:05:59+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v2 used 7.95x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1331s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil.worker] Completed body for 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v2 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.worker] 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v2 would chain to ID kind-_follower/instance-i9covkiz 1331s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil.worker] Chaining from 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v2 to '_follower' kind-_follower/instance-i9covkiz v1 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.job] '_follower' kind-_follower/instance-i9covkiz v1 is adopting successor phases from 'EncapsulatedJob' kind-EncapsulatedJob/instance-bpvbpt4v v2 of: [{'kind-Job/instance-67qr9tq8'}] 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.worker] Starting the next job 1331s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore'. 1331s [2026-01-30T07:05:59+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3) from description '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running job 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3 used 0.41% disk (4.0 KiB [4096B] used, 976.6 KiB [1000000B] requested). 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1331s [2026-01-30T07:05:59+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1331s [2026-01-30T07:05:59+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v3 used 11.14x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1331s [2026-01-30T07:05:59+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 1331s self.evaluatePromisedRequirements() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 1331s ].getValue() 1331s ~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 1331s return func(*self._args) 1331s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 1331s 1331s [2026-01-30T07:05:59+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s [2026-01-30T07:06:00+0000] [MainThread] [D] [pydot] pydot initializing 1331s [2026-01-30T07:06:00+0000] [MainThread] [D] [pydot] pydot 4.0.1 1331s [2026-01-30T07:06:00+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1331s <========= 1331s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v4 with ID kind-EncapsulatedJob/instance-bpvbpt4v to 1 1331s WARNING  toil.job:job.py:1413 We have increased the default memory of the failed job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v4 to 2147483648 bytes 1331s WARNING  toil.job:job.py:1421 We have increased the disk of the failed job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v4 to the default of 2147483648 bytes 1331s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v5 1331s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-bpvbpt4v', result_status=1) 1331s DEBUG  toil.leader:leader.py:1620 Added job: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v5 to updated jobs 1331s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1331s DEBUG  toil.leader:leader.py:606 Updating status of job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v5 with result status: 1 1331s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:910 Issuing the command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-bpvbpt4v with disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 1331s INFO  toil.leader:leader.py:1132 Issued job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v5 with job batch system ID: 3 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 0.1, accelerators: [], preemptible: True 1331s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobIssuedMessage with message: JobIssuedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-bpvbpt4v', toil_batch_id=3) 1331s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.QueueSizeMessage with message: QueueSizeMessage(queue_size=1) 1331s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:786 Attempting to run job command: _toil_worker _follower file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-bpvbpt4v 1331s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:817 Launched job 3 as child 10127 1331s 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-gw3/testPromisesWithNonCachingFile0/jobstore kind-EncapsulatedJob/instance-bpvbpt4v. 1331s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:888 Child 10127 for job 3 succeeded 1331s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:1008 Ran jobID: 3 with exit value: 1 1331s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v5 1331s Exit reason: None 1331s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobCompletedMessage with message: JobCompletedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-bpvbpt4v', exit_code=1) 1331s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.ExternalBatchIdMessage with message: ExternalBatchIdMessage(toil_batch_id=3, external_batch_id='10127', batch_system='SingleMachineBatchSystem') 1331s DEBUG  toil.leader:leader.py:1455 Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v5 continues to exist (i.e. has more to do) 1331s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v7 1331s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-EncapsulatedJob/instance-bpvbpt4v" follows: 1331s =========> 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '9758239f-8230-4707-9a89-f88f4814da8c', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpzhq9eyr4', '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} 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funcgb66nmmu 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.worker] Parsed job description 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1331s [2026-01-30T07:06:01+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. 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1331s [2026-01-30T07:06:01+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. 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore'. 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6) from description '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running job 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1331s [2026-01-30T07:06:01+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 used 6.03x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1331s [2026-01-30T07:06:01+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 1331s self.evaluatePromisedRequirements() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 1331s ].getValue() 1331s ~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 1331s return func(*self._args) 1331s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 1331s 1331s [2026-01-30T07:06:01+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [pydot] pydot initializing 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [pydot] pydot 4.0.1 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1331s <========= 1331s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v7 with ID kind-EncapsulatedJob/instance-bpvbpt4v to 0 1331s DEBUG  toil.job:job.py:1507 New job version: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 1331s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-EncapsulatedJob/instance-bpvbpt4v', result_status=1) 1331s DEBUG  toil.leader:leader.py:1620 Added job: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 to updated jobs 1331s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1331s DEBUG  toil.leader:leader.py:606 Updating status of job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 with result status: 1 1331s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_follower', job_id='kind-EncapsulatedJob/instance-bpvbpt4v') 1331s DEBUG  toil.leader:leader.py:1735 Found new failed successors: kind-Job/instance-67qr9tq8 of job: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 1331s DEBUG  toil.leader:leader.py:1779 Totally failed job: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 is marking direct predecessor: '_writer' kind-_writer/instance-icv7qr07 v4 as having failed jobs 1331s DEBUG  toil.leader:leader.py:1846 Cleaning the predecessors of kind-EncapsulatedJob/instance-bpvbpt4v 1331s DEBUG  toil.toilState:toilState.py:283 Successors: one fewer for kind-_writer/instance-icv7qr07, now have 0 1331s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobUpdatedMessage with message: JobUpdatedMessage(job_id='kind-_writer/instance-icv7qr07', result_status=0) 1331s WARNING  toil.leader:leader.py:643 Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 is completely failed 1331s DEBUG  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:06:02: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 1331s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:06:02: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 used 6.03x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1331s DEBUG  toil.leader:leader.py:735 Built the jobs list, currently have 1 jobs to update and 0 jobs issued 1331s DEBUG  toil.leader:leader.py:606 Updating status of job '_writer' kind-_writer/instance-icv7qr07 v4 with result status: 0 1331s DEBUG  toil.leader:leader.py:597 Job kind-_writer/instance-icv7qr07 is being processed as completely failed 1331s DEBUG  toil.bus:bus.py:386 Notifying toil.bus.JobFailedMessage with message: JobFailedMessage(job_type='_writer', job_id='kind-_writer/instance-icv7qr07') 1331s DEBUG  toil.leader:leader.py:1735 Found new failed successors: of job: '_writer' kind-_writer/instance-icv7qr07 v4 1331s DEBUG  toil.leader:leader.py:969 Finished the main loop: no jobs left to run. 1331s DEBUG  toil.serviceManager:serviceManager.py:236 Waiting for service manager thread to finish ... 1331s DEBUG  toil.serviceManager:serviceManager.py:261 Received signal to quit starting services. 1331s DEBUG  toil.serviceManager:serviceManager.py:243 ... finished shutting down the service manager. Took 1.683164358139038 seconds 1331s DEBUG  toil.statsAndLogging:statsAndLogging.py:296 Waiting for stats and logging collator thread to finish ... 1331s DEBUG  toil.statsAndLogging:statsAndLogging.py:300 ... finished collating stats and logs. Took 0.6425068378448486 seconds 1331s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1331s INFO  toil.leader:leader.py:317 Finished toil run with 2 failed jobs. 1331s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_writer' kind-_writer/instance-icv7qr07 v4 '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 1331s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1331s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1331s DEBUG  toil.common:common.py:1800 Shutting down batch system ... 1331s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:317 Daddy thread cleaning up 0 remaining children for batch system 4395914682160... 1331s DEBUG  toil.batchSystems.singleMachine:singleMachine.py:325 Daddy thread for batch system 4395914682160 finishing because no children should now exist 1331s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:503 Attempting worker cleanup 1331s DEBUG  toil.lib.threading:threading.py:109 Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1331s DEBUG  toil.deferred:deferred.py:215 Cleaning up deferred functions system 1331s DEBUG  toil.deferred:deferred.py:159 Opened with own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funcv08fz0_j 1331s DEBUG  toil.deferred:deferred.py:291 Running orphaned deferred functions 1331s DEBUG  toil.deferred:deferred.py:369 Ran orphaned deferred functions from 0 abandoned state files 1331s DEBUG  toil.deferred:deferred.py:167 Removing own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funcv08fz0_j 1331s DEBUG  toil.lib.threading:threading.py:109 Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1331s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:517 Deleting workflow directory /tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/workdir/toilwf-687cdbabed03577e875959feb6b5cc2e 1331s DEBUG  toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:521 Deleting coordination directory /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e 1331s DEBUG  toil.common:common.py:1802 ... finished shutting down the batch system in 0.20757818222045898 seconds. 1331s INFO  toil.lib.history:history.py:530 Workflow 9758239f-8230-4707-9a89-f88f4814da8c stopped. Success: False 1331s =========================== short test summary info ============================ 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:603: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:217: Configure AWS credentials to include this test. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:189: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1115: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1127: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:621: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:825: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:800: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:151: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:160: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:313: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:202: Configure AWS credentials to include this test. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1467: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1446: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1079: Configure AWS credentials to include this test. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:450: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:238: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:421: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:405: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:380: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:529: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:264: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:585: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:960: Configure AWS credentials to include this test. 1331s SKIPPED [13] ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py:1139: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:32: Consumes unauthenticated Docker Hub pulls if run 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:38: Consumes unauthenticated Docker Hub pulls if run 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:45: Consumes unauthenticated Docker Hub pulls if run 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:26: Consumes unauthenticated Docker Hub pulls if run 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:731: Install Toil with the 'server' extra to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:646: Install Toil with the 'server' extra to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:697: Install Toil with the 'server' extra to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:706: Install Toil with the 'server' extra to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:685: Install Toil with the 'server' extra to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:676: Install Toil with the 'server' extra to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:721: Install Toil with the 'server' extra to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:619: Install Toil with the 'server' extra to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:600: Install Toil with the 'server' extra to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:668: Install Toil with the 'server' extra to include this test. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s SKIPPED [7] ../../../../usr/lib/python3/dist-packages/_pytest/unittest.py:498: Configure AWS credentials to include this test. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s 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. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:541: Install Toil with the 'server' extra to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:535: Install Toil with the 'server' extra to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:526: Install Toil with the 'server' extra to include this test. 1331s 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. 1331s 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. 1331s 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. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py:255: Install Toil with the 'wdl' extra to include this test. 1331s SKIPPED [3] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:96: Install Toil with the 'server' extra to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:245: Install Toil with the 'server' extra to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1568: Configure AWS credentials to include this test. 1331s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:48: Install Toil with the 'server' extra to include this test. 1331s FAILED lib/dockerTest.py::TestDocker::testDockerClean - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean0/working/test.txt' 1331s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_FORGO0/working/test.txt' 1331s FAILED docs/scriptsTest.py::ToilDocumentationTest::testDocker - RuntimeError: [2026-01-30T07:01:44+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of f2610e60-b924-43fb-a299-a65233bde05f in file:/tmp/tmpv_fc012jtutorial_docker 1331s [2026-01-30T07:01:45+0000] [MainThread] [I] [toil.lib.history] Workflow f2610e60-b924-43fb-a299-a65233bde05f is a run of /usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py 1331s [2026-01-30T07:01:45+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:01:45+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1331s [2026-01-30T07:01:45+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1331s [2026-01-30T07:01:46+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpv_fc012jtutorial_docker kind-apiDockerCall/instance-af6gzttt. 1331s [2026-01-30T07:01:46+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v1 1331s Exit reason: None 1331s [2026-01-30T07:01:46+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v2 1331s [2026-01-30T07:01:46+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-af6gzttt" follows: 1331s =========> 1331s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v1 1331s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-af6gzttt v1) from description 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v1 1331s [2026-01-30T07:01:46+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s PermissionError: [Errno 13] Permission denied 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1331s resp = conn.urlopen( 1331s method=request.method, 1331s ...<9 lines>... 1331s chunked=chunked, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1331s retries = retries.increment( 1331s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1331s raise reraise(type(error), error, _stacktrace) 1331s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1331s raise value.with_traceback(tb) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1331s return self.version(api_version=False)["ApiVersion"] 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1331s return self._result(self._get(url), json=True) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1331s return f(self, *args, **kwargs) 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1331s return self.get(url, **self._set_request_timeout(kwargs)) 1331s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1331s return self.request("GET", url, **kwargs) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1331s resp = self.send(prep, **send_kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1331s r = adapter.send(request, **kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1331s raise ConnectionError(err, request=request) 1331s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s The above exception was the direct cause of the following exception: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1331s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1331s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1331s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1331s return cls( 1331s timeout=timeout, 1331s ...<3 lines>... 1331s **kwargs_from_env(**kwargs) 1331s ) 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1331s self.api = APIClient(*args, **kwargs) 1331s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1331s self._version = self._retrieve_server_version() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1331s raise DockerException( 1331s f'Error while fetching server API version: {e}' 1331s ) from e 1331s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s [2026-01-30T07:01:46+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s <========= 1331s [2026-01-30T07:01:46+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v2 with ID kind-apiDockerCall/instance-af6gzttt to 1 1331s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 1331s [2026-01-30T07:01:46+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1331s [2026-01-30T07:01:48+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmpv_fc012jtutorial_docker kind-apiDockerCall/instance-af6gzttt. 1331s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v3 1331s Exit reason: None 1331s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v5 1331s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-af6gzttt" follows: 1331s =========> 1331s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v4 1331s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-af6gzttt v4) from description 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v4 1331s [2026-01-30T07:01:47+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s PermissionError: [Errno 13] Permission denied 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1331s resp = conn.urlopen( 1331s method=request.method, 1331s ...<9 lines>... 1331s chunked=chunked, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1331s retries = retries.increment( 1331s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1331s raise reraise(type(error), error, _stacktrace) 1331s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1331s raise value.with_traceback(tb) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1331s return self.version(api_version=False)["ApiVersion"] 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1331s return self._result(self._get(url), json=True) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1331s return f(self, *args, **kwargs) 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1331s return self.get(url, **self._set_request_timeout(kwargs)) 1331s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1331s return self.request("GET", url, **kwargs) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1331s resp = self.send(prep, **send_kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1331s r = adapter.send(request, **kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1331s raise ConnectionError(err, request=request) 1331s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s The above exception was the direct cause of the following exception: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1331s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1331s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1331s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1331s return cls( 1331s timeout=timeout, 1331s ...<3 lines>... 1331s **kwargs_from_env(**kwargs) 1331s ) 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1331s self.api = APIClient(*args, **kwargs) 1331s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1331s self._version = self._retrieve_server_version() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1331s raise DockerException( 1331s f'Error while fetching server API version: {e}' 1331s ) from e 1331s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s [2026-01-30T07:01:47+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s <========= 1331s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v5 with ID kind-apiDockerCall/instance-af6gzttt to 0 1331s [2026-01-30T07:01:48+0000] [MainThread] [W] [toil.leader] Job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v6 is completely failed 1331s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1331s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1331s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v6 1331s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1331s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1331s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.lib.history] Workflow f2610e60-b924-43fb-a299-a65233bde05f stopped. Success: False 1331s [2026-01-30T07:01:51+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/tmpv_fc012jtutorial_docker) 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py", line 20, in 1331s toil.start(align) 1331s ~~~~~~~~~~^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1331s return self._runMainLoop(rootJobDescription) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1331s ).run() 1331s ~~~^^ 1331s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1331s raise FailedJobsException( 1331s ...<3 lines>... 1331s ) 1331s toil.exceptions.FailedJobsException: The job store '/tmp/tmpv_fc012jtutorial_docker' contains 1 failed jobs: 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v6 1331s Log from job "'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v6" follows: 1331s =========> 1331s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v4 1331s [2026-01-30T07:01:47+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-af6gzttt v4) from description 'apiDockerCall' kind-apiDockerCall/instance-af6gzttt v4 1331s [2026-01-30T07:01:47+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s PermissionError: [Errno 13] Permission denied 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1331s resp = conn.urlopen( 1331s method=request.method, 1331s ...<9 lines>... 1331s chunked=chunked, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1331s retries = retries.increment( 1331s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1331s raise reraise(type(error), error, _stacktrace) 1331s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1331s raise value.with_traceback(tb) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1331s return self.version(api_version=False)["ApiVersion"] 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1331s return self._result(self._get(url), json=True) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1331s return f(self, *args, **kwargs) 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1331s return self.get(url, **self._set_request_timeout(kwargs)) 1331s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1331s return self.request("GET", url, **kwargs) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1331s resp = self.send(prep, **send_kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1331s r = adapter.send(request, **kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1331s raise ConnectionError(err, request=request) 1331s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s The above exception was the direct cause of the following exception: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1331s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1331s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1331s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1331s return cls( 1331s timeout=timeout, 1331s ...<3 lines>... 1331s **kwargs_from_env(**kwargs) 1331s ) 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1331s self.api = APIClient(*args, **kwargs) 1331s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1331s self._version = self._retrieve_server_version() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1331s raise DockerException( 1331s f'Error while fetching server API version: {e}' 1331s ) from e 1331s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s [2026-01-30T07:01:47+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s <========= 1331s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_STOP0/working/test.txt' 1331s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerClean_CRx_RM0/working/test.txt' 1331s FAILED lib/dockerTest.py::TestDocker::testDockerPipeChain - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerPipeChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v6 1331s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v6" follows: 1331s =========> 1331s [2026-01-30T07:02:12+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:02:12+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:02:12+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v4 1331s [2026-01-30T07:02:13+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-2zr83ctl v4 1331s [2026-01-30T07:02:13+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s PermissionError: [Errno 13] Permission denied 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1331s resp = conn.urlopen( 1331s method=request.method, 1331s ...<9 lines>... 1331s chunked=chunked, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1331s retries = retries.increment( 1331s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1331s raise reraise(type(error), error, _stacktrace) 1331s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1331s raise value.with_traceback(tb) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1331s return self.version(api_version=False)["ApiVersion"] 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1331s return self._result(self._get(url), json=True) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1331s return f(self, *args, **kwargs) 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1331s return self.get(url, **self._set_request_timeout(kwargs)) 1331s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1331s return self.request("GET", url, **kwargs) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1331s resp = self.send(prep, **send_kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1331s r = adapter.send(request, **kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1331s raise ConnectionError(err, request=request) 1331s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s The above exception was the direct cause of the following exception: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1331s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1331s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1331s return apiDockerCall( 1331s job, 1331s ...<2 lines>... 1331s privileged=True, 1331s ) 1331s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1331s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1331s return cls( 1331s timeout=timeout, 1331s ...<3 lines>... 1331s **kwargs_from_env(**kwargs) 1331s ) 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1331s self.api = APIClient(*args, **kwargs) 1331s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1331s self._version = self._retrieve_server_version() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1331s raise DockerException( 1331s f'Error while fetching server API version: {e}' 1331s ) from e 1331s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s [2026-01-30T07:02:13+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s <========= 1331s FAILED lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerPipeChainErrorDetect0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v6 1331s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v6" follows: 1331s =========> 1331s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v4 1331s [2026-01-30T07:02:22+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-stk221sm v4 1331s [2026-01-30T07:02:23+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s PermissionError: [Errno 13] Permission denied 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1331s resp = conn.urlopen( 1331s method=request.method, 1331s ...<9 lines>... 1331s chunked=chunked, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1331s retries = retries.increment( 1331s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1331s raise reraise(type(error), error, _stacktrace) 1331s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1331s raise value.with_traceback(tb) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1331s return self.version(api_version=False)["ApiVersion"] 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1331s return self._result(self._get(url), json=True) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1331s return f(self, *args, **kwargs) 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1331s return self.get(url, **self._set_request_timeout(kwargs)) 1331s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1331s return self.request("GET", url, **kwargs) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1331s resp = self.send(prep, **send_kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1331s r = adapter.send(request, **kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1331s raise ConnectionError(err, request=request) 1331s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s The above exception was the direct cause of the following exception: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1331s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1331s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1331s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1331s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1331s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1331s return cls( 1331s timeout=timeout, 1331s ...<3 lines>... 1331s **kwargs_from_env(**kwargs) 1331s ) 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1331s self.api = APIClient(*args, **kwargs) 1331s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1331s self._version = self._retrieve_server_version() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1331s raise DockerException( 1331s f'Error while fetching server API version: {e}' 1331s ) from e 1331s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s [2026-01-30T07:02:23+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s <========= 1331s FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChain - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testNonCachingDockerChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v6 1331s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v6" follows: 1331s =========> 1331s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4 1331s [2026-01-30T07:02:28+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4 1331s [2026-01-30T07:02:28+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-6ztzu3qa v4 used 1.00x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1331s [2026-01-30T07:02:28+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s PermissionError: [Errno 13] Permission denied 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1331s resp = conn.urlopen( 1331s method=request.method, 1331s ...<9 lines>... 1331s chunked=chunked, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1331s retries = retries.increment( 1331s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1331s raise reraise(type(error), error, _stacktrace) 1331s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1331s raise value.with_traceback(tb) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1331s return self.version(api_version=False)["ApiVersion"] 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1331s return self._result(self._get(url), json=True) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1331s return f(self, *args, **kwargs) 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1331s return self.get(url, **self._set_request_timeout(kwargs)) 1331s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1331s return self.request("GET", url, **kwargs) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1331s resp = self.send(prep, **send_kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1331s r = adapter.send(request, **kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1331s raise ConnectionError(err, request=request) 1331s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s The above exception was the direct cause of the following exception: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1331s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1331s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1331s return apiDockerCall( 1331s job, 1331s ...<2 lines>... 1331s privileged=True, 1331s ) 1331s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1331s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1331s return cls( 1331s timeout=timeout, 1331s ...<3 lines>... 1331s **kwargs_from_env(**kwargs) 1331s ) 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1331s self.api = APIClient(*args, **kwargs) 1331s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1331s self._version = self._retrieve_server_version() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1331s raise DockerException( 1331s f'Error while fetching server API version: {e}' 1331s ) from e 1331s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s [2026-01-30T07:02:28+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s <========= 1331s FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testNonCachingDockerChainError0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v6 1331s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v6" follows: 1331s =========> 1331s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v4 1331s [2026-01-30T07:02:34+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 v4 1331s [2026-01-30T07:02:34+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-kanj6ak1 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. 1331s [2026-01-30T07:02:34+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s PermissionError: [Errno 13] Permission denied 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1331s resp = conn.urlopen( 1331s method=request.method, 1331s ...<9 lines>... 1331s chunked=chunked, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1331s retries = retries.increment( 1331s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1331s raise reraise(type(error), error, _stacktrace) 1331s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1331s raise value.with_traceback(tb) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1331s return self.version(api_version=False)["ApiVersion"] 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1331s return self._result(self._get(url), json=True) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1331s return f(self, *args, **kwargs) 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1331s return self.get(url, **self._set_request_timeout(kwargs)) 1331s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1331s return self.request("GET", url, **kwargs) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1331s resp = self.send(prep, **send_kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1331s r = adapter.send(request, **kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1331s raise ConnectionError(err, request=request) 1331s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s The above exception was the direct cause of the following exception: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1331s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1331s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1331s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1331s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1331s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1331s return cls( 1331s timeout=timeout, 1331s ...<3 lines>... 1331s **kwargs_from_env(**kwargs) 1331s ) 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1331s self.api = APIClient(*args, **kwargs) 1331s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1331s self._version = self._retrieve_server_version() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1331s raise DockerException( 1331s f'Error while fetching server API version: {e}' 1331s ) from e 1331s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s [2026-01-30T07:02:34+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s <========= 1331s FAILED lib/dockerTest.py::TestDocker::testDockerLogs - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v6 1331s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v6" follows: 1331s =========> 1331s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v4 1331s [2026-01-30T07:02:40+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-40spkqys v4 1331s [2026-01-30T07:02:40+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s PermissionError: [Errno 13] Permission denied 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1331s resp = conn.urlopen( 1331s method=request.method, 1331s ...<9 lines>... 1331s chunked=chunked, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1331s retries = retries.increment( 1331s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1331s raise reraise(type(error), error, _stacktrace) 1331s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1331s raise value.with_traceback(tb) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1331s return self.version(api_version=False)["ApiVersion"] 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1331s return self._result(self._get(url), json=True) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1331s return f(self, *args, **kwargs) 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1331s return self.get(url, **self._set_request_timeout(kwargs)) 1331s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1331s return self.request("GET", url, **kwargs) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1331s resp = self.send(prep, **send_kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1331s r = adapter.send(request, **kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1331s raise ConnectionError(err, request=request) 1331s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s The above exception was the direct cause of the following exception: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1331s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1331s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1331s out = apiDockerCall( 1331s job, 1331s ...<8 lines>... 1331s demux=demux, 1331s ) 1331s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1331s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1331s return cls( 1331s timeout=timeout, 1331s ...<3 lines>... 1331s **kwargs_from_env(**kwargs) 1331s ) 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1331s self.api = APIClient(*args, **kwargs) 1331s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1331s self._version = self._retrieve_server_version() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1331s raise DockerException( 1331s f'Error while fetching server API version: {e}' 1331s ) from e 1331s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s [2026-01-30T07:02:40+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s <========= 1331s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Stream - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v6 1331s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v6" follows: 1331s =========> 1331s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v4 1331s [2026-01-30T07:02:50+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-sxbjohmq v4 1331s [2026-01-30T07:02:50+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s PermissionError: [Errno 13] Permission denied 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1331s resp = conn.urlopen( 1331s method=request.method, 1331s ...<9 lines>... 1331s chunked=chunked, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1331s retries = retries.increment( 1331s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1331s raise reraise(type(error), error, _stacktrace) 1331s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1331s raise value.with_traceback(tb) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1331s return self.version(api_version=False)["ApiVersion"] 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1331s return self._result(self._get(url), json=True) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1331s return f(self, *args, **kwargs) 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1331s return self.get(url, **self._set_request_timeout(kwargs)) 1331s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1331s return self.request("GET", url, **kwargs) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1331s resp = self.send(prep, **send_kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1331s r = adapter.send(request, **kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1331s raise ConnectionError(err, request=request) 1331s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s The above exception was the direct cause of the following exception: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1331s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1331s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1331s out = apiDockerCall( 1331s job, 1331s ...<8 lines>... 1331s demux=demux, 1331s ) 1331s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1331s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1331s return cls( 1331s timeout=timeout, 1331s ...<3 lines>... 1331s **kwargs_from_env(**kwargs) 1331s ) 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1331s self.api = APIClient(*args, **kwargs) 1331s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1331s self._version = self._retrieve_server_version() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1331s raise DockerException( 1331s f'Error while fetching server API version: {e}' 1331s ) from e 1331s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s [2026-01-30T07:02:50+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s <========= 1331s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Demux0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v6 1331s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v6" follows: 1331s =========> 1331s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:02:55+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v4 1331s [2026-01-30T07:02:56+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-o3abbidv v4 1331s [2026-01-30T07:02:56+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s PermissionError: [Errno 13] Permission denied 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1331s resp = conn.urlopen( 1331s method=request.method, 1331s ...<9 lines>... 1331s chunked=chunked, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1331s retries = retries.increment( 1331s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1331s raise reraise(type(error), error, _stacktrace) 1331s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1331s raise value.with_traceback(tb) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1331s return self.version(api_version=False)["ApiVersion"] 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1331s return self._result(self._get(url), json=True) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1331s return f(self, *args, **kwargs) 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1331s return self.get(url, **self._set_request_timeout(kwargs)) 1331s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1331s return self.request("GET", url, **kwargs) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1331s resp = self.send(prep, **send_kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1331s r = adapter.send(request, **kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1331s raise ConnectionError(err, request=request) 1331s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s The above exception was the direct cause of the following exception: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1331s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1331s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1331s out = apiDockerCall( 1331s job, 1331s ...<8 lines>... 1331s demux=demux, 1331s ) 1331s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1331s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1331s return cls( 1331s timeout=timeout, 1331s ...<3 lines>... 1331s **kwargs_from_env(**kwargs) 1331s ) 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1331s self.api = APIClient(*args, **kwargs) 1331s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1331s self._version = self._retrieve_server_version() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1331s raise DockerException( 1331s f'Error while fetching server API version: {e}' 1331s ) from e 1331s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s [2026-01-30T07:02:56+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s <========= 1331s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/testDockerLogs_Demux_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v6 1331s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v6" follows: 1331s =========> 1331s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v4 1331s [2026-01-30T07:03:02+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-m1zzytz9 v4 1331s [2026-01-30T07:03:02+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s PermissionError: [Errno 13] Permission denied 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1331s resp = conn.urlopen( 1331s method=request.method, 1331s ...<9 lines>... 1331s chunked=chunked, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1331s retries = retries.increment( 1331s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1331s raise reraise(type(error), error, _stacktrace) 1331s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1331s raise value.with_traceback(tb) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1331s response = self._make_request( 1331s conn, 1331s ...<10 lines>... 1331s **response_kw, 1331s ) 1331s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1331s conn.request( 1331s ~~~~~~~~~~~~^ 1331s method, 1331s ^^^^^^^ 1331s ...<6 lines>... 1331s enforce_content_length=enforce_content_length, 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1331s self.endheaders() 1331s ~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1331s self._send_output(message_body, encode_chunked=encode_chunked) 1331s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1331s self.send(msg) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1331s self.connect() 1331s ~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1331s sock.connect(self.unix_socket) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1331s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s During handling of the above exception, another exception occurred: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1331s return self.version(api_version=False)["ApiVersion"] 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1331s return self._result(self._get(url), json=True) 1331s ~~~~~~~~~^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1331s return f(self, *args, **kwargs) 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1331s return self.get(url, **self._set_request_timeout(kwargs)) 1331s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1331s return self.request("GET", url, **kwargs) 1331s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1331s resp = self.send(prep, **send_kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1331s r = adapter.send(request, **kwargs) 1331s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1331s raise ConnectionError(err, request=request) 1331s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s The above exception was the direct cause of the following exception: 1331s 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1331s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1331s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1331s out = apiDockerCall( 1331s job, 1331s ...<8 lines>... 1331s demux=demux, 1331s ) 1331s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1331s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1331s return cls( 1331s timeout=timeout, 1331s ...<3 lines>... 1331s **kwargs_from_env(**kwargs) 1331s ) 1331s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1331s self.api = APIClient(*args, **kwargs) 1331s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1331s self._version = self._retrieve_server_version() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1331s raise DockerException( 1331s f'Error while fetching server API version: {e}' 1331s ) from e 1331s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1331s 1331s [2026-01-30T07:03:02+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s <========= 1331s FAILED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore' contains 2 failed jobs: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8, '_writer' kind-_writer/instance-0jjweo4g v4 1331s Log from job "'_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v8" follows: 1331s =========> 1331s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'ddb3944d-bb71-491a-8af0-2530f6b8aa01', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpibd3pj3m', '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} 1331s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121/deferred/funcnzj665b2 1331s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.worker] Parsed job description 1331s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 1331s [2026-01-30T07:05:48+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 1331s [2026-01-30T07:05:48+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1331s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1331s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1331s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1331s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1331s [2026-01-30T07:05:49+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1331s [2026-01-30T07:05:49+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1331s [2026-01-30T07:05:49+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1331s [2026-01-30T07:05:49+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. 1331s [2026-01-30T07:05:50+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1331s [2026-01-30T07:05:50+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1331s [2026-01-30T07:05:50+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. 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithJobStoreFileOb0/jobstore'. 1331s [2026-01-30T07:05:50+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6) from description '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-5ac0b62c6ed85c87a0cd6357680f3121 has lockable filesystem type: tmpfs 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Starting job ('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6) with ID (kind-EncapsulatedJob/instance-zzj5b9s8). 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running job 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Actually running job ('_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6) with ID (kind-EncapsulatedJob/instance-zzj5b9s8) which wants 2147483648 of our 100589039616 bytes. 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Max space: 100589039616 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total file size: 1536 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total job disk requirement size: 2147483648 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Total immutable reference size: 0 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.cachingFileStore] Available space with job: 100589039616 bytes 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1331s [2026-01-30T07:05:50+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-zzj5b9s8 v6 used 4.50x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1331s [2026-01-30T07:05:50+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 1331s self.evaluatePromisedRequirements() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 1331s ].getValue() 1331s ~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 1331s return func(*self._args) 1331s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 1331s 1331s [2026-01-30T07:05:50+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [pydot] pydot initializing 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [pydot] pydot 4.0.1 1331s [2026-01-30T07:05:50+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1331s <========= 1331s FAILED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore' contains 2 failed jobs: '_writer' kind-_writer/instance-icv7qr07 v4, '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8 1331s Log from job "'_follower' kind-EncapsulatedJob/instance-bpvbpt4v v8" follows: 1331s =========> 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '9758239f-8230-4707-9a89-f88f4814da8c', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore', 'workDir': '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/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/tmpzhq9eyr4', '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} 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Opened with own state file /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e/deferred/funcgb66nmmu 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.worker] Parsed job description 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.job] New job version: '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil.worker] Working on job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.job] Loading user module ModuleDescriptor(dirPath='/usr/lib/python3/dist-packages', name='toil.test.src.promisedRequirementTest', fromVirtualEnv=False). 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] Total machine size: 4 core(s) 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] CPU quota/period not available from cgroups v1 or cgroups v2 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] CPU affinity available 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] CPU affinity is restricted to 4 cores 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] cpu_count: 4 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1331s [2026-01-30T07:06:01+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. 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker registry of quay.io/ucsc_cgl as TOIL_DOCKER_REGISTRY is not set. 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil] Using default docker name of toil as TOIL_DOCKER_NAME is not set. 1331s [2026-01-30T07:06:01+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. 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/tmp/pytest-of-ubuntu/pytest-0/popen-gw3/testPromisesWithNonCachingFile0/jobstore'. 1331s [2026-01-30T07:06:01+0000] [MainThread] [I] [toil.worker] Loaded body Job('_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6) from description '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.lib.threading] Detected that /run/lock/toilwf-687cdbabed03577e875959feb6b5cc2e has lockable filesystem type: tmpfs 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running job 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 used 0.00% disk (4.0 KiB [4096B] used, 2.0 GiB [2147483648B] requested). 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running own deferred functions 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Out of deferred functions! 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Running orphaned deferred functions 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files 1331s [2026-01-30T07:06:01+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_follower' kind-EncapsulatedJob/instance-bpvbpt4v v6 used 6.03x more CPU than the requested 0.1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1331s [2026-01-30T07:06:01+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1331s Traceback (most recent call last): 1331s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1331s job._runner( 1331s ~~~~~~~~~~~^ 1331s jobGraph=None, 1331s ^^^^^^^^^^^^^^ 1331s ...<2 lines>... 1331s defer=defer, 1331s ^^^^^^^^^^^^ 1331s ) 1331s ^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1331s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1331s return self.run(fileStore) 1331s ~~~~~~~~^^^^^^^^^^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3514, in run 1331s self.evaluatePromisedRequirements() 1331s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 3502, in evaluatePromisedRequirements 1331s ].getValue() 1331s ~~~~~~~~^^ 1331s File "/usr/lib/python3/dist-packages/toil/job.py", line 4335, in getValue 1331s return func(*self._args) 1331s SystemError: /usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py:140: unknown opcode 128 1331s 1331s [2026-01-30T07:06:01+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [pydot] pydot initializing 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [pydot] pydot 4.0.1 1331s [2026-01-30T07:06:01+0000] [MainThread] [D] [pydot.core] pydot core module initializing 1331s <========= 1331s ERROR src/importExportFileTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py'. 1331s Hint: make sure your test modules/packages have valid Python names. 1331s Traceback: 1331s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 1331s mod = import_path( 1331s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 1331s importlib.import_module(module_name) 1331s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 1331s return _bootstrap._gcd_import(name[level:], package, level) 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s :1398: in _gcd_import 1331s ??? 1331s :1371: in _find_and_load 1331s ??? 1331s :1342: in _find_and_load_unlocked 1331s ??? 1331s :938: in _load_unlocked 1331s ??? 1331s :759: in exec_module 1331s ??? 1331s :491: in _call_with_frames_removed 1331s ??? 1331s /usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py:30: in 1331s from pytest_subtests import SubTests 1331s E ModuleNotFoundError: No module named 'pytest_subtests' 1331s ERROR src/jobEncapsulationTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py'. 1331s Hint: make sure your test modules/packages have valid Python names. 1331s Traceback: 1331s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 1331s mod = import_path( 1331s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 1331s importlib.import_module(module_name) 1331s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 1331s return _bootstrap._gcd_import(name[level:], package, level) 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s :1398: in _gcd_import 1331s ??? 1331s :1371: in _find_and_load 1331s ??? 1331s :1342: in _find_and_load_unlocked 1331s ??? 1331s :938: in _load_unlocked 1331s ??? 1331s :759: in exec_module 1331s ??? 1331s :491: in _call_with_frames_removed 1331s ??? 1331s /usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py:17: in 1331s from toil.test.src.jobTest import fn1Test 1331s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 1331s from pytest_subtests import SubTests 1331s E ModuleNotFoundError: No module named 'pytest_subtests' 1331s ERROR src/jobTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobTest.py'. 1331s Hint: make sure your test modules/packages have valid Python names. 1331s Traceback: 1331s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 1331s mod = import_path( 1331s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 1331s importlib.import_module(module_name) 1331s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 1331s return _bootstrap._gcd_import(name[level:], package, level) 1331s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1331s :1398: in _gcd_import 1331s ??? 1331s :1371: in _find_and_load 1331s ??? 1331s :1342: in _find_and_load_unlocked 1331s ??? 1331s :938: in _load_unlocked 1331s ??? 1331s :759: in exec_module 1331s ??? 1331s :491: in _call_with_frames_removed 1331s ??? 1331s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 1331s from pytest_subtests import SubTests 1331s E ModuleNotFoundError: No module named 'pytest_subtests' 1331s = 15 failed, 224 passed, 136 skipped, 3 errors, 24 subtests passed in 1071.38s (0:17:51) = 1331s E: pybuild pybuild:483: test: plugin pyproject failed with: exit code=1: cd /tmp/autopkgtest.cjJpnO/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 1331s I: pybuild base:384: cd /tmp/autopkgtest.cjJpnO/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 1342s ============================= test session starts ============================== 1342s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.13 1342s cachedir: .pytest_cache 1342s rootdir: /tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build 1342s configfile: setup.cfg 1342s plugins: typeguard-4.4.4, xdist-3.8.0, pytest_httpserver-1.1.3, cwltest-2.6.20251216093331, timeout-2.4.0 1342s created: 4/4 workers 1342s 4 workers [375 items] 1342s 1342s scheduling tests via LoadScopeScheduling 1342s 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_default_gpu_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1342s [gw0] [ 0%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 0%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 0%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 1%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 1%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 1%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 1%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 2%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 3%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 3%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 3%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 4%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 4%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 4%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 5%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 6%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 7%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 7%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 7%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 8%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 8%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 8%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 8%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 9%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 9%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 9%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 9%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw1] [ 10%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw1] [ 10%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw3] [ 10%] PASSED batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_default_gpu_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1342s batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_get_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1342s [gw3] [ 10%] PASSED batchSystems/test_slurm.py::SlurmTest::test_PartitionSet_get_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1342s batchSystems/test_slurm.py::SlurmTest::test_any_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1342s [gw3] [ 11%] PASSED batchSystems/test_slurm.py::SlurmTest::test_any_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1342s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1342s [gw0] [ 11%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw1] [ 11%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw1] [ 12%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw1] [ 12%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw3] [ 12%] 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 1342s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_mix_sacct_scontrol <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1342s [gw3] [ 12%] 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 1342s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1342s [gw3] [ 13%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1342s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1342s [gw1] [ 13%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw1] [ 13%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw1] [ 13%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw1] [ 14%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw1] [ 14%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw1] [ 14%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw1] [ 14%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw1] [ 15%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 15%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 15%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 16%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 16%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw1] [ 16%] SKIPPED jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s docs/scriptsTest.py::ToilDocumentationTest::testArguments <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1342s [gw0] [ 16%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 17%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 17%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw0] [ 17%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw0] [ 17%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw0] [ 18%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw0] [ 18%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw0] [ 18%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw0] [ 18%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw0] [ 19%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw0] [ 19%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw0] [ 19%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw2] [ 20%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw3] [ 20%] 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 1342s 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 1342s jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw0] [ 20%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw0] [ 20%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw0] [ 21%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw3] [ 21%] 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 1342s 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 1342s [gw3] [ 21%] 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 1342s jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s [gw0] [ 21%] SKIPPED jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1342s lib/dockerTest.py::TestDocker::testDockerClean <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1342s batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_some_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1342s [gw3] [ 22%] PASSED batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_some_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1342s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_argument_list_too_big <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1342s [gw2] [ 22%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw2] [ 22%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [gw2] [ 22%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1342s [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 1343s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw2] [ 23%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1343s jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1343s [gw3] [ 23%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw2] [ 24%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1343s jobStores/jobStoreTest.py::FileJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1343s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw3] [ 24%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_none_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw3] [ 25%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw3] [ 26%] PASSED batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [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 1343s batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_not_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [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 1343s batchSystems/test_slurm.py::SlurmTest::test_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw3] [ 27%] PASSED batchSystems/test_slurm.py::SlurmTest::test_option_detector <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_export <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw3] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_export <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw3] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_partition <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_time <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s [gw3] [ 28%] PASSED batchSystems/test_slurm.py::SlurmTest::test_prepareSbatch_time <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_slurm.py 1343s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1343s [gw2] [ 28%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testImportFtpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1344s jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1344s [gw2] [ 29%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1347s jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1347s [gw1] [ 29%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testArguments <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1349s docs/scriptsTest.py::ToilDocumentationTest::testDocker <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1349s [gw3] [ 29%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1350s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1350s [gw0] [ 29%] FAILED lib/dockerTest.py::TestDocker::testDockerClean <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1355s lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1358s [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 1358s [gw0] [ 30%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1360s lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1361s [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 1361s [gw1] [ 30%] FAILED docs/scriptsTest.py::ToilDocumentationTest::testDocker <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1365s docs/scriptsTest.py::ToilDocumentationTest::testDynamic <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1365s [gw0] [ 30%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1367s lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1373s [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 1373s [gw0] [ 31%] FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1373s lib/dockerTest.py::TestDocker::testDockerPipeChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1373s [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 1373s [gw2] [ 31%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1374s jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1374s [gw2] [ 31%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1380s jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1385s [gw3] [ 31%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1385s [gw0] [ 32%] FAILED lib/dockerTest.py::TestDocker::testDockerPipeChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1387s lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1393s [gw3] [ 32%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1398s [gw3] [ 32%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1398s [gw0] [ 32%] FAILED lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1398s lib/dockerTest.py::TestDocker::testNonCachingDockerChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1399s [gw3] [ 32%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1399s [gw3] [ 32%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1404s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1404s [gw3] [ 32%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1406s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1406s [gw0] [ 32%] FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChain <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1407s lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1407s [gw1] [ 33%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testDynamic <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1408s docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1408s [gw3] [ 33%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1411s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1411s [gw1] [ 33%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1413s docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1413s [gw3] [ 33%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1414s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1414s [gw0] [ 34%] FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1416s lib/dockerTest.py::TestDocker::testDockerLogs <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1416s [gw3] [ 34%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1422s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1422s [gw1] [ 34%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testEncapsulation2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1422s docs/scriptsTest.py::ToilDocumentationTest::testHelloworld <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1422s [gw0] [ 34%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1434s lib/dockerTest.py::TestDocker::testDockerLogs_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1434s [gw2] [ 35%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 35%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 35%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 36%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 36%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 36%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 36%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 37%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 37%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 37%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 37%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 38%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 38%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 38%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_does_not_leak_symlinks <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 38%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_does_not_leak_symlinks <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_init_preserves_symlink_path <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 39%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_init_preserves_symlink_path <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::test_symlink_read_control <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s [gw2] [ 39%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_symlink_read_control <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1434s [gw2] [ 39%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1434s [gw2] [ 40%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1434s [gw2] [ 40%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1434s [gw2] [ 40%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1434s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1434s [gw2] [ 40%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1435s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1435s [gw2] [ 41%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1435s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1435s [gw2] [ 41%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1435s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1435s [gw2] [ 41%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1435s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1435s [gw2] [ 41%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1435s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1435s [gw2] [ 42%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1435s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1435s [gw2] [ 42%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1435s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1435s [gw2] [ 42%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1436s jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1436s [gw2] [ 42%] PASSED jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1436s src/dockerCheckTest.py::DockerCheckTest::testApplianceParser <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1436s [gw2] [ 43%] PASSED src/dockerCheckTest.py::DockerCheckTest::testApplianceParser <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1436s src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1436s [gw2] [ 43%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1436s src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1436s [gw1] [ 43%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testHelloworld <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1437s docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1437s [gw2] [ 44%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1437s src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1437s [gw2] [ 44%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1437s src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1437s [gw2] [ 44%] PASSED src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1437s src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1437s [gw2] [ 44%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1437s src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1437s [gw2] [ 45%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1437s src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1437s [gw2] [ 45%] PASSED src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1437s src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1437s [gw2] [ 45%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1437s src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1437s [gw2] [ 45%] SKIPPED src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1438s src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1438s [gw2] [ 46%] PASSED src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo <- ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py 1438s provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s [gw2] [ 46%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s [gw2] [ 46%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s [gw2] [ 46%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s [gw2] [ 47%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s [gw2] [ 47%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s [gw2] [ 47%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s [gw2] [ 48%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s [gw2] [ 48%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s [gw2] [ 48%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s [gw2] [ 48%] PASSED provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1438s server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1438s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1438s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1438s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1438s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1438s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 49%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 50%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 51%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 51%] SKIPPED server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 51%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 52%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 52%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 52%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 52%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 53%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 53%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 53%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 53%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 54%] SKIPPED server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 54%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 54%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 54%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 55%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 55%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 55%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 56%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 56%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 56%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s [gw2] [ 56%] SKIPPED server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1439s provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1439s [gw2] [ 57%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1439s provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1439s [gw2] [ 57%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1439s provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1439s [gw2] [ 57%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1440s provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1440s [gw2] [ 57%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1440s provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1440s [gw0] [ 58%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1440s lib/dockerTest.py::TestDocker::testDockerLogs_Demux <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1440s [gw2] [ 58%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1440s provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1440s [gw2] [ 58%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1440s provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1440s [gw2] [ 58%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1440s provisioners/clusterScalerTest.py::BinPackingTest::testSorting <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1440s [gw2] [ 59%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testSorting <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1440s provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1440s [gw2] [ 59%] PASSED provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/clusterScalerTest.py 1440s src/miscTests.py::TestMisc::testIDStability <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1440s [gw2] [ 59%] PASSED src/miscTests.py::TestMisc::testIDStability <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1440s src/miscTests.py::TestMisc::test_atomic_install <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1440s [gw2] [ 60%] PASSED src/miscTests.py::TestMisc::test_atomic_install <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1440s src/miscTests.py::TestMisc::test_atomic_install_dev <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1440s [gw2] [ 60%] PASSED src/miscTests.py::TestMisc::test_atomic_install_dev <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1440s src/miscTests.py::TestMisc::test_atomic_context_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1440s [gw2] [ 60%] PASSED src/miscTests.py::TestMisc::test_atomic_context_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1440s src/miscTests.py::TestMisc::test_atomic_context_error <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1440s [gw2] [ 60%] PASSED src/miscTests.py::TestMisc::test_atomic_context_error <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1440s src/miscTests.py::TestMisc::test_call_command_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1440s [gw2] [ 61%] PASSED src/miscTests.py::TestMisc::test_call_command_ok <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1440s src/miscTests.py::TestMisc::test_call_command_err <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1440s [gw2] [ 61%] PASSED src/miscTests.py::TestMisc::test_call_command_err <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1440s lib/test_url.py::TestURLAccess::test_get_url_access <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 1440s [gw2] [ 61%] PASSED lib/test_url.py::TestURLAccess::test_get_url_access <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 1440s lib/test_url.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 1440s [gw2] [ 61%] SKIPPED lib/test_url.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 1440s lib/test_url.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 1440s [gw2] [ 62%] SKIPPED lib/test_url.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 1440s lib/test_url.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 1440s [gw2] [ 62%] SKIPPED lib/test_url.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 1440s lib/test_url.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 1440s [gw2] [ 62%] SKIPPED lib/test_url.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 1440s lib/test_url.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 1440s [gw2] [ 62%] SKIPPED lib/test_url.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_url.py 1440s lib/url_plugin_test.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 1440s [gw2] [ 63%] PASSED lib/url_plugin_test.py::TestURLAccess::test_get_is_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 1440s lib/url_plugin_test.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 1440s [gw2] [ 63%] PASSED lib/url_plugin_test.py::TestURLAccess::test_get_size <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 1440s lib/url_plugin_test.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 1440s [gw2] [ 63%] PASSED lib/url_plugin_test.py::TestURLAccess::test_list_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 1440s lib/url_plugin_test.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 1440s [gw2] [ 64%] PASSED lib/url_plugin_test.py::TestURLAccess::test_open_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 1440s lib/url_plugin_test.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 1441s [gw2] [ 64%] PASSED lib/url_plugin_test.py::TestURLAccess::test_read_from_url <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 1441s lib/url_plugin_test.py::TestURLAccess::test_url_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 1441s [gw2] [ 64%] PASSED lib/url_plugin_test.py::TestURLAccess::test_url_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/url_plugin_test.py 1441s src/retainTempDirTest.py::TestCleanWorkDir::testNever <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 1441s [gw1] [ 64%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1445s docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1445s [gw2] [ 65%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testNever <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 1448s src/retainTempDirTest.py::TestCleanWorkDir::testAlways <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 1448s [gw1] [ 65%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testInvokeworkflow2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1448s docs/scriptsTest.py::ToilDocumentationTest::testJobFunctions <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1448s [gw2] [ 65%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testAlways <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 1450s src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 1450s [gw0] [ 65%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1454s lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1454s [gw1] [ 66%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testJobFunctions <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1459s docs/scriptsTest.py::ToilDocumentationTest::testManaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1459s [gw2] [ 66%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 1462s src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithNoError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 1462s [gw0] [ 66%] FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py 1462s utils/utilsTest.py::TestUtils::test_config_functionality <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1462s [gw1] [ 66%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testManaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1464s docs/scriptsTest.py::ToilDocumentationTest::testManaging2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1464s [gw0] [ 67%] PASSED utils/utilsTest.py::TestUtils::test_config_functionality <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1466s utils/utilsTest.py::TestUtils::testUtilsSort <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1466s [gw2] [ 67%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnErrorWithNoError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 1470s src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 1470s [gw1] [ 67%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testManaging2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1477s docs/scriptsTest.py::ToilDocumentationTest::testPromises <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1477s [gw2] [ 68%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithError <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 1477s src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithSuccess <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 1477s [gw1] [ 68%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testPromises <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1483s docs/scriptsTest.py::ToilDocumentationTest::testPromises2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1483s [gw2] [ 68%] PASSED src/retainTempDirTest.py::TestCleanWorkDir::testOnSuccessWithSuccess <- ../../../../usr/lib/python3/dist-packages/toil/test/src/retainTempDirTest.py 1483s lib/aws/test_utils.py::TagGenerationTest::test_build_tag <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 1483s [gw2] [ 68%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_build_tag <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 1483s lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 1483s [gw2] [ 69%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 1483s lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 1483s [gw2] [ 69%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 1483s lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 1483s [gw2] [ 69%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 1483s lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 1483s [gw2] [ 69%] PASSED lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/aws/test_utils.py 1496s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1508s [gw2] [ 70%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1523s [gw2] [ 70%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1535s [gw2] [ 70%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1543s [gw2] [ 70%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1550s [gw2] [ 70%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1559s [gw2] [ 70%] SUBPASSED[Now testing readGlobalFileWith: mutable=True symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1566s [gw2] [ 70%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=True] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1566s [gw2] [ 70%] SUBPASSED[Now testing readGlobalFileWith: mutable=False symlink=False] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1566s [gw2] [ 70%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1575s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1575s [gw2] [ 70%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1581s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1581s [gw1] [ 70%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testPromises2 <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1585s docs/scriptsTest.py::ToilDocumentationTest::testQuickstart <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1585s [gw1] [ 70%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testQuickstart <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1590s docs/scriptsTest.py::ToilDocumentationTest::testRequirements <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1590s [gw2] [ 71%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1594s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1594s [gw1] [ 71%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testRequirements <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1599s docs/scriptsTest.py::ToilDocumentationTest::testStaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1599s [gw1] [ 71%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testStaging <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1601s docs/scriptsTest.py::ToilDocumentationTest::testStats <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1601s [gw2] [ 72%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1610s src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1610s [gw2] [ 72%] SUBPASSED[Testing readwrite file permissions 1610s [executable: True] 1610s [caching: True] 1619s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1619s [gw2] [ 72%] SUBPASSED[Testing readwrite file permissions 1619s [executable: True] 1619s [caching: False] 1629s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1629s [gw1] [ 72%] PASSED docs/scriptsTest.py::ToilDocumentationTest::testStats <- ../../../../usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py 1629s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1629s [gw1] [ 72%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1629s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1629s [gw1] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1629s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1629s [gw1] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1629s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1629s [gw1] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1630s src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1630s [gw1] [ 73%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1630s src/resourceTest.py::TestResource::testStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 1630s [gw1] [ 74%] PASSED src/resourceTest.py::TestResource::testStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 1630s src/resourceTest.py::TestResource::testPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 1630s [gw1] [ 74%] PASSED src/resourceTest.py::TestResource::testPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 1630s src/resourceTest.py::TestResource::testStandAloneInPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 1630s [gw1] [ 74%] PASSED src/resourceTest.py::TestResource::testStandAloneInPackage <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 1630s src/resourceTest.py::TestResource::testBuiltIn <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 1630s [gw1] [ 74%] PASSED src/resourceTest.py::TestResource::testBuiltIn <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 1630s src/resourceTest.py::TestResource::testNonPyStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 1630s [gw1] [ 75%] PASSED src/resourceTest.py::TestResource::testNonPyStandAlone <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resourceTest.py 1633s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 1633s [gw2] [ 75%] SUBPASSED[Testing readwrite file permissions 1633s [executable: False] 1633s [caching: True] 1635s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1635s [gw1] [ 75%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 1638s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithClassMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 1638s [gw2] [ 75%] SUBPASSED[Testing readwrite file permissions 1638s [executable: False] 1638s [caching: False] 1638s ] src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1638s [gw2] [ 75%] PASSED src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1638s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1638s [gw2] [ 75%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testImportReadFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1638s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1638s [gw2] [ 76%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1638s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1638s [gw2] [ 76%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1638s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1638s [gw2] [ 76%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1638s src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1638s [gw2] [ 76%] SKIPPED src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1638s src/miscTests.py::TestPanic::test_panic_by_hand <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1638s [gw2] [ 77%] PASSED src/miscTests.py::TestPanic::test_panic_by_hand <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1638s src/miscTests.py::TestPanic::test_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1638s [gw2] [ 77%] PASSED src/miscTests.py::TestPanic::test_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1638s src/miscTests.py::TestPanic::test_panic_with_secondary <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1638s [gw2] [ 77%] PASSED src/miscTests.py::TestPanic::test_panic_with_secondary <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1638s src/miscTests.py::TestPanic::test_nested_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1638s [gw2] [ 77%] PASSED src/miscTests.py::TestPanic::test_nested_panic <- ../../../../usr/lib/python3/dist-packages/toil/test/src/miscTests.py 1638s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_many_all_exist <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 1638s [gw2] [ 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 1638s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 1638s [gw2] [ 78%] PASSED batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_exists <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 1638s batchSystems/test_gridengine.py::GridEngineTest::test_coalesce_job_exit_codes_one_still_running <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/test_gridengine.py 1638s [gw2] [ 78%] 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 1638s lib/test_conversions.py::ConversionTest::test_convert <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 1638s [gw2] [ 78%] PASSED lib/test_conversions.py::ConversionTest::test_convert <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 1638s lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 1638s [gw2] [ 79%] PASSED lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 1638s lib/test_conversions.py::ConversionTest::test_human2bytes <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 1638s [gw2] [ 79%] PASSED lib/test_conversions.py::ConversionTest::test_human2bytes <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_conversions.py 1638s lib/test_history.py::TestHistory::test_history_submittable_detection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 1639s [gw2] [ 79%] PASSED lib/test_history.py::TestHistory::test_history_submittable_detection <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 1639s lib/test_history.py::TestHistory::test_history_deletion <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 1639s [gw2] [ 80%] PASSED lib/test_history.py::TestHistory::test_history_deletion <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 1639s lib/test_history.py::TestHistory::test_history_size_limit <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 1639s [gw1] [ 80%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithClassMethod <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 1646s src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithLambda <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 1646s [gw1] [ 80%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testDeferredFunctionRunsWithLambda <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 1649s src/deferredFunctionTest.py::TestDeferredFunction::testBatchSystemCleanupCanHandleWorkerDeaths <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 1649s [gw2] [ 80%] PASSED lib/test_history.py::TestHistory::test_history_size_limit <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_history.py 1649s server/serverTest.py::ToilWESServerBenchTest::test_get_service_info <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1649s [gw2] [ 81%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_get_service_info <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1649s server/serverTest.py::ToilWESServerBenchTest::test_health <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1649s [gw2] [ 81%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_health <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1649s server/serverTest.py::ToilWESServerBenchTest::test_home <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1649s [gw2] [ 81%] SKIPPED server/serverTest.py::ToilWESServerBenchTest::test_home <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1652s src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 1652s [gw1] [ 81%] PASSED src/deferredFunctionTest.py::TestDeferredFunction::testBatchSystemCleanupCanHandleWorkerDeaths <- ../../../../usr/lib/python3/dist-packages/toil/test/src/deferredFunctionTest.py 1652s src/busTest.py::TestMessageBus::test_enum_ints_in_file <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 1652s [gw1] [ 82%] PASSED src/busTest.py::TestMessageBus::test_enum_ints_in_file <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 1652s src/busTest.py::TestMessageBus::test_cross_thread_messaging <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 1652s [gw1] [ 82%] PASSED src/busTest.py::TestMessageBus::test_cross_thread_messaging <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 1654s src/busTest.py::TestMessageBus::test_restart_without_bus_path <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 1654s [gw2] [ 82%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 1658s src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 1658s [gw0] [ 82%] PASSED utils/utilsTest.py::TestUtils::testUtilsSort <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1662s utils/utilsTest.py::TestUtils::testUnicodeSupport <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1662s [gw0] [ 83%] PASSED utils/utilsTest.py::TestUtils::testUnicodeSupport <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1665s utils/utilsTest.py::TestUtils::testGetPIDStatus <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1665s [gw1] [ 83%] PASSED src/busTest.py::TestMessageBus::test_restart_without_bus_path <- ../../../../usr/lib/python3/dist-packages/toil/test/src/busTest.py 1677s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 1677s [gw0] [ 83%] PASSED utils/utilsTest.py::TestUtils::testGetPIDStatus <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1683s utils/utilsTest.py::TestUtils::testGetStatusFailedToilWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1683s [gw3] [ 84%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1685s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1685s [gw1] [ 84%] PASSED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 1687s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 1687s [gw2] [ 84%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 1688s src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 1688s [gw0] [ 84%] PASSED utils/utilsTest.py::TestUtils::testGetStatusFailedToilWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1693s utils/utilsTest.py::TestUtils::testGetStatusFailedCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1693s [gw2] [ 85%] PASSED src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobFileStoreTest.py 1693s src/promisedRequirementTest.py::TestMesosPromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 1693s [gw2] [ 85%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::test_omp_threads <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batchSystemTest.py 1693s src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 1693s [gw2] [ 85%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 1693s src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 1693s [gw2] [ 85%] SKIPPED src/promisedRequirementTest.py::TestMesosPromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 1701s utils/toilDebugTest.py::TestDebugJob::test_run_job <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 1701s [gw3] [ 86%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1702s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1702s [gw0] [ 86%] PASSED utils/utilsTest.py::TestUtils::testGetStatusFailedCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1705s utils/utilsTest.py::TestUtils::testGetStatusSuccessfulCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1705s [gw1] [ 86%] PASSED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithJobStoreFileObjects <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 1708s src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 1708s [gw2] [ 86%] PASSED utils/toilDebugTest.py::TestDebugJob::test_run_job <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 1713s utils/toilDebugTest.py::TestDebugJob::test_print_job_info <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 1713s [gw3] [ 87%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1716s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1716s [gw0] [ 87%] PASSED utils/utilsTest.py::TestUtils::testGetStatusSuccessfulCWLWF <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1719s utils/utilsTest.py::TestUtils::testPrintJobLog <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1719s [gw3] [ 87%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1721s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1721s [gw2] [ 88%] PASSED utils/toilDebugTest.py::TestDebugJob::test_print_job_info <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 1721s utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 1721s [gw2] [ 88%] SKIPPED utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 1721s __init__.py::toil.test.make_tests <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1721s [gw2] [ 88%] PASSED __init__.py::toil.test.make_tests <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1722s __init__.py::toil.test.timeLimit <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1722s [gw1] [ 88%] PASSED src/promisedRequirementTest.py::TestSingleMachinePromisedRequirements::testPromisesWithNonCachingFileStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisedRequirementTest.py 1723s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 1723s [gw3] [ 89%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1723s src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1723s [gw1] [ 89%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 1723s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 1723s [gw2] [ 89%] PASSED __init__.py::toil.test.timeLimit <- ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py 1724s src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 1724s [gw2] [ 89%] PASSED src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 1724s src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 1724s [gw2] [ 90%] PASSED src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobDescriptionTest.py 1724s batchSystems/batch_system_plugin_test.py::BatchSystemPluginTest::test_batchsystem_plugin_installable <- ../../../../usr/lib/python3/dist-packages/toil/test/batchSystems/batch_system_plugin_test.py 1724s [gw2] [ 90%] 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 1724s 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 1724s [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 1724s jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1724s [gw2] [ 90%] SKIPPED jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName <- ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py 1724s lib/test_misc.py::UserNameAvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 1724s [gw2] [ 91%] PASSED lib/test_misc.py::UserNameAvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 1724s lib/test_misc.py::UserNameUnvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 1724s [gw2] [ 91%] PASSED lib/test_misc.py::UserNameUnvailableTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 1724s lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 1724s [gw2] [ 91%] PASSED lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name <- ../../../../usr/lib/python3/dist-packages/toil/test/lib/test_misc.py 1724s mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue <- ../../../../usr/lib/python3/dist-packages/toil/test/mesos/MesosDataStructuresTest.py 1724s [gw2] [ 92%] PASSED mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue <- ../../../../usr/lib/python3/dist-packages/toil/test/mesos/MesosDataStructuresTest.py 1724s provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/provisionerTest.py 1724s [gw2] [ 92%] PASSED provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing <- ../../../../usr/lib/python3/dist-packages/toil/test/provisioners/provisionerTest.py 1724s server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1724s [gw2] [ 92%] SKIPPED server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1724s server/serverTest.py::FileStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1724s [gw2] [ 92%] SKIPPED server/serverTest.py::FileStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1724s server/serverTest.py::FileStateStoreURLTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1724s [gw2] [ 93%] SKIPPED server/serverTest.py::FileStateStoreURLTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1729s src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried <- ../../../../usr/lib/python3/dist-packages/toil/test/src/checkpointTest.py 1729s [gw3] [ 93%] SUBPASSED[Testing readwrite file permissions 1729s [executable: True] 1729s [caching: True] 1729s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1729s [gw0] [ 93%] PASSED utils/utilsTest.py::TestUtils::testPrintJobLog <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1733s utils/utilsTest.py::TestUtils::testRestartAttribute <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1733s [gw1] [ 93%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 1734s src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 1734s [gw3] [ 93%] SUBPASSED[Testing readwrite file permissions 1734s [executable: True] 1734s [caching: False] 1735s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1735s [gw1] [ 94%] PASSED src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain <- ../../../../usr/lib/python3/dist-packages/toil/test/src/userDefinedJobArgTypeTest.py 1735s src/threadingTest.py::TestThreading::testGlobalMutexOrdering <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 1735s [gw2] [ 94%] PASSED src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried <- ../../../../usr/lib/python3/dist-packages/toil/test/src/checkpointTest.py 1739s src/environmentTest.py::EnvironmentTest::test_environment <- ../../../../usr/lib/python3/dist-packages/toil/test/src/environmentTest.py 1739s [gw3] [ 94%] SUBPASSED[Testing readwrite file permissions 1739s [executable: False] 1739s [caching: True] 1744s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1744s [gw3] [ 94%] SUBPASSED[Testing readwrite file permissions 1744s [executable: False] 1744s [caching: False] 1744s ] src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1744s [gw3] [ 94%] PASSED src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions <- ../../../../usr/lib/python3/dist-packages/toil/test/src/fileStoreTest.py 1744s server/serverTest.py::AWSStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1744s [gw3] [ 94%] SKIPPED server/serverTest.py::AWSStateStoreTest::test_state_store <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1744s server/serverTest.py::AWSStateStoreTest::test_state_store_paths <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1744s [gw3] [ 94%] SKIPPED server/serverTest.py::AWSStateStoreTest::test_state_store_paths <- ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py 1752s src/promisesTest.py::CachedUnpicklingJobStoreTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 1752s [gw1] [ 95%] PASSED src/threadingTest.py::TestThreading::testGlobalMutexOrdering <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 1759s src/threadingTest.py::TestThreading::testLastProcessStanding <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 1759s [gw2] [ 95%] PASSED src/environmentTest.py::EnvironmentTest::test_environment <- ../../../../usr/lib/python3/dist-packages/toil/test/src/environmentTest.py 1760s src/helloWorldTest.py::HelloWorldTest::testHelloWorld <- ../../../../usr/lib/python3/dist-packages/toil/test/src/helloWorldTest.py 1760s [gw3] [ 95%] PASSED src/promisesTest.py::CachedUnpicklingJobStoreTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 1766s src/promisesTest.py::ChainedIndexedPromisesTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 1766s [gw3] [ 96%] PASSED src/promisesTest.py::ChainedIndexedPromisesTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 1767s src/promisesTest.py::PathIndexingPromiseTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 1767s [gw1] [ 96%] PASSED src/threadingTest.py::TestThreading::testLastProcessStanding <- ../../../../usr/lib/python3/dist-packages/toil/test/src/threadingTest.py 1771s src/jobServiceTest.py::TestJobService::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 1771s [gw3] [ 96%] PASSED src/promisesTest.py::PathIndexingPromiseTest::test <- ../../../../usr/lib/python3/dist-packages/toil/test/src/promisesTest.py 1772s src/systemTest.py::TestSystem::testAtomicityOfNonEmptyDirectoryRenames <- ../../../../usr/lib/python3/dist-packages/toil/test/src/systemTest.py 1772s [gw2] [ 96%] PASSED src/helloWorldTest.py::HelloWorldTest::testHelloWorld <- ../../../../usr/lib/python3/dist-packages/toil/test/src/helloWorldTest.py 1778s src/jobServiceTest.py::TestPerfectServicet::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 1778s [gw3] [ 97%] PASSED src/systemTest.py::TestSystem::testAtomicityOfNonEmptyDirectoryRenames <- ../../../../usr/lib/python3/dist-packages/toil/test/src/systemTest.py 1779s src/workerTest.py::WorkerTests::testNextChainable <- ../../../../usr/lib/python3/dist-packages/toil/test/src/workerTest.py 1779s [gw3] [ 97%] PASSED src/workerTest.py::WorkerTests::testNextChainable <- ../../../../usr/lib/python3/dist-packages/toil/test/src/workerTest.py 1779s utils/toilKillTest.py::TestToilKill::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 1780s [gw3] [ 97%] SKIPPED utils/toilKillTest.py::TestToilKill::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 1780s [gw0] [ 97%] PASSED utils/utilsTest.py::TestUtils::testRestartAttribute <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py 1781s options/options.py::OptionsTest::test_caching_option_priority <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 1781s [gw0] [ 98%] PASSED options/options.py::OptionsTest::test_caching_option_priority <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 1781s options/options.py::OptionsTest::test_default_caching_slurm <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 1808s [gw0] [ 98%] PASSED options/options.py::OptionsTest::test_default_caching_slurm <- ../../../../usr/lib/python3/dist-packages/toil/test/options/options.py 1808s [gw2] [ 98%] PASSED src/jobServiceTest.py::TestPerfectServicet::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 1821s src/resumabilityTest.py::TestResumability::test_chaining <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resumabilityTest.py 1821s [gw2] [ 98%] PASSED src/resumabilityTest.py::TestResumability::test_chaining <- ../../../../usr/lib/python3/dist-packages/toil/test/src/resumabilityTest.py 1821s utils/toilKillTest.py::TestToilKillWithAWSJobStore::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 1897s [gw2] [ 99%] SKIPPED utils/toilKillTest.py::TestToilKillWithAWSJobStore::test_cwl_toil_kill <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilKillTest.py 1897s [gw1] [ 99%] PASSED src/jobServiceTest.py::TestJobService::testServiceWithCheckpoints <- ../../../../usr/lib/python3/dist-packages/toil/test/src/jobServiceTest.py 1903s src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger <- ../../../../usr/lib/python3/dist-packages/toil/test/src/realtimeLoggerTest.py 1903s [gw1] [ 99%] PASSED src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger <- ../../../../usr/lib/python3/dist-packages/toil/test/src/realtimeLoggerTest.py 1918s utils/toilDebugTest.py::testFetchJobStoreFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 1920s [gw1] [100%] PASSED utils/toilDebugTest.py::testFetchJobStoreFiles <- ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py 1920s 1920s ==================================== ERRORS ==================================== 1920s _________________ ERROR collecting src/importExportFileTest.py _________________ 1920s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py'. 1920s Hint: make sure your test modules/packages have valid Python names. 1920s Traceback: 1920s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 1920s mod = import_path( 1920s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 1920s importlib.import_module(module_name) 1920s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1920s return _bootstrap._gcd_import(name[level:], package, level) 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s :1387: in _gcd_import 1920s ??? 1920s :1360: in _find_and_load 1920s ??? 1920s :1331: in _find_and_load_unlocked 1920s ??? 1920s :935: in _load_unlocked 1920s ??? 1920s :1023: in exec_module 1920s ??? 1920s :488: in _call_with_frames_removed 1920s ??? 1920s /usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py:30: in 1920s from pytest_subtests import SubTests 1920s E ModuleNotFoundError: No module named 'pytest_subtests' 1920s _________________ ERROR collecting src/jobEncapsulationTest.py _________________ 1920s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py'. 1920s Hint: make sure your test modules/packages have valid Python names. 1920s Traceback: 1920s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 1920s mod = import_path( 1920s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 1920s importlib.import_module(module_name) 1920s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1920s return _bootstrap._gcd_import(name[level:], package, level) 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s :1387: in _gcd_import 1920s ??? 1920s :1360: in _find_and_load 1920s ??? 1920s :1331: in _find_and_load_unlocked 1920s ??? 1920s :935: in _load_unlocked 1920s ??? 1920s :1023: in exec_module 1920s ??? 1920s :488: in _call_with_frames_removed 1920s ??? 1920s /usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py:17: in 1920s from toil.test.src.jobTest import fn1Test 1920s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 1920s from pytest_subtests import SubTests 1920s E ModuleNotFoundError: No module named 'pytest_subtests' 1920s _______________________ ERROR collecting src/jobTest.py ________________________ 1920s ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobTest.py'. 1920s Hint: make sure your test modules/packages have valid Python names. 1920s Traceback: 1920s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 1920s mod = import_path( 1920s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 1920s importlib.import_module(module_name) 1920s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1920s return _bootstrap._gcd_import(name[level:], package, level) 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s :1387: in _gcd_import 1920s ??? 1920s :1360: in _find_and_load 1920s ??? 1920s :1331: in _find_and_load_unlocked 1920s ??? 1920s :935: in _load_unlocked 1920s ??? 1920s :1023: in exec_module 1920s ??? 1920s :488: in _call_with_frames_removed 1920s ??? 1920s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 1920s from pytest_subtests import SubTests 1920s E ModuleNotFoundError: No module named 'pytest_subtests' 1920s =================================== FAILURES =================================== 1920s __________________________ TestDocker.testDockerClean __________________________ 1920s [gw0] linux -- Python 3.13.11 /usr/bin/python3.13 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 1920s toil.start(A) 1920s ~~~~~~~~~~^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1920s return self._runMainLoop(rootJobDescription) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1920s ).run() 1920s ~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1920s raise FailedJobsException( 1920s ...<3 lines>... 1920s ) 1920s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v3 1920s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v3" follows: 1920s =========> 1920s [2026-01-30T07:19:32+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:32+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:32+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v1 1920s [2026-01-30T07:19:33+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v1 1920s [2026-01-30T07:19:33+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1920s apiDockerCall( 1920s ~~~~~~~~~~~~~^ 1920s job, 1920s ^^^^ 1920s ...<6 lines>... 1920s privileged=True, 1920s ^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:33+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1920s result: TResult | None = func() 1920s ~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1920s lambda: runtest_hook(item=item, **kwds), 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1920s yield 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1920s return result.get_result() 1920s ~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1920s raise exc.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1920s res = yield 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1920s item.runtest() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1920s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1920s result = testfunction(**testargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 1920s file_stats = test_file.stat() 1920s File "/usr/lib/python3.13/pathlib/_local.py", line 517, in stat 1920s return os.stat(self, follow_symlinks=follow_symlinks) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean0/working/test.txt' 1920s ----------------------------- Captured stderr call ----------------------------- 1920s [2026-01-30T07:19:31+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of d318477f-892e-4725-858d-97609237e41c in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean0/jobstore 1920s [2026-01-30T07:19:31+0000] [MainThread] [I] [toil.lib.history] Workflow d318477f-892e-4725-858d-97609237e41c is a run of 1920s [2026-01-30T07:19:31+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:31+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1920s [2026-01-30T07:19:31+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:19:33+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1920s [2026-01-30T07:19:34+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-gw0/testDockerClean0/jobstore kind-_testDockerCleanFn/instance-_jrhl4so. 1920s [2026-01-30T07:19:34+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v1 1920s Exit reason: None 1920s [2026-01-30T07:19:34+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v2 1920s [2026-01-30T07:19:34+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-_jrhl4so" follows: 1920s =========> 1920s [2026-01-30T07:19:32+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:32+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:32+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v1 1920s [2026-01-30T07:19:33+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v1 1920s [2026-01-30T07:19:33+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1920s apiDockerCall( 1920s ~~~~~~~~~~~~~^ 1920s job, 1920s ^^^^ 1920s ...<6 lines>... 1920s privileged=True, 1920s ^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:33+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:19:34+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v2 with ID kind-_testDockerCleanFn/instance-_jrhl4so to 0 1920s [2026-01-30T07:19:34+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v3 is completely failed 1920s [2026-01-30T07:19:38+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s [2026-01-30T07:19:38+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1920s [2026-01-30T07:19:38+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v3 1920s [2026-01-30T07:19:38+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.lib.history] Workflow d318477f-892e-4725-858d-97609237e41c stopped. Success: False 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean0/jobstore) 1920s ------------------------------ Captured log call ------------------------------- 1920s INFO  toil.lib.history:history.py:369 Recording workflow creation of d318477f-892e-4725-858d-97609237e41c in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean0/jobstore 1920s INFO  toil.lib.history:history.py:399 Workflow d318477f-892e-4725-858d-97609237e41c is a run of 1920s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1920s 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-gw0/testDockerClean0/jobstore kind-_testDockerCleanFn/instance-_jrhl4so. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v1 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v2 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-_jrhl4so" follows: 1920s =========> 1920s [2026-01-30T07:19:32+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:32+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:32+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v1 1920s [2026-01-30T07:19:33+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v1 1920s [2026-01-30T07:19:33+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1920s apiDockerCall( 1920s ~~~~~~~~~~~~~^ 1920s job, 1920s ^^^^ 1920s ...<6 lines>... 1920s privileged=True, 1920s ^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:33+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v2 with ID kind-_testDockerCleanFn/instance-_jrhl4so to 0 1920s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v3 is completely failed 1920s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1920s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_jrhl4so v3 1920s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1920s INFO  toil.lib.history:history.py:530 Workflow d318477f-892e-4725-858d-97609237e41c stopped. Success: False 1920s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean0/jobstore) 1920s _____________________ TestDocker.testDockerClean_CRx_FORGO _____________________ 1920s [gw0] linux -- Python 3.13.11 /usr/bin/python3.13 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 1920s toil.start(A) 1920s ~~~~~~~~~~^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1920s return self._runMainLoop(rootJobDescription) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1920s ).run() 1920s ~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1920s raise FailedJobsException( 1920s ...<3 lines>... 1920s ) 1920s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_FORGO0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v3 1920s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v3" follows: 1920s =========> 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v1 1920s [2026-01-30T07:19:41+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v1 1920s [2026-01-30T07:19:41+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1920s apiDockerCall( 1920s ~~~~~~~~~~~~~^ 1920s job, 1920s ^^^^ 1920s ...<6 lines>... 1920s privileged=True, 1920s ^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:41+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1920s result: TResult | None = func() 1920s ~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1920s lambda: runtest_hook(item=item, **kwds), 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1920s yield 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1920s return result.get_result() 1920s ~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1920s raise exc.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1920s res = yield 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1920s item.runtest() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1920s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1920s result = testfunction(**testargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 133, in testDockerClean_CRx_FORGO 1920s self.testDockerClean( 1920s ~~~~~~~~~~~~~~~~~~~~^ 1920s tmp_path, caching=False, detached=False, rm=True, deferParam=FORGO 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 1920s file_stats = test_file.stat() 1920s File "/usr/lib/python3.13/pathlib/_local.py", line 517, in stat 1920s return os.stat(self, follow_symlinks=follow_symlinks) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_FORGO0/working/test.txt' 1920s ----------------------------- Captured stderr call ----------------------------- 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 109aa9aa-3c30-4e63-9f36-a77a1f4bca05 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_FORGO0/jobstore 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.lib.history] Workflow 109aa9aa-3c30-4e63-9f36-a77a1f4bca05 is a run of 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:19:41+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1920s [2026-01-30T07:19:42+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-gw0/testDockerClean_CRx_FORGO0/jobstore kind-_testDockerCleanFn/instance-jp3nizfa. 1920s [2026-01-30T07:19:42+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v1 1920s Exit reason: None 1920s [2026-01-30T07:19:42+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v2 1920s [2026-01-30T07:19:42+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-jp3nizfa" follows: 1920s =========> 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v1 1920s [2026-01-30T07:19:41+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v1 1920s [2026-01-30T07:19:41+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1920s apiDockerCall( 1920s ~~~~~~~~~~~~~^ 1920s job, 1920s ^^^^ 1920s ...<6 lines>... 1920s privileged=True, 1920s ^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:41+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:19:42+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v2 with ID kind-_testDockerCleanFn/instance-jp3nizfa to 0 1920s [2026-01-30T07:19:42+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v3 is completely failed 1920s [2026-01-30T07:19:46+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s [2026-01-30T07:19:46+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1920s [2026-01-30T07:19:46+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v3 1920s [2026-01-30T07:19:46+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1920s [2026-01-30T07:19:46+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1920s [2026-01-30T07:19:46+0000] [MainThread] [I] [toil.lib.history] Workflow 109aa9aa-3c30-4e63-9f36-a77a1f4bca05 stopped. Success: False 1920s [2026-01-30T07:19:46+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_FORGO0/jobstore) 1920s ------------------------------ Captured log call ------------------------------- 1920s INFO  toil.lib.history:history.py:369 Recording workflow creation of 109aa9aa-3c30-4e63-9f36-a77a1f4bca05 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_FORGO0/jobstore 1920s INFO  toil.lib.history:history.py:399 Workflow 109aa9aa-3c30-4e63-9f36-a77a1f4bca05 is a run of 1920s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1920s 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-gw0/testDockerClean_CRx_FORGO0/jobstore kind-_testDockerCleanFn/instance-jp3nizfa. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v1 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v2 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-jp3nizfa" follows: 1920s =========> 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v1 1920s [2026-01-30T07:19:41+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v1 1920s [2026-01-30T07:19:41+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1920s apiDockerCall( 1920s ~~~~~~~~~~~~~^ 1920s job, 1920s ^^^^ 1920s ...<6 lines>... 1920s privileged=True, 1920s ^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:41+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v2 with ID kind-_testDockerCleanFn/instance-jp3nizfa to 0 1920s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v3 is completely failed 1920s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1920s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-jp3nizfa v3 1920s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1920s INFO  toil.lib.history:history.py:530 Workflow 109aa9aa-3c30-4e63-9f36-a77a1f4bca05 stopped. Success: False 1920s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_FORGO0/jobstore) 1920s _______________________ ToilDocumentationTest.testDocker _______________________ 1920s [gw1] linux -- Python 3.13.11 /usr/bin/python3.13 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor 1920s yield 1920s File "/usr/lib/python3.13/unittest/case.py", line 651, in run 1920s self._callTestMethod(testMethod) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod 1920s if method() is not None: 1920s ~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py", line 161, in testDocker 1920s self.checkExitCode("tutorial_docker.py") 1920s ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/test/docs/scriptsTest.py", line 50, in checkExitCode 1920s raise RuntimeError(stderr) 1920s RuntimeError: [2026-01-30T07:19:37+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 23938669-3606-4f16-a889-9c47b99ca8d4 in file:/tmp/tmp_4g6ykietutorial_docker 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil.lib.history] Workflow 23938669-3606-4f16-a889-9c47b99ca8d4 is a run of /usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:19:38+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmp_4g6ykietutorial_docker kind-apiDockerCall/instance-5la714qj. 1920s [2026-01-30T07:19:38+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v1 1920s Exit reason: None 1920s [2026-01-30T07:19:38+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v2 1920s [2026-01-30T07:19:38+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-5la714qj" follows: 1920s =========> 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v1 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-5la714qj v1) from description 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v1 1920s [2026-01-30T07:19:37+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:37+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:19:38+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v2 with ID kind-apiDockerCall/instance-5la714qj to 1 1920s [2026-01-30T07:19:38+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 1920s [2026-01-30T07:19:38+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:19:41+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmp_4g6ykietutorial_docker kind-apiDockerCall/instance-5la714qj. 1920s [2026-01-30T07:19:41+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v3 1920s Exit reason: None 1920s [2026-01-30T07:19:41+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v5 1920s [2026-01-30T07:19:41+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-5la714qj" follows: 1920s =========> 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v4 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-5la714qj v4) from description 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v4 1920s [2026-01-30T07:19:39+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:39+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:19:41+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v5 with ID kind-apiDockerCall/instance-5la714qj to 0 1920s [2026-01-30T07:19:41+0000] [MainThread] [W] [toil.leader] Job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v6 is completely failed 1920s [2026-01-30T07:19:44+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s [2026-01-30T07:19:44+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1920s [2026-01-30T07:19:44+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v6 1920s [2026-01-30T07:19:44+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1920s [2026-01-30T07:19:45+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1920s [2026-01-30T07:19:45+0000] [MainThread] [I] [toil.lib.history] Workflow 23938669-3606-4f16-a889-9c47b99ca8d4 stopped. Success: False 1920s [2026-01-30T07:19:45+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/tmp_4g6ykietutorial_docker) 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py", line 20, in 1920s toil.start(align) 1920s ~~~~~~~~~~^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1920s return self._runMainLoop(rootJobDescription) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1920s ).run() 1920s ~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1920s raise FailedJobsException( 1920s ...<3 lines>... 1920s ) 1920s toil.exceptions.FailedJobsException: The job store '/tmp/tmp_4g6ykietutorial_docker' contains 1 failed jobs: 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v6 1920s Log from job "'apiDockerCall' kind-apiDockerCall/instance-5la714qj v6" follows: 1920s =========> 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v4 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-5la714qj v4) from description 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v4 1920s [2026-01-30T07:19:39+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:39+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s 1920s ---------------------------- Captured stdout setup ----------------------------- 1920s 1920s 1920s [TEST] toil.test.docs.scriptsTest.ToilDocumentationTest:testDocker (Jan 29 2026 23:19:35:973338 PST) 1920s 1920s 1920s _____________________ TestDocker.testDockerClean_CRx_STOP ______________________ 1920s [gw0] linux -- Python 3.13.11 /usr/bin/python3.13 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 1920s toil.start(A) 1920s ~~~~~~~~~~^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1920s return self._runMainLoop(rootJobDescription) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1920s ).run() 1920s ~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1920s raise FailedJobsException( 1920s ...<3 lines>... 1920s ) 1920s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_STOP0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v3 1920s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v3" follows: 1920s =========> 1920s [2026-01-30T07:19:47+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:47+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:47+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v1 1920s [2026-01-30T07:19:49+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v1 1920s [2026-01-30T07:19:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 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. 1920s [2026-01-30T07:19:49+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1920s apiDockerCall( 1920s ~~~~~~~~~~~~~^ 1920s job, 1920s ^^^^ 1920s ...<6 lines>... 1920s privileged=True, 1920s ^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:49+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1920s result: TResult | None = func() 1920s ~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1920s lambda: runtest_hook(item=item, **kwds), 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1920s yield 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1920s return result.get_result() 1920s ~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1920s raise exc.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1920s res = yield 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1920s item.runtest() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1920s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1920s result = testfunction(**testargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 138, in testDockerClean_CRx_STOP 1920s self.testDockerClean( 1920s ~~~~~~~~~~~~~~~~~~~~^ 1920s tmp_path, caching=False, detached=False, rm=True, deferParam=STOP 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 1920s file_stats = test_file.stat() 1920s File "/usr/lib/python3.13/pathlib/_local.py", line 517, in stat 1920s return os.stat(self, follow_symlinks=follow_symlinks) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_STOP0/working/test.txt' 1920s ----------------------------- Captured stderr call ----------------------------- 1920s [2026-01-30T07:19:46+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 007476f8-53ec-4309-9381-ced8d393456b in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_STOP0/jobstore 1920s [2026-01-30T07:19:46+0000] [MainThread] [I] [toil.lib.history] Workflow 007476f8-53ec-4309-9381-ced8d393456b is a run of 1920s [2026-01-30T07:19:46+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:46+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1920s [2026-01-30T07:19:46+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:19:48+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1920s [2026-01-30T07:19:49+0000] [Thread-13 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:19:49: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 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. 1920s [2026-01-30T07:19:49+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-gw0/testDockerClean_CRx_STOP0/jobstore kind-_testDockerCleanFn/instance-_39pbz27. 1920s [2026-01-30T07:19:49+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v1 1920s Exit reason: None 1920s [2026-01-30T07:19:49+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v2 1920s [2026-01-30T07:19:49+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-_39pbz27" follows: 1920s =========> 1920s [2026-01-30T07:19:47+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:47+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:47+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v1 1920s [2026-01-30T07:19:49+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v1 1920s [2026-01-30T07:19:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 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. 1920s [2026-01-30T07:19:49+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1920s apiDockerCall( 1920s ~~~~~~~~~~~~~^ 1920s job, 1920s ^^^^ 1920s ...<6 lines>... 1920s privileged=True, 1920s ^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:49+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:19:49+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v2 with ID kind-_testDockerCleanFn/instance-_39pbz27 to 0 1920s [2026-01-30T07:19:49+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v3 is completely failed 1920s [2026-01-30T07:19:53+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s [2026-01-30T07:19:53+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1920s [2026-01-30T07:19:53+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v3 1920s [2026-01-30T07:19:53+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1920s [2026-01-30T07:19:53+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1920s [2026-01-30T07:19:53+0000] [MainThread] [I] [toil.lib.history] Workflow 007476f8-53ec-4309-9381-ced8d393456b stopped. Success: False 1920s [2026-01-30T07:19:53+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_STOP0/jobstore) 1920s ------------------------------ Captured log call ------------------------------- 1920s INFO  toil.lib.history:history.py:369 Recording workflow creation of 007476f8-53ec-4309-9381-ced8d393456b in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_STOP0/jobstore 1920s INFO  toil.lib.history:history.py:399 Workflow 007476f8-53ec-4309-9381-ced8d393456b is a run of 1920s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1920s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:19:49: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 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. 1920s 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-gw0/testDockerClean_CRx_STOP0/jobstore kind-_testDockerCleanFn/instance-_39pbz27. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v1 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v2 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-_39pbz27" follows: 1920s =========> 1920s [2026-01-30T07:19:47+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:47+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:47+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v1 1920s [2026-01-30T07:19:49+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v1 1920s [2026-01-30T07:19:49+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 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. 1920s [2026-01-30T07:19:49+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1920s apiDockerCall( 1920s ~~~~~~~~~~~~~^ 1920s job, 1920s ^^^^ 1920s ...<6 lines>... 1920s privileged=True, 1920s ^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:49+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v2 with ID kind-_testDockerCleanFn/instance-_39pbz27 to 0 1920s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v3 is completely failed 1920s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1920s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-_39pbz27 v3 1920s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1920s INFO  toil.lib.history:history.py:530 Workflow 007476f8-53ec-4309-9381-ced8d393456b stopped. Success: False 1920s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_STOP0/jobstore) 1920s ______________________ TestDocker.testDockerClean_CRx_RM _______________________ 1920s [gw0] linux -- Python 3.13.11 /usr/bin/python3.13 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 97, in testDockerClean 1920s toil.start(A) 1920s ~~~~~~~~~~^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1920s return self._runMainLoop(rootJobDescription) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1920s ).run() 1920s ~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1920s raise FailedJobsException( 1920s ...<3 lines>... 1920s ) 1920s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_RM0/jobstore' contains 1 failed jobs: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v3 1920s Log from job "'_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v3" follows: 1920s =========> 1920s [2026-01-30T07:19:54+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:54+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:54+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v1 1920s [2026-01-30T07:19:55+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v1 1920s [2026-01-30T07:19:55+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1920s apiDockerCall( 1920s ~~~~~~~~~~~~~^ 1920s job, 1920s ^^^^ 1920s ...<6 lines>... 1920s privileged=True, 1920s ^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:55+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1920s result: TResult | None = func() 1920s ~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1920s lambda: runtest_hook(item=item, **kwds), 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1920s yield 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1920s return result.get_result() 1920s ~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1920s raise exc.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1920s res = yield 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1920s item.runtest() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1920s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1920s result = testfunction(**testargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 143, in testDockerClean_CRx_RM 1920s self.testDockerClean( 1920s ~~~~~~~~~~~~~~~~~~~~^ 1920s tmp_path, caching=False, detached=False, rm=True, deferParam=RM 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 103, in testDockerClean 1920s file_stats = test_file.stat() 1920s File "/usr/lib/python3.13/pathlib/_local.py", line 517, in stat 1920s return os.stat(self, follow_symlinks=follow_symlinks) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_RM0/working/test.txt' 1920s ----------------------------- Captured stderr call ----------------------------- 1920s [2026-01-30T07:19:53+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 067a256c-0a22-4618-97c4-7d8dd63a98cd in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_RM0/jobstore 1920s [2026-01-30T07:19:53+0000] [MainThread] [I] [toil.lib.history] Workflow 067a256c-0a22-4618-97c4-7d8dd63a98cd is a run of 1920s [2026-01-30T07:19:53+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:53+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1920s [2026-01-30T07:19:53+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:19:55+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1920s [2026-01-30T07:19:57+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-gw0/testDockerClean_CRx_RM0/jobstore kind-_testDockerCleanFn/instance-0sh7czit. 1920s [2026-01-30T07:19:57+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v1 1920s Exit reason: None 1920s [2026-01-30T07:19:57+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v2 1920s [2026-01-30T07:19:57+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerCleanFn/instance-0sh7czit" follows: 1920s =========> 1920s [2026-01-30T07:19:54+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:54+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:54+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v1 1920s [2026-01-30T07:19:55+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v1 1920s [2026-01-30T07:19:55+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1920s apiDockerCall( 1920s ~~~~~~~~~~~~~^ 1920s job, 1920s ^^^^ 1920s ...<6 lines>... 1920s privileged=True, 1920s ^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:55+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:19:57+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v2 with ID kind-_testDockerCleanFn/instance-0sh7czit to 0 1920s [2026-01-30T07:19:57+0000] [MainThread] [W] [toil.leader] Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v3 is completely failed 1920s [2026-01-30T07:20:01+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s [2026-01-30T07:20:01+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1920s [2026-01-30T07:20:01+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v3 1920s [2026-01-30T07:20:01+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1920s [2026-01-30T07:20:01+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1920s [2026-01-30T07:20:01+0000] [MainThread] [I] [toil.lib.history] Workflow 067a256c-0a22-4618-97c4-7d8dd63a98cd stopped. Success: False 1920s [2026-01-30T07:20:01+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_RM0/jobstore) 1920s ------------------------------ Captured log call ------------------------------- 1920s INFO  toil.lib.history:history.py:369 Recording workflow creation of 067a256c-0a22-4618-97c4-7d8dd63a98cd in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_RM0/jobstore 1920s INFO  toil.lib.history:history.py:399 Workflow 067a256c-0a22-4618-97c4-7d8dd63a98cd is a run of 1920s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1920s 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-gw0/testDockerClean_CRx_RM0/jobstore kind-_testDockerCleanFn/instance-0sh7czit. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v1 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v2 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerCleanFn/instance-0sh7czit" follows: 1920s =========> 1920s [2026-01-30T07:19:54+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:54+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:54+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v1 1920s [2026-01-30T07:19:55+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v1) from description '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v1 1920s [2026-01-30T07:19:55+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 408, in _testDockerCleanFn 1920s apiDockerCall( 1920s ~~~~~~~~~~~~~^ 1920s job, 1920s ^^^^ 1920s ...<6 lines>... 1920s privileged=True, 1920s ^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:55+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v2 with ID kind-_testDockerCleanFn/instance-0sh7czit to 0 1920s WARNING  toil.leader:leader.py:643 Job '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v3 is completely failed 1920s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1920s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerCleanFn' kind-_testDockerCleanFn/instance-0sh7czit v3 1920s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1920s INFO  toil.lib.history:history.py:530 Workflow 067a256c-0a22-4618-97c4-7d8dd63a98cd stopped. Success: False 1920s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_RM0/jobstore) 1920s ________________________ TestDocker.testDockerPipeChain ________________________ 1920s [gw0] linux -- Python 3.13.11 /usr/bin/python3.13 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1920s result: TResult | None = func() 1920s ~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1920s lambda: runtest_hook(item=item, **kwds), 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1920s yield 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1920s return result.get_result() 1920s ~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1920s raise exc.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1920s res = yield 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1920s item.runtest() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1920s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1920s result = testfunction(**testargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 310, in testDockerPipeChain 1920s rv = Job.Runner.startToil(A, options) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1920s return toil.start(job) 1920s ~~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1920s return self._runMainLoop(rootJobDescription) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1920s ).run() 1920s ~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1920s raise FailedJobsException( 1920s ...<3 lines>... 1920s ) 1920s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerPipeChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v6 1920s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v6" follows: 1920s =========> 1920s [2026-01-30T07:20:07+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:07+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:07+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v4 1920s [2026-01-30T07:20:08+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v4 1920s [2026-01-30T07:20:08+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1920s return apiDockerCall( 1920s job, 1920s ...<2 lines>... 1920s privileged=True, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:08+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s ----------------------------- Captured stderr call ----------------------------- 1920s [2026-01-30T07:20:01+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 872aacc2-060e-46eb-bff1-30e22376fd64 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerPipeChain0/jobstore 1920s [2026-01-30T07:20:02+0000] [MainThread] [I] [toil.lib.history] Workflow 872aacc2-060e-46eb-bff1-30e22376fd64 is a run of 1920s [2026-01-30T07:20:02+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:02+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1920s [2026-01-30T07:20:02+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:20:04+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1920s [2026-01-30T07:20:06+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-gw0/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-cazc6fwq. 1920s [2026-01-30T07:20:06+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v1 1920s Exit reason: None 1920s [2026-01-30T07:20:06+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v2 1920s [2026-01-30T07:20:06+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-cazc6fwq" follows: 1920s =========> 1920s [2026-01-30T07:20:04+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:04+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v1 1920s [2026-01-30T07:20:05+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v1 1920s [2026-01-30T07:20:05+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1920s return apiDockerCall( 1920s job, 1920s ...<2 lines>... 1920s privileged=True, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:05+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:20:06+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v2 with ID kind-_testDockerPipeChainFn/instance-cazc6fwq to 1 1920s [2026-01-30T07:20:06+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:20:09+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-gw0/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-cazc6fwq. 1920s [2026-01-30T07:20:09+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v3 1920s Exit reason: None 1920s [2026-01-30T07:20:09+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v5 1920s [2026-01-30T07:20:09+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-cazc6fwq" follows: 1920s =========> 1920s [2026-01-30T07:20:07+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:07+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:07+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v4 1920s [2026-01-30T07:20:08+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v4 1920s [2026-01-30T07:20:08+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1920s return apiDockerCall( 1920s job, 1920s ...<2 lines>... 1920s privileged=True, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:08+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:20:09+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v5 with ID kind-_testDockerPipeChainFn/instance-cazc6fwq to 0 1920s [2026-01-30T07:20:09+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v6 is completely failed 1920s [2026-01-30T07:20:13+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s [2026-01-30T07:20:13+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1920s [2026-01-30T07:20:13+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v6 1920s [2026-01-30T07:20:13+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1920s [2026-01-30T07:20:13+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1920s [2026-01-30T07:20:13+0000] [MainThread] [I] [toil.lib.history] Workflow 872aacc2-060e-46eb-bff1-30e22376fd64 stopped. Success: False 1920s [2026-01-30T07:20:13+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerPipeChain0/jobstore) 1920s ------------------------------ Captured log call ------------------------------- 1920s INFO  toil.lib.history:history.py:369 Recording workflow creation of 872aacc2-060e-46eb-bff1-30e22376fd64 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerPipeChain0/jobstore 1920s INFO  toil.lib.history:history.py:399 Workflow 872aacc2-060e-46eb-bff1-30e22376fd64 is a run of 1920s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1920s 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-gw0/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-cazc6fwq. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v1 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v2 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-cazc6fwq" follows: 1920s =========> 1920s [2026-01-30T07:20:04+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:04+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:04+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v1 1920s [2026-01-30T07:20:05+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v1 1920s [2026-01-30T07:20:05+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1920s return apiDockerCall( 1920s job, 1920s ...<2 lines>... 1920s privileged=True, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:05+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v2 with ID kind-_testDockerPipeChainFn/instance-cazc6fwq to 1 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s 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-gw0/testDockerPipeChain0/jobstore kind-_testDockerPipeChainFn/instance-cazc6fwq. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v3 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v5 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-cazc6fwq" follows: 1920s =========> 1920s [2026-01-30T07:20:07+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:07+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:07+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v4 1920s [2026-01-30T07:20:08+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v4 1920s [2026-01-30T07:20:08+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1920s return apiDockerCall( 1920s job, 1920s ...<2 lines>... 1920s privileged=True, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:08+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v5 with ID kind-_testDockerPipeChainFn/instance-cazc6fwq to 0 1920s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v6 is completely failed 1920s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1920s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v6 1920s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1920s INFO  toil.lib.history:history.py:530 Workflow 872aacc2-060e-46eb-bff1-30e22376fd64 stopped. Success: False 1920s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerPipeChain0/jobstore) 1920s _________________ TestDocker.testDockerPipeChainErrorDetection _________________ 1920s [gw0] linux -- Python 3.13.11 /usr/bin/python3.13 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1920s result: TResult | None = func() 1920s ~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1920s lambda: runtest_hook(item=item, **kwds), 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1920s yield 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1920s return result.get_result() 1920s ~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1920s raise exc.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1920s res = yield 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1920s item.runtest() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1920s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1920s result = testfunction(**testargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 332, in testDockerPipeChainErrorDetection 1920s rv = Job.Runner.startToil(A, options) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1920s return toil.start(job) 1920s ~~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1920s return self._runMainLoop(rootJobDescription) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1920s ).run() 1920s ~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1920s raise FailedJobsException( 1920s ...<3 lines>... 1920s ) 1920s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerPipeChainErrorDetect0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v6 1920s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v6" follows: 1920s =========> 1920s [2026-01-30T07:20:19+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:19+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v4 1920s [2026-01-30T07:20:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v4 1920s [2026-01-30T07:20:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1920s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1920s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s ----------------------------- Captured stderr call ----------------------------- 1920s [2026-01-30T07:20:14+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of c123ea9d-4c68-4bd0-a5f3-b8c5856a3b14 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerPipeChainErrorDetect0/jobstore 1920s [2026-01-30T07:20:14+0000] [MainThread] [I] [toil.lib.history] Workflow c123ea9d-4c68-4bd0-a5f3-b8c5856a3b14 is a run of 1920s [2026-01-30T07:20:14+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:14+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1920s [2026-01-30T07:20:14+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:20:16+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1920s [2026-01-30T07:20:18+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-gw0/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7. 1920s [2026-01-30T07:20:18+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v1 1920s Exit reason: None 1920s [2026-01-30T07:20:18+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v2 1920s [2026-01-30T07:20:18+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7" follows: 1920s =========> 1920s [2026-01-30T07:20:15+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:15+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:15+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v1 1920s [2026-01-30T07:20:17+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v1 1920s [2026-01-30T07:20:17+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1920s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1920s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:17+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:20:18+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v2 with ID kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 to 1 1920s [2026-01-30T07:20:18+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:20:22+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-gw0/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7. 1920s [2026-01-30T07:20:22+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v3 1920s Exit reason: None 1920s [2026-01-30T07:20:22+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v5 1920s [2026-01-30T07:20:22+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7" follows: 1920s =========> 1920s [2026-01-30T07:20:19+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:19+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v4 1920s [2026-01-30T07:20:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v4 1920s [2026-01-30T07:20:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1920s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1920s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:20:22+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v5 with ID kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 to 0 1920s [2026-01-30T07:20:22+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v6 is completely failed 1920s [2026-01-30T07:20:25+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s [2026-01-30T07:20:25+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1920s [2026-01-30T07:20:25+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v6 1920s [2026-01-30T07:20:25+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1920s [2026-01-30T07:20:26+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1920s [2026-01-30T07:20:26+0000] [MainThread] [I] [toil.lib.history] Workflow c123ea9d-4c68-4bd0-a5f3-b8c5856a3b14 stopped. Success: False 1920s [2026-01-30T07:20:26+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerPipeChainErrorDetect0/jobstore) 1920s ------------------------------ Captured log call ------------------------------- 1920s INFO  toil.lib.history:history.py:369 Recording workflow creation of c123ea9d-4c68-4bd0-a5f3-b8c5856a3b14 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerPipeChainErrorDetect0/jobstore 1920s INFO  toil.lib.history:history.py:399 Workflow c123ea9d-4c68-4bd0-a5f3-b8c5856a3b14 is a run of 1920s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1920s 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-gw0/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v1 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v2 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7" follows: 1920s =========> 1920s [2026-01-30T07:20:15+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:15+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:15+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v1 1920s [2026-01-30T07:20:17+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v1 1920s [2026-01-30T07:20:17+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1920s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1920s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:17+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v2 with ID kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 to 1 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s 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-gw0/testDockerPipeChainErrorDetect0/jobstore kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v3 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v5 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7" follows: 1920s =========> 1920s [2026-01-30T07:20:19+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:19+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v4 1920s [2026-01-30T07:20:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v4 1920s [2026-01-30T07:20:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1920s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1920s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v5 with ID kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 to 0 1920s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v6 is completely failed 1920s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1920s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v6 1920s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1920s INFO  toil.lib.history:history.py:530 Workflow c123ea9d-4c68-4bd0-a5f3-b8c5856a3b14 stopped. Success: False 1920s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerPipeChainErrorDetect0/jobstore) 1920s _____________________ TestDocker.testNonCachingDockerChain _____________________ 1920s [gw0] linux -- Python 3.13.11 /usr/bin/python3.13 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1920s result: TResult | None = func() 1920s ~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1920s lambda: runtest_hook(item=item, **kwds), 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1920s yield 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1920s return result.get_result() 1920s ~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1920s raise exc.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1920s res = yield 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1920s item.runtest() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1920s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1920s result = testfunction(**testargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 336, in testNonCachingDockerChain 1920s self.testDockerPipeChain(tmp_path, caching=True) 1920s ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 310, in testDockerPipeChain 1920s rv = Job.Runner.startToil(A, options) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1920s return toil.start(job) 1920s ~~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1920s return self._runMainLoop(rootJobDescription) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1920s ).run() 1920s ~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1920s raise FailedJobsException( 1920s ...<3 lines>... 1920s ) 1920s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testNonCachingDockerChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v6 1920s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v6" follows: 1920s =========> 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v4 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v4 1920s [2026-01-30T07:20:30+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr 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. 1920s [2026-01-30T07:20:30+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1920s return apiDockerCall( 1920s job, 1920s ...<2 lines>... 1920s privileged=True, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:30+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s ----------------------------- Captured stderr call ----------------------------- 1920s [2026-01-30T07:20:26+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 49b383f3-5b0f-498b-be72-82da520651d9 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testNonCachingDockerChain0/jobstore 1920s [2026-01-30T07:20:26+0000] [MainThread] [I] [toil.lib.history] Workflow 49b383f3-5b0f-498b-be72-82da520651d9 is a run of 1920s [2026-01-30T07:20:26+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:26+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1920s [2026-01-30T07:20:26+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:20:28+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1920s [2026-01-30T07:20:29+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-gw0/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-1hcrl_qr. 1920s [2026-01-30T07:20:29+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v1 1920s Exit reason: None 1920s [2026-01-30T07:20:29+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v2 1920s [2026-01-30T07:20:29+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-1hcrl_qr" follows: 1920s =========> 1920s [2026-01-30T07:20:27+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:27+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:27+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v1 1920s [2026-01-30T07:20:28+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v1 1920s [2026-01-30T07:20:28+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1920s return apiDockerCall( 1920s job, 1920s ...<2 lines>... 1920s privileged=True, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:28+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:20:29+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v2 with ID kind-_testDockerPipeChainFn/instance-1hcrl_qr to 1 1920s [2026-01-30T07:20:29+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:20:31+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-gw0/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-1hcrl_qr. 1920s [2026-01-30T07:20:31+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v3 1920s Exit reason: None 1920s [2026-01-30T07:20:31+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v5 1920s [2026-01-30T07:20:31+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainFn/instance-1hcrl_qr" follows: 1920s =========> 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v4 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v4 1920s [2026-01-30T07:20:30+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr 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. 1920s [2026-01-30T07:20:30+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1920s return apiDockerCall( 1920s job, 1920s ...<2 lines>... 1920s privileged=True, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:30+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:20:31+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v5 with ID kind-_testDockerPipeChainFn/instance-1hcrl_qr to 0 1920s [2026-01-30T07:20:31+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v6 is completely failed 1920s [2026-01-30T07:20:31+0000] [Thread-29 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:20:31: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr 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. 1920s [2026-01-30T07:20:34+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s [2026-01-30T07:20:34+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1920s [2026-01-30T07:20:34+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v6 1920s [2026-01-30T07:20:34+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1920s [2026-01-30T07:20:34+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1920s [2026-01-30T07:20:35+0000] [MainThread] [I] [toil.lib.history] Workflow 49b383f3-5b0f-498b-be72-82da520651d9 stopped. Success: False 1920s [2026-01-30T07:20:35+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testNonCachingDockerChain0/jobstore) 1920s ------------------------------ Captured log call ------------------------------- 1920s INFO  toil.lib.history:history.py:369 Recording workflow creation of 49b383f3-5b0f-498b-be72-82da520651d9 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testNonCachingDockerChain0/jobstore 1920s INFO  toil.lib.history:history.py:399 Workflow 49b383f3-5b0f-498b-be72-82da520651d9 is a run of 1920s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1920s 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-gw0/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-1hcrl_qr. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v1 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v2 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-1hcrl_qr" follows: 1920s =========> 1920s [2026-01-30T07:20:27+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:27+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:27+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v1 1920s [2026-01-30T07:20:28+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v1) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v1 1920s [2026-01-30T07:20:28+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1920s return apiDockerCall( 1920s job, 1920s ...<2 lines>... 1920s privileged=True, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:28+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v2 with ID kind-_testDockerPipeChainFn/instance-1hcrl_qr to 1 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s 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-gw0/testNonCachingDockerChain0/jobstore kind-_testDockerPipeChainFn/instance-1hcrl_qr. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v3 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v5 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainFn/instance-1hcrl_qr" follows: 1920s =========> 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v4 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v4 1920s [2026-01-30T07:20:30+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr 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. 1920s [2026-01-30T07:20:30+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1920s return apiDockerCall( 1920s job, 1920s ...<2 lines>... 1920s privileged=True, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:30+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v5 with ID kind-_testDockerPipeChainFn/instance-1hcrl_qr to 0 1920s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v6 is completely failed 1920s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:20:31: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr 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. 1920s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1920s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v6 1920s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1920s INFO  toil.lib.history:history.py:530 Workflow 49b383f3-5b0f-498b-be72-82da520651d9 stopped. Success: False 1920s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testNonCachingDockerChain0/jobstore) 1920s ______________ TestDocker.testNonCachingDockerChainErrorDetection ______________ 1920s [gw0] linux -- Python 3.13.11 /usr/bin/python3.13 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1920s result: TResult | None = func() 1920s ~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1920s lambda: runtest_hook(item=item, **kwds), 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1920s yield 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1920s return result.get_result() 1920s ~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1920s raise exc.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1920s res = yield 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1920s item.runtest() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1920s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1920s result = testfunction(**testargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 339, in testNonCachingDockerChainErrorDetection 1920s self.testDockerPipeChainErrorDetection(tmp_path, caching=True) 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 332, in testDockerPipeChainErrorDetection 1920s rv = Job.Runner.startToil(A, options) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1920s return toil.start(job) 1920s ~~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1920s return self._runMainLoop(rootJobDescription) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1920s ).run() 1920s ~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1920s raise FailedJobsException( 1920s ...<3 lines>... 1920s ) 1920s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testNonCachingDockerChainError0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v6 1920s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v6" follows: 1920s =========> 1920s [2026-01-30T07:20:37+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:37+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:37+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v4 1920s [2026-01-30T07:20:38+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v4 1920s [2026-01-30T07:20:38+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt 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. 1920s [2026-01-30T07:20:38+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1920s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1920s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:38+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s ----------------------------- Captured stderr call ----------------------------- 1920s [2026-01-30T07:20:35+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of b4cdb10a-d381-4928-be7b-07caa23882e8 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testNonCachingDockerChainError0/jobstore 1920s [2026-01-30T07:20:35+0000] [MainThread] [I] [toil.lib.history] Workflow b4cdb10a-d381-4928-be7b-07caa23882e8 is a run of 1920s [2026-01-30T07:20:35+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:35+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1920s [2026-01-30T07:20:35+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:20:36+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-gw0/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt. 1920s [2026-01-30T07:20:36+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v1 1920s Exit reason: None 1920s [2026-01-30T07:20:36+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v2 1920s [2026-01-30T07:20:36+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt" follows: 1920s =========> 1920s [2026-01-30T07:20:35+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:35+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:35+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v1 1920s [2026-01-30T07:20:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v1 1920s [2026-01-30T07:20:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1920s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1920s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:20:36+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v2 with ID kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt to 1 1920s [2026-01-30T07:20:36+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 1920s [2026-01-30T07:20:36+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:20:38+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-gw0/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt. 1920s [2026-01-30T07:20:38+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v3 1920s Exit reason: None 1920s [2026-01-30T07:20:38+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v5 1920s [2026-01-30T07:20:38+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt" follows: 1920s =========> 1920s [2026-01-30T07:20:37+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:37+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:37+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v4 1920s [2026-01-30T07:20:38+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v4 1920s [2026-01-30T07:20:38+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt 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. 1920s [2026-01-30T07:20:38+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1920s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1920s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:38+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:20:38+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v5 with ID kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt to 0 1920s [2026-01-30T07:20:38+0000] [MainThread] [W] [toil.leader] Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v6 is completely failed 1920s [2026-01-30T07:20:38+0000] [Thread-33 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:20:38: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt 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. 1920s [2026-01-30T07:20:42+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s [2026-01-30T07:20:42+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1920s [2026-01-30T07:20:42+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v6 1920s [2026-01-30T07:20:42+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1920s [2026-01-30T07:20:42+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1920s [2026-01-30T07:20:42+0000] [MainThread] [I] [toil.lib.history] Workflow b4cdb10a-d381-4928-be7b-07caa23882e8 stopped. Success: False 1920s [2026-01-30T07:20:42+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testNonCachingDockerChainError0/jobstore) 1920s ------------------------------ Captured log call ------------------------------- 1920s INFO  toil.lib.history:history.py:369 Recording workflow creation of b4cdb10a-d381-4928-be7b-07caa23882e8 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testNonCachingDockerChainError0/jobstore 1920s INFO  toil.lib.history:history.py:399 Workflow b4cdb10a-d381-4928-be7b-07caa23882e8 is a run of 1920s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s 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-gw0/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v1 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v2 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt" follows: 1920s =========> 1920s [2026-01-30T07:20:35+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:35+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:35+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v1 1920s [2026-01-30T07:20:36+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v1) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v1 1920s [2026-01-30T07:20:36+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1920s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1920s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:36+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v2 with ID kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt to 1 1920s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s 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-gw0/testNonCachingDockerChainError0/jobstore kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v3 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v5 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt" follows: 1920s =========> 1920s [2026-01-30T07:20:37+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:37+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:37+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v4 1920s [2026-01-30T07:20:38+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v4 1920s [2026-01-30T07:20:38+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt 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. 1920s [2026-01-30T07:20:38+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1920s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1920s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:38+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v5 with ID kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt to 0 1920s WARNING  toil.leader:leader.py:643 Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v6 is completely failed 1920s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:20:38: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt 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. 1920s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1920s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v6 1920s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1920s INFO  toil.lib.history:history.py:530 Workflow b4cdb10a-d381-4928-be7b-07caa23882e8 stopped. Success: False 1920s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testNonCachingDockerChainError0/jobstore) 1920s __________________________ TestDocker.testDockerLogs ___________________________ 1920s [gw0] linux -- Python 3.13.11 /usr/bin/python3.13 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1920s result: TResult | None = func() 1920s ~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1920s lambda: runtest_hook(item=item, **kwds), 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1920s yield 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1920s return result.get_result() 1920s ~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1920s raise exc.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1920s res = yield 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1920s item.runtest() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1920s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1920s result = testfunction(**testargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 1920s rv = Job.Runner.startToil(A, options) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1920s return toil.start(job) 1920s ~~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1920s return self._runMainLoop(rootJobDescription) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1920s ).run() 1920s ~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1920s raise FailedJobsException( 1920s ...<3 lines>... 1920s ) 1920s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v6 1920s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v6" follows: 1920s =========> 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v4 1920s [2026-01-30T07:20:45+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v4 1920s [2026-01-30T07:20:45+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:45+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s ----------------------------- Captured stderr call ----------------------------- 1920s [2026-01-30T07:20:43+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of e4132395-c274-4653-aca3-bc7a177b7d63 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs0/jobstore 1920s [2026-01-30T07:20:43+0000] [MainThread] [I] [toil.lib.history] Workflow e4132395-c274-4653-aca3-bc7a177b7d63 is a run of 1920s [2026-01-30T07:20:43+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:43+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1920s [2026-01-30T07:20:43+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:20:44+0000] [Thread-37 (statsAndLoggingAggregator)] [W] [toil.statsAndLogging] Got message from job at time 01-30-2026 07:20:44: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v1 used 1.12x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1920s [2026-01-30T07:20:44+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-gw0/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-_k8nu84j. 1920s [2026-01-30T07:20:44+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v1 1920s Exit reason: None 1920s [2026-01-30T07:20:44+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v2 1920s [2026-01-30T07:20:44+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-_k8nu84j" follows: 1920s =========> 1920s [2026-01-30T07:20:43+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:43+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:43+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v1 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v1 1920s [2026-01-30T07:20:44+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v1 used 1.12x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1920s [2026-01-30T07:20:44+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:44+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:20:44+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v2 with ID kind-_testDockerLogsFn/instance-_k8nu84j to 1 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:20:45+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-gw0/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-_k8nu84j. 1920s [2026-01-30T07:20:45+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v3 1920s Exit reason: None 1920s [2026-01-30T07:20:45+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v5 1920s [2026-01-30T07:20:45+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-_k8nu84j" follows: 1920s =========> 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v4 1920s [2026-01-30T07:20:45+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v4 1920s [2026-01-30T07:20:45+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:45+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:20:45+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v5 with ID kind-_testDockerLogsFn/instance-_k8nu84j to 0 1920s [2026-01-30T07:20:45+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v6 is completely failed 1920s [2026-01-30T07:20:49+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s [2026-01-30T07:20:49+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1920s [2026-01-30T07:20:49+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v6 1920s [2026-01-30T07:20:49+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1920s [2026-01-30T07:20:50+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1920s [2026-01-30T07:20:50+0000] [MainThread] [I] [toil.lib.history] Workflow e4132395-c274-4653-aca3-bc7a177b7d63 stopped. Success: False 1920s [2026-01-30T07:20:50+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs0/jobstore) 1920s ------------------------------ Captured log call ------------------------------- 1920s INFO  toil.lib.history:history.py:369 Recording workflow creation of e4132395-c274-4653-aca3-bc7a177b7d63 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs0/jobstore 1920s INFO  toil.lib.history:history.py:399 Workflow e4132395-c274-4653-aca3-bc7a177b7d63 is a run of 1920s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s WARNING  toil.statsAndLogging:statsAndLogging.py:193 Got message from job at time 01-30-2026 07:20:44: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v1 used 1.12x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1920s 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-gw0/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-_k8nu84j. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v1 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v2 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-_k8nu84j" follows: 1920s =========> 1920s [2026-01-30T07:20:43+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:43+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:43+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v1 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v1 1920s [2026-01-30T07:20:44+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v1 used 1.12x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched. 1920s [2026-01-30T07:20:44+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:44+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v2 with ID kind-_testDockerLogsFn/instance-_k8nu84j to 1 1920s INFO  toil.leader:leader.py:1231 0 jobs are running, 0 jobs are issued and waiting to run 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s 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-gw0/testDockerLogs0/jobstore kind-_testDockerLogsFn/instance-_k8nu84j. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v3 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v5 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-_k8nu84j" follows: 1920s =========> 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v4 1920s [2026-01-30T07:20:45+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v4 1920s [2026-01-30T07:20:45+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:45+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v5 with ID kind-_testDockerLogsFn/instance-_k8nu84j to 0 1920s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v6 is completely failed 1920s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1920s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v6 1920s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1920s INFO  toil.lib.history:history.py:530 Workflow e4132395-c274-4653-aca3-bc7a177b7d63 stopped. Success: False 1920s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs0/jobstore) 1920s _______________________ TestDocker.testDockerLogs_Stream _______________________ 1920s [gw0] linux -- Python 3.13.11 /usr/bin/python3.13 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1920s result: TResult | None = func() 1920s ~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1920s lambda: runtest_hook(item=item, **kwds), 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1920s yield 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1920s return result.get_result() 1920s ~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1920s raise exc.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1920s res = yield 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1920s item.runtest() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1920s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1920s result = testfunction(**testargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 366, in testDockerLogs_Stream 1920s self.testDockerLogs(tmp_path, stream=True, demux=False) 1920s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 1920s rv = Job.Runner.startToil(A, options) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1920s return toil.start(job) 1920s ~~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1920s return self._runMainLoop(rootJobDescription) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1920s ).run() 1920s ~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1920s raise FailedJobsException( 1920s ...<3 lines>... 1920s ) 1920s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v6 1920s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v6" follows: 1920s =========> 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v4 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v4 1920s [2026-01-30T07:21:04+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:04+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s ----------------------------- Captured stderr call ----------------------------- 1920s [2026-01-30T07:20:51+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 279cd0ab-da66-45d2-abf1-37bd935e0eb6 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Stream0/jobstore 1920s [2026-01-30T07:20:51+0000] [MainThread] [I] [toil.lib.history] Workflow 279cd0ab-da66-45d2-abf1-37bd935e0eb6 is a run of 1920s [2026-01-30T07:20:52+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:52+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1920s [2026-01-30T07:20:52+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:20:54+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1920s [2026-01-30T07:21:02+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-gw0/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-qylgpejb. 1920s [2026-01-30T07:21:02+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v1 1920s Exit reason: None 1920s [2026-01-30T07:21:02+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v2 1920s [2026-01-30T07:21:02+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-qylgpejb" follows: 1920s =========> 1920s [2026-01-30T07:20:59+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:59+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:59+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v1 1920s [2026-01-30T07:21:01+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v1 1920s [2026-01-30T07:21:01+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:01+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:21:02+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v2 with ID kind-_testDockerLogsFn/instance-qylgpejb to 1 1920s [2026-01-30T07:21:02+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:21:04+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-gw0/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-qylgpejb. 1920s [2026-01-30T07:21:04+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v3 1920s Exit reason: None 1920s [2026-01-30T07:21:04+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v5 1920s [2026-01-30T07:21:04+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-qylgpejb" follows: 1920s =========> 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v4 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v4 1920s [2026-01-30T07:21:04+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:04+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:21:04+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v5 with ID kind-_testDockerLogsFn/instance-qylgpejb to 0 1920s [2026-01-30T07:21:04+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v6 is completely failed 1920s [2026-01-30T07:21:08+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s [2026-01-30T07:21:08+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1920s [2026-01-30T07:21:08+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v6 1920s [2026-01-30T07:21:08+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1920s [2026-01-30T07:21:08+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1920s [2026-01-30T07:21:08+0000] [MainThread] [I] [toil.lib.history] Workflow 279cd0ab-da66-45d2-abf1-37bd935e0eb6 stopped. Success: False 1920s [2026-01-30T07:21:09+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Stream0/jobstore) 1920s ------------------------------ Captured log call ------------------------------- 1920s INFO  toil.lib.history:history.py:369 Recording workflow creation of 279cd0ab-da66-45d2-abf1-37bd935e0eb6 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Stream0/jobstore 1920s INFO  toil.lib.history:history.py:399 Workflow 279cd0ab-da66-45d2-abf1-37bd935e0eb6 is a run of 1920s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1920s 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-gw0/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-qylgpejb. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v1 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v2 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-qylgpejb" follows: 1920s =========> 1920s [2026-01-30T07:20:59+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:59+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:59+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v1 1920s [2026-01-30T07:21:01+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v1 1920s [2026-01-30T07:21:01+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:01+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v2 with ID kind-_testDockerLogsFn/instance-qylgpejb to 1 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s 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-gw0/testDockerLogs_Stream0/jobstore kind-_testDockerLogsFn/instance-qylgpejb. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v3 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v5 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-qylgpejb" follows: 1920s =========> 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v4 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v4 1920s [2026-01-30T07:21:04+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:04+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v5 with ID kind-_testDockerLogsFn/instance-qylgpejb to 0 1920s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v6 is completely failed 1920s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1920s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v6 1920s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1920s INFO  toil.lib.history:history.py:530 Workflow 279cd0ab-da66-45d2-abf1-37bd935e0eb6 stopped. Success: False 1920s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Stream0/jobstore) 1920s _______________________ TestDocker.testDockerLogs_Demux ________________________ 1920s [gw0] linux -- Python 3.13.11 /usr/bin/python3.13 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1920s result: TResult | None = func() 1920s ~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1920s lambda: runtest_hook(item=item, **kwds), 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1920s yield 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1920s return result.get_result() 1920s ~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1920s raise exc.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1920s res = yield 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1920s item.runtest() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1920s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1920s result = testfunction(**testargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 369, in testDockerLogs_Demux 1920s self.testDockerLogs(tmp_path, stream=False, demux=True) 1920s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 1920s rv = Job.Runner.startToil(A, options) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1920s return toil.start(job) 1920s ~~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1920s return self._runMainLoop(rootJobDescription) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1920s ).run() 1920s ~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1920s raise FailedJobsException( 1920s ...<3 lines>... 1920s ) 1920s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Demux0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v6 1920s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v6" follows: 1920s =========> 1920s [2026-01-30T07:21:12+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:12+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:12+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v4 1920s [2026-01-30T07:21:13+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v4 1920s [2026-01-30T07:21:13+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:13+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s ----------------------------- Captured stderr call ----------------------------- 1920s [2026-01-30T07:21:09+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 1ffdc9ce-0739-403e-a430-a91a37ad8f7d in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Demux0/jobstore 1920s [2026-01-30T07:21:09+0000] [MainThread] [I] [toil.lib.history] Workflow 1ffdc9ce-0739-403e-a430-a91a37ad8f7d is a run of 1920s [2026-01-30T07:21:09+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:09+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1920s [2026-01-30T07:21:09+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:21:11+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1920s [2026-01-30T07:21:11+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-gw0/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-6pkxt67e. 1920s [2026-01-30T07:21:11+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v1 1920s Exit reason: None 1920s [2026-01-30T07:21:11+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v2 1920s [2026-01-30T07:21:11+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-6pkxt67e" follows: 1920s =========> 1920s [2026-01-30T07:21:09+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:09+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:09+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v1 1920s [2026-01-30T07:21:10+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v1 1920s [2026-01-30T07:21:10+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:10+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:21:11+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v2 with ID kind-_testDockerLogsFn/instance-6pkxt67e to 1 1920s [2026-01-30T07:21:11+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:21:13+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-gw0/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-6pkxt67e. 1920s [2026-01-30T07:21:13+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v3 1920s Exit reason: None 1920s [2026-01-30T07:21:13+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v5 1920s [2026-01-30T07:21:13+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-6pkxt67e" follows: 1920s =========> 1920s [2026-01-30T07:21:12+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:12+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:12+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v4 1920s [2026-01-30T07:21:13+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v4 1920s [2026-01-30T07:21:13+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:13+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:21:13+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v5 with ID kind-_testDockerLogsFn/instance-6pkxt67e to 0 1920s [2026-01-30T07:21:13+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v6 is completely failed 1920s [2026-01-30T07:21:18+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s [2026-01-30T07:21:18+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1920s [2026-01-30T07:21:18+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v6 1920s [2026-01-30T07:21:18+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1920s [2026-01-30T07:21:18+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1920s [2026-01-30T07:21:18+0000] [MainThread] [I] [toil.lib.history] Workflow 1ffdc9ce-0739-403e-a430-a91a37ad8f7d stopped. Success: False 1920s [2026-01-30T07:21:19+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Demux0/jobstore) 1920s ------------------------------ Captured log call ------------------------------- 1920s INFO  toil.lib.history:history.py:369 Recording workflow creation of 1ffdc9ce-0739-403e-a430-a91a37ad8f7d in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Demux0/jobstore 1920s INFO  toil.lib.history:history.py:399 Workflow 1ffdc9ce-0739-403e-a430-a91a37ad8f7d is a run of 1920s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1920s 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-gw0/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-6pkxt67e. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v1 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v2 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-6pkxt67e" follows: 1920s =========> 1920s [2026-01-30T07:21:09+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:09+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:09+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v1 1920s [2026-01-30T07:21:10+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v1 1920s [2026-01-30T07:21:10+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:10+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v2 with ID kind-_testDockerLogsFn/instance-6pkxt67e to 1 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s 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-gw0/testDockerLogs_Demux0/jobstore kind-_testDockerLogsFn/instance-6pkxt67e. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v3 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v5 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-6pkxt67e" follows: 1920s =========> 1920s [2026-01-30T07:21:12+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:12+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:12+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v4 1920s [2026-01-30T07:21:13+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v4 1920s [2026-01-30T07:21:13+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:13+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v5 with ID kind-_testDockerLogsFn/instance-6pkxt67e to 0 1920s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v6 is completely failed 1920s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1920s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v6 1920s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1920s INFO  toil.lib.history:history.py:530 Workflow 1ffdc9ce-0739-403e-a430-a91a37ad8f7d stopped. Success: False 1920s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Demux0/jobstore) 1920s ____________________ TestDocker.testDockerLogs_Demux_Stream ____________________ 1920s [gw0] linux -- Python 3.13.11 /usr/bin/python3.13 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353, in from_call 1920s result: TResult | None = func() 1920s ~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245, in 1920s lambda: runtest_hook(item=item, **kwds), 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 850, in pytest_runtest_call 1920s yield 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 900, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 53, in run_old_style_hookwrapper 1920s return result.get_result() 1920s ~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 103, in get_result 1920s raise exc.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 38, in run_old_style_hookwrapper 1920s res = yield 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall 1920s teardown.throw(exception) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 268, in pytest_runtest_call 1920s return (yield) 1920s ^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179, in pytest_runtest_call 1920s item.runtest() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720, in runtest 1920s self.ihook.pytest_pyfunc_call(pyfuncitem=self) 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__ 1920s return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) 1920s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec 1920s return self._inner_hookexec(hook_name, methods, kwargs, firstresult) 1920s ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall 1920s raise exception 1920s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall 1920s res = hook_impl.function(*args) 1920s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166, in pytest_pyfunc_call 1920s result = testfunction(**testargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 372, in testDockerLogs_Demux_Stream 1920s self.testDockerLogs(tmp_path, stream=True, demux=True) 1920s ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 362, in testDockerLogs 1920s rv = Job.Runner.startToil(A, options) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 2568, in startToil 1920s return toil.start(job) 1920s ~~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1920s return self._runMainLoop(rootJobDescription) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1920s ).run() 1920s ~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1920s raise FailedJobsException( 1920s ...<3 lines>... 1920s ) 1920s toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Demux_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v6 1920s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v6" follows: 1920s =========> 1920s [2026-01-30T07:21:23+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:23+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:23+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v4 1920s [2026-01-30T07:21:25+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v4 1920s [2026-01-30T07:21:25+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:25+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s ----------------------------- Captured stderr call ----------------------------- 1920s [2026-01-30T07:21:19+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 67d6352f-7fae-4969-b88c-efef7895e310 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Demux_Stream0/jobstore 1920s [2026-01-30T07:21:19+0000] [MainThread] [I] [toil.lib.history] Workflow 67d6352f-7fae-4969-b88c-efef7895e310 is a run of 1920s [2026-01-30T07:21:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:19+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1920s [2026-01-30T07:21:19+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:21:21+0000] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run 1920s [2026-01-30T07:21:22+0000] [Thread-46 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker _testDockerLogsFn file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-cvbheaoj. 1920s [2026-01-30T07:21:22+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v1 1920s Exit reason: None 1920s [2026-01-30T07:21:22+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v2 1920s [2026-01-30T07:21:22+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-cvbheaoj" follows: 1920s =========> 1920s [2026-01-30T07:21:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:21+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v1 1920s [2026-01-30T07:21:21+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v1 1920s [2026-01-30T07:21:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:21:22+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v2 with ID kind-_testDockerLogsFn/instance-cvbheaoj to 1 1920s [2026-01-30T07:21:22+0000] [MainThread] [I] [toil.leader] Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:21:26+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-1/popen-gw0/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-cvbheaoj. 1920s [2026-01-30T07:21:26+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v3 1920s Exit reason: None 1920s [2026-01-30T07:21:26+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v5 1920s [2026-01-30T07:21:26+0000] [MainThread] [W] [toil.leader] Log from job "kind-_testDockerLogsFn/instance-cvbheaoj" follows: 1920s =========> 1920s [2026-01-30T07:21:23+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:23+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:23+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v4 1920s [2026-01-30T07:21:25+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v4 1920s [2026-01-30T07:21:25+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:25+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:21:26+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v5 with ID kind-_testDockerLogsFn/instance-cvbheaoj to 0 1920s [2026-01-30T07:21:26+0000] [MainThread] [W] [toil.leader] Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v6 is completely failed 1920s [2026-01-30T07:21:30+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s [2026-01-30T07:21:30+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1920s [2026-01-30T07:21:30+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v6 1920s [2026-01-30T07:21:30+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1920s [2026-01-30T07:21:30+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1920s [2026-01-30T07:21:30+0000] [MainThread] [I] [toil.lib.history] Workflow 67d6352f-7fae-4969-b88c-efef7895e310 stopped. Success: False 1920s [2026-01-30T07:21:30+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Demux_Stream0/jobstore) 1920s ------------------------------ Captured log call ------------------------------- 1920s INFO  toil.lib.history:history.py:369 Recording workflow creation of 67d6352f-7fae-4969-b88c-efef7895e310 in file:/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Demux_Stream0/jobstore 1920s INFO  toil.lib.history:history.py:399 Workflow 67d6352f-7fae-4969-b88c-efef7895e310 is a run of 1920s INFO  toil:__init__.py:480 Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:141 Starting real-time logging. 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s INFO  toil.leader:leader.py:1231 1 jobs are running, 0 jobs are issued and waiting to run 1920s 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-gw0/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-cvbheaoj. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v1 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v2 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-cvbheaoj" follows: 1920s =========> 1920s [2026-01-30T07:21:21+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:21+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:21+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v1 1920s [2026-01-30T07:21:21+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v1) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v1 1920s [2026-01-30T07:21:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v2 with ID kind-_testDockerLogsFn/instance-cvbheaoj to 1 1920s INFO  toil.leader:leader.py:1132 Issued job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s 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-gw0/testDockerLogs_Demux_Stream0/jobstore kind-_testDockerLogsFn/instance-cvbheaoj. 1920s WARNING  toil.leader:leader.py:861 Job failed with exit value 1: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v3 1920s Exit reason: None 1920s WARNING  toil.leader:statsAndLogging.py:98 The job seems to have left a log file, indicating failure: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v5 1920s WARNING  toil.leader:statsAndLogging.py:101 Log from job "kind-_testDockerLogsFn/instance-cvbheaoj" follows: 1920s =========> 1920s [2026-01-30T07:21:23+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:23+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:23+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v4 1920s [2026-01-30T07:21:25+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v4 1920s [2026-01-30T07:21:25+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:25+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s WARNING  toil.job:job.py:1395 Due to failure we are reducing the remaining try count of job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v5 with ID kind-_testDockerLogsFn/instance-cvbheaoj to 0 1920s WARNING  toil.leader:leader.py:643 Job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v6 is completely failed 1920s INFO  toil.jobStores.abstractJobStore:abstractJobStore.py:459 Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s INFO  toil.leader:leader.py:317 Finished toil run with 1 failed jobs. 1920s INFO  toil.leader:leader.py:337 Failed jobs at end of the run: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v6 1920s INFO  toil.realtimeLogger:realtimeLogger.py:183 Stopping real-time logging server. 1920s INFO  toil.realtimeLogger:realtimeLogger.py:187 Joining real-time logging server thread. 1920s INFO  toil.lib.history:history.py:530 Workflow 67d6352f-7fae-4969-b88c-efef7895e310 stopped. Success: False 1920s INFO  toil.common:common.py:1111 Successfully deleted the job store: FileJobStore(/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Demux_Stream0/jobstore) 1920s =========================== short test summary info ============================ 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:603: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:217: Configure AWS credentials to include this test. 1920s 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. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:189: Configure AWS credentials to include this test. 1920s 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. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1115: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1127: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:621: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:825: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:800: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:151: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:160: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:313: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:202: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1467: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1446: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1079: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:450: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:238: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:421: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:405: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:380: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:529: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:264: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:585: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:960: Configure AWS credentials to include this test. 1920s SKIPPED [13] ../../../../usr/lib/python3/dist-packages/toil/test/__init__.py:1139: Configure AWS credentials to include this test. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:32: Consumes unauthenticated Docker Hub pulls if run 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:38: Consumes unauthenticated Docker Hub pulls if run 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:45: Consumes unauthenticated Docker Hub pulls if run 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/src/dockerCheckTest.py:26: Consumes unauthenticated Docker Hub pulls if run 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:731: Install Toil with the 'server' extra to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:646: Install Toil with the 'server' extra to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:697: Install Toil with the 'server' extra to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:706: Install Toil with the 'server' extra to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:685: Install Toil with the 'server' extra to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:676: Install Toil with the 'server' extra to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:721: Install Toil with the 'server' extra to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:619: Install Toil with the 'server' extra to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:600: Install Toil with the 'server' extra to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:668: Install Toil with the 'server' extra to include this test. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s SKIPPED [7] ../../../../usr/lib/python3/dist-packages/_pytest/unittest.py:498: Configure AWS credentials to include this test. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s 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. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:541: Install Toil with the 'server' extra to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:535: Install Toil with the 'server' extra to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:526: Install Toil with the 'server' extra to include this test. 1920s 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. 1920s 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. 1920s 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. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py:255: Install Toil with the 'wdl' extra to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/jobStores/jobStoreTest.py:1568: Configure AWS credentials to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:48: Install Toil with the 'server' extra to include this test. 1920s SKIPPED [3] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:96: Install Toil with the 'server' extra to include this test. 1920s SKIPPED [1] ../../../../usr/lib/python3/dist-packages/toil/test/server/serverTest.py:245: Install Toil with the 'server' extra to include this test. 1920s FAILED lib/dockerTest.py::TestDocker::testDockerClean - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean0/working/test.txt' 1920s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_FORGO - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_FORGO0/working/test.txt' 1920s FAILED docs/scriptsTest.py::ToilDocumentationTest::testDocker - RuntimeError: [2026-01-30T07:19:37+0000] [MainThread] [I] [toil.lib.history] Recording workflow creation of 23938669-3606-4f16-a889-9c47b99ca8d4 in file:/tmp/tmp_4g6ykietutorial_docker 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil.lib.history] Workflow 23938669-3606-4f16-a889-9c47b99ca8d4 is a run of /usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v1 with job batch system ID: 1 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:19:38+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmp_4g6ykietutorial_docker kind-apiDockerCall/instance-5la714qj. 1920s [2026-01-30T07:19:38+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v1 1920s Exit reason: None 1920s [2026-01-30T07:19:38+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v2 1920s [2026-01-30T07:19:38+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-5la714qj" follows: 1920s =========> 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v1 1920s [2026-01-30T07:19:37+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-5la714qj v1) from description 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v1 1920s [2026-01-30T07:19:37+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:37+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:19:38+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v2 with ID kind-apiDockerCall/instance-5la714qj to 1 1920s [2026-01-30T07:19:38+0000] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run 1920s [2026-01-30T07:19:38+0000] [MainThread] [I] [toil.leader] Issued job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v3 with job batch system ID: 2 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False 1920s [2026-01-30T07:19:41+0000] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker apiDockerCall file:/tmp/tmp_4g6ykietutorial_docker kind-apiDockerCall/instance-5la714qj. 1920s [2026-01-30T07:19:41+0000] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v3 1920s Exit reason: None 1920s [2026-01-30T07:19:41+0000] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v5 1920s [2026-01-30T07:19:41+0000] [MainThread] [W] [toil.leader] Log from job "kind-apiDockerCall/instance-5la714qj" follows: 1920s =========> 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v4 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-5la714qj v4) from description 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v4 1920s [2026-01-30T07:19:39+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:39+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s [2026-01-30T07:19:41+0000] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v5 with ID kind-apiDockerCall/instance-5la714qj to 0 1920s [2026-01-30T07:19:41+0000] [MainThread] [W] [toil.leader] Job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v6 is completely failed 1920s [2026-01-30T07:19:44+0000] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///tmp/autopkgtest.cjJpnO/autopkgtest_tmp/build/failed.log... 1920s [2026-01-30T07:19:44+0000] [MainThread] [I] [toil.leader] Finished toil run with 1 failed jobs. 1920s [2026-01-30T07:19:44+0000] [MainThread] [I] [toil.leader] Failed jobs at end of the run: 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v6 1920s [2026-01-30T07:19:44+0000] [MainThread] [I] [toil.realtimeLogger] Stopping real-time logging server. 1920s [2026-01-30T07:19:45+0000] [MainThread] [I] [toil.realtimeLogger] Joining real-time logging server thread. 1920s [2026-01-30T07:19:45+0000] [MainThread] [I] [toil.lib.history] Workflow 23938669-3606-4f16-a889-9c47b99ca8d4 stopped. Success: False 1920s [2026-01-30T07:19:45+0000] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/tmp/tmp_4g6ykietutorial_docker) 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/test/docs/scripts/tutorial_docker.py", line 20, in 1920s toil.start(align) 1920s ~~~~~~~~~~^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1185, in start 1920s return self._runMainLoop(rootJobDescription) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/common.py", line 1795, in _runMainLoop 1920s ).run() 1920s ~~~^^ 1920s File "/usr/lib/python3/dist-packages/toil/leader.py", line 341, in run 1920s raise FailedJobsException( 1920s ...<3 lines>... 1920s ) 1920s toil.exceptions.FailedJobsException: The job store '/tmp/tmp_4g6ykietutorial_docker' contains 1 failed jobs: 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v6 1920s Log from job "'apiDockerCall' kind-apiDockerCall/instance-5la714qj v6" follows: 1920s =========> 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] Working on job 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v4 1920s [2026-01-30T07:19:39+0000] [MainThread] [I] [toil.worker] Loaded body Job('apiDockerCall' kind-apiDockerCall/instance-5la714qj v4) from description 'apiDockerCall' kind-apiDockerCall/instance-5la714qj v4 1920s [2026-01-30T07:19:39+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:19:39+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_STOP - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_STOP0/working/test.txt' 1920s FAILED lib/dockerTest.py::TestDocker::testDockerClean_CRx_RM - FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerClean_CRx_RM0/working/test.txt' 1920s FAILED lib/dockerTest.py::TestDocker::testDockerPipeChain - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerPipeChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v6 1920s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v6" follows: 1920s =========> 1920s [2026-01-30T07:20:07+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:07+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:07+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v4 1920s [2026-01-30T07:20:08+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-cazc6fwq v4 1920s [2026-01-30T07:20:08+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1920s return apiDockerCall( 1920s job, 1920s ...<2 lines>... 1920s privileged=True, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:08+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s FAILED lib/dockerTest.py::TestDocker::testDockerPipeChainErrorDetection - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerPipeChainErrorDetect0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v6 1920s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v6" follows: 1920s =========> 1920s [2026-01-30T07:20:19+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:19+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:19+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v4 1920s [2026-01-30T07:20:20+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-oqfkh7n7 v4 1920s [2026-01-30T07:20:21+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1920s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1920s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:21+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChain - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testNonCachingDockerChain0/jobstore' contains 1 failed jobs: '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v6 1920s Log from job "'_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v6" follows: 1920s =========> 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v4 1920s [2026-01-30T07:20:30+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v4) from description '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr v4 1920s [2026-01-30T07:20:30+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainFn' kind-_testDockerPipeChainFn/instance-1hcrl_qr 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. 1920s [2026-01-30T07:20:30+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 423, in _testDockerPipeChainFn 1920s return apiDockerCall( 1920s job, 1920s ...<2 lines>... 1920s privileged=True, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:30+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s FAILED lib/dockerTest.py::TestDocker::testNonCachingDockerChainErrorDetection - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testNonCachingDockerChainError0/jobstore' contains 1 failed jobs: '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v6 1920s Log from job "'_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v6" follows: 1920s =========> 1920s [2026-01-30T07:20:37+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:37+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:37+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v4 1920s [2026-01-30T07:20:38+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v4) from description '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt v4 1920s [2026-01-30T07:20:38+0000] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job '_testDockerPipeChainErrorFn' kind-_testDockerPipeChainErrorFn/instance-ksq6vyxt 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. 1920s [2026-01-30T07:20:38+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 435, in _testDockerPipeChainErrorFn 1920s apiDockerCall(job, image="quay.io/ucsc_cgl/spooky_test", parameters=parameters) 1920s ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:38+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s FAILED lib/dockerTest.py::TestDocker::testDockerLogs - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v6 1920s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v6" follows: 1920s =========> 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:20:44+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v4 1920s [2026-01-30T07:20:45+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-_k8nu84j v4 1920s [2026-01-30T07:20:45+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:20:45+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Stream - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v6 1920s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v6" follows: 1920s =========> 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v4 1920s [2026-01-30T07:21:03+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-qylgpejb v4 1920s [2026-01-30T07:21:04+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:04+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Demux0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v6 1920s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v6" follows: 1920s =========> 1920s [2026-01-30T07:21:12+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:12+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:12+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v4 1920s [2026-01-30T07:21:13+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-6pkxt67e v4 1920s [2026-01-30T07:21:13+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:13+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s FAILED lib/dockerTest.py::TestDocker::testDockerLogs_Demux_Stream - toil.exceptions.FailedJobsException: The job store '/tmp/pytest-of-ubuntu/pytest-1/popen-gw0/testDockerLogs_Demux_Stream0/jobstore' contains 1 failed jobs: '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v6 1920s Log from job "'_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v6" follows: 1920s =========> 1920s [2026-01-30T07:21:23+0000] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- 1920s [2026-01-30T07:21:23+0000] [MainThread] [I] [toil] Running Toil version 9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c on host autopkgtest. 1920s [2026-01-30T07:21:23+0000] [MainThread] [I] [toil.worker] Working on job '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v4 1920s [2026-01-30T07:21:25+0000] [MainThread] [I] [toil.worker] Loaded body Job('_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v4) from description '_testDockerLogsFn' kind-_testDockerLogsFn/instance-cvbheaoj v4 1920s [2026-01-30T07:21:25+0000] [MainThread] [C] [toil.worker] Worker crashed with traceback: 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s PermissionError: [Errno 13] Permission denied 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 1920s resp = conn.urlopen( 1920s method=request.method, 1920s ...<9 lines>... 1920s chunked=chunked, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 1920s retries = retries.increment( 1920s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 474, in increment 1920s raise reraise(type(error), error, _stacktrace) 1920s ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/urllib3/util/util.py", line 38, in reraise 1920s raise value.with_traceback(tb) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 787, in urlopen 1920s response = self._make_request( 1920s conn, 1920s ...<10 lines>... 1920s **response_kw, 1920s ) 1920s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 493, in _make_request 1920s conn.request( 1920s ~~~~~~~~~~~~^ 1920s method, 1920s ^^^^^^^ 1920s ...<6 lines>... 1920s enforce_content_length=enforce_content_length, 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/urllib3/connection.py", line 494, in request 1920s self.endheaders() 1920s ~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 1920s self._send_output(message_body, encode_chunked=encode_chunked) 1920s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 1920s self.send(msg) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3.13/http/client.py", line 1057, in send 1920s self.connect() 1920s ~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 26, in connect 1920s sock.connect(self.unix_socket) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 1920s urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s During handling of the above exception, another exception occurred: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 223, in _retrieve_server_version 1920s return self.version(api_version=False)["ApiVersion"] 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version 1920s return self._result(self._get(url), json=True) 1920s ~~~~~~~~~^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 44, in inner 1920s return f(self, *args, **kwargs) 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 246, in _get 1920s return self.get(url, **self._set_request_timeout(kwargs)) 1920s ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 602, in get 1920s return self.request("GET", url, **kwargs) 1920s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 1920s resp = self.send(prep, **send_kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 1920s r = adapter.send(request, **kwargs) 1920s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 659, in send 1920s raise ConnectionError(err, request=request) 1920s requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s The above exception was the direct cause of the following exception: 1920s 1920s Traceback (most recent call last): 1920s File "/usr/lib/python3/dist-packages/toil/worker.py", line 595, in workerScript 1920s job._runner( 1920s ~~~~~~~~~~~^ 1920s jobGraph=None, 1920s ^^^^^^^^^^^^^^ 1920s ...<2 lines>... 1920s defer=defer, 1920s ^^^^^^^^^^^^ 1920s ) 1920s ^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3254, in _runner 1920s returnValues = self._run(jobGraph=None, fileStore=fileStore) 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3137, in _run 1920s return self.run(fileStore) 1920s ~~~~~~~~^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/toil/job.py", line 3452, in run 1920s rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) 1920s File "/usr/lib/python3/dist-packages/toil/test/lib/dockerTest.py", line 469, in _testDockerLogsFn 1920s out = apiDockerCall( 1920s job, 1920s ...<8 lines>... 1920s demux=demux, 1920s ) 1920s File "/usr/lib/python3/dist-packages/toil/lib/docker.py", line 397, in apiDockerCall 1920s client = docker.from_env(version="auto", timeout=timeout) # type: ignore[attr-defined] 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 94, in from_env 1920s return cls( 1920s timeout=timeout, 1920s ...<3 lines>... 1920s **kwargs_from_env(**kwargs) 1920s ) 1920s File "/usr/lib/python3/dist-packages/docker/client.py", line 45, in __init__ 1920s self.api = APIClient(*args, **kwargs) 1920s ~~~~~~~~~^^^^^^^^^^^^^^^^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 207, in __init__ 1920s self._version = self._retrieve_server_version() 1920s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1920s File "/usr/lib/python3/dist-packages/docker/api/client.py", line 230, in _retrieve_server_version 1920s raise DockerException( 1920s f'Error while fetching server API version: {e}' 1920s ) from e 1920s docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied')) 1920s 1920s [2026-01-30T07:21:25+0000] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host autopkgtest 1920s <========= 1920s ERROR src/importExportFileTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py'. 1920s Hint: make sure your test modules/packages have valid Python names. 1920s Traceback: 1920s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 1920s mod = import_path( 1920s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 1920s importlib.import_module(module_name) 1920s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1920s return _bootstrap._gcd_import(name[level:], package, level) 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s :1387: in _gcd_import 1920s ??? 1920s :1360: in _find_and_load 1920s ??? 1920s :1331: in _find_and_load_unlocked 1920s ??? 1920s :935: in _load_unlocked 1920s ??? 1920s :1023: in exec_module 1920s ??? 1920s :488: in _call_with_frames_removed 1920s ??? 1920s /usr/lib/python3/dist-packages/toil/test/src/importExportFileTest.py:30: in 1920s from pytest_subtests import SubTests 1920s E ModuleNotFoundError: No module named 'pytest_subtests' 1920s ERROR src/jobEncapsulationTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py'. 1920s Hint: make sure your test modules/packages have valid Python names. 1920s Traceback: 1920s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 1920s mod = import_path( 1920s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 1920s importlib.import_module(module_name) 1920s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1920s return _bootstrap._gcd_import(name[level:], package, level) 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s :1387: in _gcd_import 1920s ??? 1920s :1360: in _find_and_load 1920s ??? 1920s :1331: in _find_and_load_unlocked 1920s ??? 1920s :935: in _load_unlocked 1920s ??? 1920s :1023: in exec_module 1920s ??? 1920s :488: in _call_with_frames_removed 1920s ??? 1920s /usr/lib/python3/dist-packages/toil/test/src/jobEncapsulationTest.py:17: in 1920s from toil.test.src.jobTest import fn1Test 1920s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 1920s from pytest_subtests import SubTests 1920s E ModuleNotFoundError: No module named 'pytest_subtests' 1920s ERROR src/jobTest.py - ImportError while importing test module '/usr/lib/python3/dist-packages/toil/test/src/jobTest.py'. 1920s Hint: make sure your test modules/packages have valid Python names. 1920s Traceback: 1920s /usr/lib/python3/dist-packages/_pytest/python.py:507: in importtestmodule 1920s mod = import_path( 1920s /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path 1920s importlib.import_module(module_name) 1920s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1920s return _bootstrap._gcd_import(name[level:], package, level) 1920s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1920s :1387: in _gcd_import 1920s ??? 1920s :1360: in _find_and_load 1920s ??? 1920s :1331: in _find_and_load_unlocked 1920s ??? 1920s :935: in _load_unlocked 1920s ??? 1920s :1023: in exec_module 1920s ??? 1920s :488: in _call_with_frames_removed 1920s ??? 1920s /usr/lib/python3/dist-packages/toil/test/src/jobTest.py:37: in 1920s from pytest_subtests import SubTests 1920s E ModuleNotFoundError: No module named 'pytest_subtests' 1920s = 13 failed, 226 passed, 136 skipped, 3 errors, 24 subtests passed in 587.71s (0:09:47) = 1920s E: pybuild pybuild:483: test: plugin pyproject failed with: exit code=1: cd /tmp/autopkgtest.cjJpnO/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 1920s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13 1921s make: *** [/tmp/yD45YlVIwY/run:4: pybuild-autopkgtest] Error 25 1921s pybuild-autopkgtest: error: /tmp/yD45YlVIwY/run pybuild-autopkgtest returned exit code 2 1921s autopkgtest [07:26:55]: test pybuild-autopkgtest: -----------------------] 1922s pybuild-autopkgtest FAIL non-zero exit status 25 1922s autopkgtest [07:26:56]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 1923s autopkgtest [07:26:57]: @@@@@@@@@@@@@@@@@@@@ summary 1923s smoke-test PASS (superficial) 1923s pybuild-autopkgtest FAIL non-zero exit status 25