0s autopkgtest [05:42:48]: starting date and time: 2026-01-30 05:42:48+0000 0s autopkgtest [05:42:48]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [05:42:48]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1tf4fs8c/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src: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 -- lxd -r lxd-armhf-10.145.243.61 lxd-armhf-10.145.243.61:autopkgtest/ubuntu/resolute/armhf 21s autopkgtest [05:43:09]: testbed dpkg architecture: armhf 23s autopkgtest [05:43:11]: testbed apt version: 3.1.14 29s autopkgtest [05:43:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 31s autopkgtest [05:43:19]: testbed release detected to be: None 40s autopkgtest [05:43:28]: updating testbed package index (apt update) 42s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 42s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 42s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 42s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 42s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 42s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [103 kB] 42s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [33.0 kB] 42s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1600 kB] 43s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [118 kB] 43s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1078 kB] 43s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [10.8 kB] 43s Get:12 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.3 MB] 44s Get:13 http://ftpmaster.internal/ubuntu resolute/main Sources [1406 kB] 44s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1374 kB] 44s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.0 MB] 48s Fetched 42.3 MB in 6s (7090 kB/s) 49s Reading package lists... 56s autopkgtest [05:43:44]: upgrading testbed (apt dist-upgrade and autopurge) 58s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Calculating upgrade... 60s The following packages will be upgraded: 60s bzip2 inetutils-telnet libbz2-1.0 libsqlite3-0 telnet 60s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s Need to get 775 kB of archives. 60s After this operation, 2048 B of additional disk space will be used. 60s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf bzip2 armhf 1.0.8-6build2 [33.8 kB] 60s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libbz2-1.0 armhf 1.0.8-6build2 [31.6 kB] 60s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libsqlite3-0 armhf 3.46.1-9 [609 kB] 60s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf inetutils-telnet armhf 2:2.7-2ubuntu1 [96.8 kB] 60s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf telnet all 0.17+2.7-2ubuntu1 [3636 B] 61s Fetched 775 kB in 1s (1339 kB/s) 61s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 66512 files and directories currently installed.) 61s Preparing to unpack .../bzip2_1.0.8-6build2_armhf.deb ... 61s Unpacking bzip2 (1.0.8-6build2) over (1.0.8-6build1) ... 61s Preparing to unpack .../libbz2-1.0_1.0.8-6build2_armhf.deb ... 61s Unpacking libbz2-1.0:armhf (1.0.8-6build2) over (1.0.8-6build1) ... 61s Setting up libbz2-1.0:armhf (1.0.8-6build2) ... 61s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 66512 files and directories currently installed.) 61s Preparing to unpack .../libsqlite3-0_3.46.1-9_armhf.deb ... 61s Unpacking libsqlite3-0:armhf (3.46.1-9) over (3.46.1-8) ... 61s Preparing to unpack .../inetutils-telnet_2%3a2.7-2ubuntu1_armhf.deb ... 61s Unpacking inetutils-telnet (2:2.7-2ubuntu1) over (2:2.6-4ubuntu1) ... 61s Preparing to unpack .../telnet_0.17+2.7-2ubuntu1_all.deb ... 61s Unpacking telnet (0.17+2.7-2ubuntu1) over (0.17+2.6-4ubuntu1) ... 61s Setting up libsqlite3-0:armhf (3.46.1-9) ... 61s Setting up inetutils-telnet (2:2.7-2ubuntu1) ... 61s Setting up bzip2 (1.0.8-6build2) ... 61s Setting up telnet (0.17+2.7-2ubuntu1) ... 61s Processing triggers for man-db (2.13.1-1) ... 62s Processing triggers for libc-bin (2.42-2ubuntu4) ... 64s Reading package lists... 65s Building dependency tree... 65s Reading state information... 65s Solving dependencies... 66s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s autopkgtest [05:43:56]: rebooting testbed after setup commands that affected boot 114s autopkgtest [05:44:42]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 152s autopkgtest [05:45:20]: @@@@@@@@@@@@@@@@@@@@ apt-source toil 164s Get:1 http://ftpmaster.internal/ubuntu resolute/universe toil 9.1.0-1 (dsc) [2872 B] 164s Get:2 http://ftpmaster.internal/ubuntu resolute/universe toil 9.1.0-1 (tar) [7876 kB] 164s Get:3 http://ftpmaster.internal/ubuntu resolute/universe toil 9.1.0-1 (diff) [17.1 kB] 164s gpgv: Signature made Fri Oct 17 09:42:43 2025 UTC 164s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 164s gpgv: issuer "crusoe@debian.org" 164s gpgv: Can't check signature: No public key 164s dpkg-source: warning: cannot verify inline signature for ./toil_9.1.0-1.dsc: no acceptable signature found 164s autopkgtest [05:45:32]: testing package toil version 9.1.0-1 167s pybuild-autopkgtest SKIP Test declares architecture as not supported: armhf 167s autopkgtest [05:45:35]: build not needed 170s autopkgtest [05:45:38]: test smoke-test: preparing testbed 170s pybuild-autopkgtest SKIP Test declares architecture as not supported: armhf 172s Reading package lists... 173s Building dependency tree... 173s Reading state information... 173s Solving dependencies... 174s The following NEW packages will be installed: 174s cwl-upgrader cwltool fontconfig fontconfig-config fonts-dejavu-core 174s fonts-dejavu-mono fonts-glyphicons-halflings graphviz libaom3 libcairo2 174s libcdt6 libcgraph8 libdatrie1 libde265-0 libdeflate0 libfontconfig1 174s libfreetype6 libgd3 libgomp1 libgraphite2-3 libgvc7 libgvplugin-gd8 174s libgvplugin-pango8 libgvpr2 libharfbuzz0b libheif-plugin-aomdec 174s libheif-plugin-libde265 libheif1 libimagequant0 libjbig0 libjpeg-turbo8 174s libjpeg8 libjs-bootstrap liblerc4 libltdl7 libpango-1.0-0 174s libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpixman-1-0 174s libsharpyuv0 libthai-data libthai0 libtiff6 libwebp7 libxcb-render0 174s libxcb-shm0 libxdot4 libxpm4 libxrender1 libxslt1.1 python3-arcp 174s python3-argcomplete python3-blessed python3-cachecontrol python3-coloredlogs 174s python3-configargparse python3-cwl-utils python3-dill python3-docker 174s python3-enlighten python3-filelock python3-humanfriendly python3-lxml 174s python3-mistune python3-msgpack python3-mypy-extensions python3-networkx 174s python3-prefixed python3-prompt-toolkit python3-prov python3-psutil 174s python3-pubsub python3-pydot python3-rdflib python3-rich-argparse 174s python3-ruamel.yaml python3-ruamel.yaml.clib python3-schema-salad 174s python3-spython python3-wcwidth toil 179s 0 upgraded, 82 newly installed, 0 to remove and 0 not upgraded. 179s Need to get 27.9 MB of archives. 179s After this operation, 160 MB of additional disk space will be used. 179s Get:1 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-ruamel.yaml.clib armhf 0.2.15+ds-1 [183 kB] 179s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf python3-ruamel.yaml all 0.18.10+ds-1build1 [127 kB] 179s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf python3-msgpack armhf 1.1.2-1 [107 kB] 179s Get:4 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-cachecontrol all 0.14.3-1 [18.7 kB] 179s Get:5 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-mistune all 3.1.4-1 [35.0 kB] 179s Get:6 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-mypy-extensions all 1.1.0-1 [6716 B] 179s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-rdflib all 7.4.0-1 [431 kB] 180s Get:8 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-filelock all 3.20.3-1 [13.5 kB] 180s Get:9 http://ftpmaster.internal/ubuntu resolute/universe armhf fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 180s Get:10 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 180s Get:11 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-schema-salad armhf 8.9.20251102115403-1 [1966 kB] 180s Get:12 http://ftpmaster.internal/ubuntu resolute/universe armhf cwl-upgrader all 1.2.14-1 [16.6 kB] 180s Get:13 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-argcomplete all 3.6.3-1 [36.1 kB] 180s Get:14 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-humanfriendly all 10.0-6build1 [70.9 kB] 180s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-coloredlogs all 15.0.1-1build1 [38.4 kB] 180s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-cwl-utils all 0.40-1 [140 kB] 180s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libxslt1.1 armhf 1.1.43-0.3 [146 kB] 180s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf python3-lxml armhf 6.0.2-1 [2260 kB] 180s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf python3-networkx all 3.2.1-4ubuntu2 [11.8 MB] 181s Get:20 http://ftpmaster.internal/ubuntu resolute/universe armhf libcdt6 armhf 14.1.1-2ubuntu2 [17.3 kB] 181s Get:21 http://ftpmaster.internal/ubuntu resolute/universe armhf libcgraph8 armhf 14.1.1-2ubuntu2 [50.5 kB] 181s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libltdl7 armhf 2.5.4-9 [40.4 kB] 181s Get:23 http://ftpmaster.internal/ubuntu resolute/universe armhf libpathplan4 armhf 14.1.1-2ubuntu2 [28.1 kB] 181s Get:24 http://ftpmaster.internal/ubuntu resolute/universe armhf libxdot4 armhf 14.1.1-2ubuntu2 [21.7 kB] 181s Get:25 http://ftpmaster.internal/ubuntu resolute/universe armhf libgvc7 armhf 14.1.1-2ubuntu2 [341 kB] 181s Get:26 http://ftpmaster.internal/ubuntu resolute/universe armhf libgvpr2 armhf 14.1.1-2ubuntu2 [117 kB] 181s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.14.1+dfsg-2 [345 kB] 181s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-mono all 2.37-8build1 [502 kB] 181s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-core all 2.37-8build1 [834 kB] 181s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.17.1-3ubuntu1 [38.5 kB] 181s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libfontconfig1 armhf 2.17.1-3ubuntu1 [117 kB] 181s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libpixman-1-0 armhf 0.46.4-1 [196 kB] 181s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-render0 armhf 1.17.0-2ubuntu1 [15.5 kB] 181s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-shm0 armhf 1.17.0-2ubuntu1 [5956 B] 181s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 181s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libcairo2 armhf 1.18.4-3 [489 kB] 181s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1build1 [16.3 kB] 181s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libaom3 armhf 3.13.1-2 [1258 kB] 181s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libheif-plugin-aomdec armhf 1.21.2-1 [13.0 kB] 181s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf libde265-0 armhf 1.0.16-1build1 [159 kB] 181s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf libheif-plugin-libde265 armhf 1.21.2-1 [13.6 kB] 181s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf libheif1 armhf 1.21.2-1 [597 kB] 181s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-12ubuntu1 [129 kB] 181s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 181s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu2 [127 kB] 181s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 181s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 181s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu3 [25.3 kB] 181s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu2 [162 kB] 181s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1build1 [189 kB] 181s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 181s Get:52 http://ftpmaster.internal/ubuntu resolute/main armhf libxpm4 armhf 1:3.5.17-1build3 [31.1 kB] 181s Get:53 http://ftpmaster.internal/ubuntu resolute/main armhf libgd3 armhf 2.3.3-13ubuntu1 [109 kB] 181s Get:54 http://ftpmaster.internal/ubuntu resolute/universe armhf libgvplugin-gd8 armhf 14.1.1-2ubuntu2 [22.7 kB] 181s Get:55 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig armhf 2.17.1-3ubuntu1 [180 kB] 181s Get:56 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-11ubuntu1 [65.2 kB] 181s Get:57 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.3.1-1 [501 kB] 181s Get:58 http://ftpmaster.internal/ubuntu resolute/main armhf libthai-data all 0.1.30-1 [155 kB] 181s Get:59 http://ftpmaster.internal/ubuntu resolute/main armhf libdatrie1 armhf 0.2.14-1 [16.4 kB] 181s Get:60 http://ftpmaster.internal/ubuntu resolute/main armhf libthai0 armhf 0.1.30-1 [15.4 kB] 181s Get:61 http://ftpmaster.internal/ubuntu resolute/main armhf libpango-1.0-0 armhf 1.57.0-1 [218 kB] 181s Get:62 http://ftpmaster.internal/ubuntu resolute/main armhf libpangoft2-1.0-0 armhf 1.57.0-1 [45.2 kB] 181s Get:63 http://ftpmaster.internal/ubuntu resolute/main armhf libpangocairo-1.0-0 armhf 1.57.0-1 [25.3 kB] 181s Get:64 http://ftpmaster.internal/ubuntu resolute/universe armhf libgvplugin-pango8 armhf 14.1.1-2ubuntu2 [26.3 kB] 181s Get:65 http://ftpmaster.internal/ubuntu resolute/universe armhf graphviz armhf 14.1.1-2ubuntu2 [58.3 kB] 181s Get:66 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pydot all 4.0.1-1 [35.8 kB] 181s Get:67 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-prov all 2.1.1-1 [101 kB] 181s Get:68 http://ftpmaster.internal/ubuntu resolute/main armhf python3-psutil armhf 7.1.0-1ubuntu1 [189 kB] 181s Get:69 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-rich-argparse all 1.6.0-2 [17.2 kB] 181s Get:70 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-spython all 0.3.13-2build1 [56.4 kB] 181s Get:71 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-arcp all 0.2.1-7build1 [14.1 kB] 181s Get:72 http://ftpmaster.internal/ubuntu resolute/universe armhf cwltool all 3.1.20251031082601-1 [533 kB] 181s Get:73 http://ftpmaster.internal/ubuntu resolute/main armhf python3-wcwidth all 0.2.14+dfsg1-1build1 [26.5 kB] 181s Get:74 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-blessed all 1.21.0-1 [50.4 kB] 181s Get:75 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-configargparse all 1.7-2 [31.7 kB] 181s Get:76 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-dill all 0.4.0-1 [84.8 kB] 181s Get:77 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-docker all 7.1.0-2ubuntu1 [91.0 kB] 181s Get:78 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-prefixed all 0.7.0-1build1 [8352 B] 181s Get:79 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-enlighten armhf 1.11.2-1build1 [42.4 kB] 181s Get:80 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-prompt-toolkit all 3.0.52-2 [258 kB] 181s Get:81 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pubsub all 4.0.3-7build1 [45.0 kB] 181s Get:82 http://ftpmaster.internal/ubuntu resolute/universe armhf toil all 9.1.0-1 [1104 kB] 182s Fetched 27.9 MB in 8s (3522 kB/s) 182s Selecting previously unselected package python3-ruamel.yaml.clib. 182s (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 ... 66512 files and directories currently installed.) 182s Preparing to unpack .../00-python3-ruamel.yaml.clib_0.2.15+ds-1_armhf.deb ... 182s Unpacking python3-ruamel.yaml.clib (0.2.15+ds-1) ... 182s Selecting previously unselected package python3-ruamel.yaml. 182s Preparing to unpack .../01-python3-ruamel.yaml_0.18.10+ds-1build1_all.deb ... 182s Unpacking python3-ruamel.yaml (0.18.10+ds-1build1) ... 182s Selecting previously unselected package python3-msgpack. 182s Preparing to unpack .../02-python3-msgpack_1.1.2-1_armhf.deb ... 182s Unpacking python3-msgpack (1.1.2-1) ... 182s Selecting previously unselected package python3-cachecontrol. 182s Preparing to unpack .../03-python3-cachecontrol_0.14.3-1_all.deb ... 182s Unpacking python3-cachecontrol (0.14.3-1) ... 182s Selecting previously unselected package python3-mistune. 183s Preparing to unpack .../04-python3-mistune_3.1.4-1_all.deb ... 183s Unpacking python3-mistune (3.1.4-1) ... 183s Selecting previously unselected package python3-mypy-extensions. 183s Preparing to unpack .../05-python3-mypy-extensions_1.1.0-1_all.deb ... 183s Unpacking python3-mypy-extensions (1.1.0-1) ... 183s Selecting previously unselected package python3-rdflib. 183s Preparing to unpack .../06-python3-rdflib_7.4.0-1_all.deb ... 183s Unpacking python3-rdflib (7.4.0-1) ... 183s Selecting previously unselected package python3-filelock. 183s Preparing to unpack .../07-python3-filelock_3.20.3-1_all.deb ... 183s Unpacking python3-filelock (3.20.3-1) ... 183s Selecting previously unselected package fonts-glyphicons-halflings. 183s Preparing to unpack .../08-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 183s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 183s Selecting previously unselected package libjs-bootstrap. 183s Preparing to unpack .../09-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 183s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 183s Selecting previously unselected package python3-schema-salad. 183s Preparing to unpack .../10-python3-schema-salad_8.9.20251102115403-1_armhf.deb ... 183s Unpacking python3-schema-salad (8.9.20251102115403-1) ... 183s Selecting previously unselected package cwl-upgrader. 183s Preparing to unpack .../11-cwl-upgrader_1.2.14-1_all.deb ... 183s Unpacking cwl-upgrader (1.2.14-1) ... 183s Selecting previously unselected package python3-argcomplete. 183s Preparing to unpack .../12-python3-argcomplete_3.6.3-1_all.deb ... 183s Unpacking python3-argcomplete (3.6.3-1) ... 183s Selecting previously unselected package python3-humanfriendly. 183s Preparing to unpack .../13-python3-humanfriendly_10.0-6build1_all.deb ... 183s Unpacking python3-humanfriendly (10.0-6build1) ... 183s Selecting previously unselected package python3-coloredlogs. 183s Preparing to unpack .../14-python3-coloredlogs_15.0.1-1build1_all.deb ... 183s Unpacking python3-coloredlogs (15.0.1-1build1) ... 183s Selecting previously unselected package python3-cwl-utils. 183s Preparing to unpack .../15-python3-cwl-utils_0.40-1_all.deb ... 183s Unpacking python3-cwl-utils (0.40-1) ... 183s Selecting previously unselected package libxslt1.1:armhf. 183s Preparing to unpack .../16-libxslt1.1_1.1.43-0.3_armhf.deb ... 183s Unpacking libxslt1.1:armhf (1.1.43-0.3) ... 183s Selecting previously unselected package python3-lxml:armhf. 183s Preparing to unpack .../17-python3-lxml_6.0.2-1_armhf.deb ... 183s Unpacking python3-lxml:armhf (6.0.2-1) ... 184s Selecting previously unselected package python3-networkx. 184s Preparing to unpack .../18-python3-networkx_3.2.1-4ubuntu2_all.deb ... 184s Unpacking python3-networkx (3.2.1-4ubuntu2) ... 184s Selecting previously unselected package libcdt6:armhf. 184s Preparing to unpack .../19-libcdt6_14.1.1-2ubuntu2_armhf.deb ... 184s Unpacking libcdt6:armhf (14.1.1-2ubuntu2) ... 184s Selecting previously unselected package libcgraph8:armhf. 184s Preparing to unpack .../20-libcgraph8_14.1.1-2ubuntu2_armhf.deb ... 184s Unpacking libcgraph8:armhf (14.1.1-2ubuntu2) ... 184s Selecting previously unselected package libltdl7:armhf. 184s Preparing to unpack .../21-libltdl7_2.5.4-9_armhf.deb ... 184s Unpacking libltdl7:armhf (2.5.4-9) ... 184s Selecting previously unselected package libpathplan4:armhf. 184s Preparing to unpack .../22-libpathplan4_14.1.1-2ubuntu2_armhf.deb ... 184s Unpacking libpathplan4:armhf (14.1.1-2ubuntu2) ... 184s Selecting previously unselected package libxdot4:armhf. 184s Preparing to unpack .../23-libxdot4_14.1.1-2ubuntu2_armhf.deb ... 184s Unpacking libxdot4:armhf (14.1.1-2ubuntu2) ... 185s Selecting previously unselected package libgvc7:armhf. 185s Preparing to unpack .../24-libgvc7_14.1.1-2ubuntu2_armhf.deb ... 185s Unpacking libgvc7:armhf (14.1.1-2ubuntu2) ... 185s Selecting previously unselected package libgvpr2:armhf. 185s Preparing to unpack .../25-libgvpr2_14.1.1-2ubuntu2_armhf.deb ... 185s Unpacking libgvpr2:armhf (14.1.1-2ubuntu2) ... 185s Selecting previously unselected package libfreetype6:armhf. 185s Preparing to unpack .../26-libfreetype6_2.14.1+dfsg-2_armhf.deb ... 185s Unpacking libfreetype6:armhf (2.14.1+dfsg-2) ... 185s Selecting previously unselected package fonts-dejavu-mono. 185s Preparing to unpack .../27-fonts-dejavu-mono_2.37-8build1_all.deb ... 185s Unpacking fonts-dejavu-mono (2.37-8build1) ... 185s Selecting previously unselected package fonts-dejavu-core. 185s Preparing to unpack .../28-fonts-dejavu-core_2.37-8build1_all.deb ... 185s Unpacking fonts-dejavu-core (2.37-8build1) ... 185s Selecting previously unselected package fontconfig-config. 185s Preparing to unpack .../29-fontconfig-config_2.17.1-3ubuntu1_armhf.deb ... 185s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 185s Selecting previously unselected package libfontconfig1:armhf. 185s Preparing to unpack .../30-libfontconfig1_2.17.1-3ubuntu1_armhf.deb ... 185s Unpacking libfontconfig1:armhf (2.17.1-3ubuntu1) ... 185s Selecting previously unselected package libpixman-1-0:armhf. 185s Preparing to unpack .../31-libpixman-1-0_0.46.4-1_armhf.deb ... 185s Unpacking libpixman-1-0:armhf (0.46.4-1) ... 185s Selecting previously unselected package libxcb-render0:armhf. 185s Preparing to unpack .../32-libxcb-render0_1.17.0-2ubuntu1_armhf.deb ... 185s Unpacking libxcb-render0:armhf (1.17.0-2ubuntu1) ... 185s Selecting previously unselected package libxcb-shm0:armhf. 185s Preparing to unpack .../33-libxcb-shm0_1.17.0-2ubuntu1_armhf.deb ... 185s Unpacking libxcb-shm0:armhf (1.17.0-2ubuntu1) ... 185s Selecting previously unselected package libxrender1:armhf. 185s Preparing to unpack .../34-libxrender1_1%3a0.9.12-1_armhf.deb ... 185s Unpacking libxrender1:armhf (1:0.9.12-1) ... 185s Selecting previously unselected package libcairo2:armhf. 185s Preparing to unpack .../35-libcairo2_1.18.4-3_armhf.deb ... 185s Unpacking libcairo2:armhf (1.18.4-3) ... 185s Selecting previously unselected package libsharpyuv0:armhf. 186s Preparing to unpack .../36-libsharpyuv0_1.5.0-0.1build1_armhf.deb ... 186s Unpacking libsharpyuv0:armhf (1.5.0-0.1build1) ... 186s Selecting previously unselected package libaom3:armhf. 186s Preparing to unpack .../37-libaom3_3.13.1-2_armhf.deb ... 186s Unpacking libaom3:armhf (3.13.1-2) ... 186s Selecting previously unselected package libheif-plugin-aomdec:armhf. 186s Preparing to unpack .../38-libheif-plugin-aomdec_1.21.2-1_armhf.deb ... 186s Unpacking libheif-plugin-aomdec:armhf (1.21.2-1) ... 186s Selecting previously unselected package libde265-0:armhf. 186s Preparing to unpack .../39-libde265-0_1.0.16-1build1_armhf.deb ... 186s Unpacking libde265-0:armhf (1.0.16-1build1) ... 186s Selecting previously unselected package libheif-plugin-libde265:armhf. 186s Preparing to unpack .../40-libheif-plugin-libde265_1.21.2-1_armhf.deb ... 186s Unpacking libheif-plugin-libde265:armhf (1.21.2-1) ... 186s Selecting previously unselected package libheif1:armhf. 186s Preparing to unpack .../41-libheif1_1.21.2-1_armhf.deb ... 186s Unpacking libheif1:armhf (1.21.2-1) ... 186s Selecting previously unselected package libgomp1:armhf. 186s Preparing to unpack .../42-libgomp1_15.2.0-12ubuntu1_armhf.deb ... 186s Unpacking libgomp1:armhf (15.2.0-12ubuntu1) ... 186s Selecting previously unselected package libimagequant0:armhf. 186s Preparing to unpack .../43-libimagequant0_2.18.0-1build1_armhf.deb ... 186s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 186s Selecting previously unselected package libjpeg-turbo8:armhf. 186s Preparing to unpack .../44-libjpeg-turbo8_2.1.5-4ubuntu2_armhf.deb ... 186s Unpacking libjpeg-turbo8:armhf (2.1.5-4ubuntu2) ... 186s Selecting previously unselected package libjpeg8:armhf. 186s Preparing to unpack .../45-libjpeg8_8c-2ubuntu11_armhf.deb ... 186s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 186s Selecting previously unselected package libdeflate0:armhf. 186s Preparing to unpack .../46-libdeflate0_1.23-2_armhf.deb ... 186s Unpacking libdeflate0:armhf (1.23-2) ... 186s Selecting previously unselected package libjbig0:armhf. 186s Preparing to unpack .../47-libjbig0_2.1-6.1ubuntu3_armhf.deb ... 186s Unpacking libjbig0:armhf (2.1-6.1ubuntu3) ... 186s Selecting previously unselected package liblerc4:armhf. 186s Preparing to unpack .../48-liblerc4_4.0.0+ds-5ubuntu2_armhf.deb ... 186s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 186s Selecting previously unselected package libwebp7:armhf. 186s Preparing to unpack .../49-libwebp7_1.5.0-0.1build1_armhf.deb ... 186s Unpacking libwebp7:armhf (1.5.0-0.1build1) ... 186s Selecting previously unselected package libtiff6:armhf. 186s Preparing to unpack .../50-libtiff6_4.7.0-3ubuntu3_armhf.deb ... 186s Unpacking libtiff6:armhf (4.7.0-3ubuntu3) ... 186s Selecting previously unselected package libxpm4:armhf. 186s Preparing to unpack .../51-libxpm4_1%3a3.5.17-1build3_armhf.deb ... 186s Unpacking libxpm4:armhf (1:3.5.17-1build3) ... 186s Selecting previously unselected package libgd3:armhf. 186s Preparing to unpack .../52-libgd3_2.3.3-13ubuntu1_armhf.deb ... 186s Unpacking libgd3:armhf (2.3.3-13ubuntu1) ... 186s Selecting previously unselected package libgvplugin-gd8:armhf. 186s Preparing to unpack .../53-libgvplugin-gd8_14.1.1-2ubuntu2_armhf.deb ... 186s Unpacking libgvplugin-gd8:armhf (14.1.1-2ubuntu2) ... 186s Selecting previously unselected package fontconfig. 186s Preparing to unpack .../54-fontconfig_2.17.1-3ubuntu1_armhf.deb ... 186s Unpacking fontconfig (2.17.1-3ubuntu1) ... 186s Selecting previously unselected package libgraphite2-3:armhf. 186s Preparing to unpack .../55-libgraphite2-3_1.3.14-11ubuntu1_armhf.deb ... 186s Unpacking libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 186s Selecting previously unselected package libharfbuzz0b:armhf. 186s Preparing to unpack .../56-libharfbuzz0b_12.3.1-1_armhf.deb ... 186s Unpacking libharfbuzz0b:armhf (12.3.1-1) ... 186s Selecting previously unselected package libthai-data. 186s Preparing to unpack .../57-libthai-data_0.1.30-1_all.deb ... 186s Unpacking libthai-data (0.1.30-1) ... 186s Selecting previously unselected package libdatrie1:armhf. 187s Preparing to unpack .../58-libdatrie1_0.2.14-1_armhf.deb ... 187s Unpacking libdatrie1:armhf (0.2.14-1) ... 187s Selecting previously unselected package libthai0:armhf. 187s Preparing to unpack .../59-libthai0_0.1.30-1_armhf.deb ... 187s Unpacking libthai0:armhf (0.1.30-1) ... 187s Selecting previously unselected package libpango-1.0-0:armhf. 187s Preparing to unpack .../60-libpango-1.0-0_1.57.0-1_armhf.deb ... 187s Unpacking libpango-1.0-0:armhf (1.57.0-1) ... 187s Selecting previously unselected package libpangoft2-1.0-0:armhf. 187s Preparing to unpack .../61-libpangoft2-1.0-0_1.57.0-1_armhf.deb ... 187s Unpacking libpangoft2-1.0-0:armhf (1.57.0-1) ... 187s Selecting previously unselected package libpangocairo-1.0-0:armhf. 187s Preparing to unpack .../62-libpangocairo-1.0-0_1.57.0-1_armhf.deb ... 187s Unpacking libpangocairo-1.0-0:armhf (1.57.0-1) ... 187s Selecting previously unselected package libgvplugin-pango8:armhf. 187s Preparing to unpack .../63-libgvplugin-pango8_14.1.1-2ubuntu2_armhf.deb ... 187s Unpacking libgvplugin-pango8:armhf (14.1.1-2ubuntu2) ... 187s Selecting previously unselected package graphviz. 187s Preparing to unpack .../64-graphviz_14.1.1-2ubuntu2_armhf.deb ... 187s Unpacking graphviz (14.1.1-2ubuntu2) ... 187s Selecting previously unselected package python3-pydot. 187s Preparing to unpack .../65-python3-pydot_4.0.1-1_all.deb ... 187s Unpacking python3-pydot (4.0.1-1) ... 187s Selecting previously unselected package python3-prov. 187s Preparing to unpack .../66-python3-prov_2.1.1-1_all.deb ... 187s Unpacking python3-prov (2.1.1-1) ... 187s Selecting previously unselected package python3-psutil. 187s Preparing to unpack .../67-python3-psutil_7.1.0-1ubuntu1_armhf.deb ... 187s Unpacking python3-psutil (7.1.0-1ubuntu1) ... 187s Selecting previously unselected package python3-rich-argparse. 187s Preparing to unpack .../68-python3-rich-argparse_1.6.0-2_all.deb ... 187s Unpacking python3-rich-argparse (1.6.0-2) ... 187s Selecting previously unselected package python3-spython. 187s Preparing to unpack .../69-python3-spython_0.3.13-2build1_all.deb ... 187s Unpacking python3-spython (0.3.13-2build1) ... 187s Selecting previously unselected package python3-arcp. 187s Preparing to unpack .../70-python3-arcp_0.2.1-7build1_all.deb ... 187s Unpacking python3-arcp (0.2.1-7build1) ... 187s Selecting previously unselected package cwltool. 187s Preparing to unpack .../71-cwltool_3.1.20251031082601-1_all.deb ... 187s Unpacking cwltool (3.1.20251031082601-1) ... 188s Selecting previously unselected package python3-wcwidth. 188s Preparing to unpack .../72-python3-wcwidth_0.2.14+dfsg1-1build1_all.deb ... 188s Unpacking python3-wcwidth (0.2.14+dfsg1-1build1) ... 188s Selecting previously unselected package python3-blessed. 188s Preparing to unpack .../73-python3-blessed_1.21.0-1_all.deb ... 188s Unpacking python3-blessed (1.21.0-1) ... 188s Selecting previously unselected package python3-configargparse. 188s Preparing to unpack .../74-python3-configargparse_1.7-2_all.deb ... 188s Unpacking python3-configargparse (1.7-2) ... 188s Selecting previously unselected package python3-dill. 188s Preparing to unpack .../75-python3-dill_0.4.0-1_all.deb ... 188s Unpacking python3-dill (0.4.0-1) ... 188s Selecting previously unselected package python3-docker. 188s Preparing to unpack .../76-python3-docker_7.1.0-2ubuntu1_all.deb ... 188s Unpacking python3-docker (7.1.0-2ubuntu1) ... 188s Selecting previously unselected package python3-prefixed. 188s Preparing to unpack .../77-python3-prefixed_0.7.0-1build1_all.deb ... 188s Unpacking python3-prefixed (0.7.0-1build1) ... 188s Selecting previously unselected package python3-enlighten. 188s Preparing to unpack .../78-python3-enlighten_1.11.2-1build1_armhf.deb ... 188s Unpacking python3-enlighten (1.11.2-1build1) ... 188s Selecting previously unselected package python3-prompt-toolkit. 188s Preparing to unpack .../79-python3-prompt-toolkit_3.0.52-2_all.deb ... 188s Unpacking python3-prompt-toolkit (3.0.52-2) ... 188s Selecting previously unselected package python3-pubsub. 188s Preparing to unpack .../80-python3-pubsub_4.0.3-7build1_all.deb ... 188s Unpacking python3-pubsub (4.0.3-7build1) ... 188s Selecting previously unselected package toil. 188s Preparing to unpack .../81-toil_9.1.0-1_all.deb ... 188s Unpacking toil (9.1.0-1) ... 188s Setting up libxdot4:armhf (14.1.1-2ubuntu2) ... 188s Setting up libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 188s Setting up python3-configargparse (1.7-2) ... 188s Setting up python3-arcp (0.2.1-7build1) ... 189s Setting up libcdt6:armhf (14.1.1-2ubuntu2) ... 189s Setting up libpixman-1-0:armhf (0.46.4-1) ... 189s Setting up libsharpyuv0:armhf (1.5.0-0.1build1) ... 189s Setting up libaom3:armhf (3.13.1-2) ... 189s Setting up python3-filelock (3.20.3-1) ... 189s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 189s Setting up libxpm4:armhf (1:3.5.17-1build3) ... 189s Setting up libxrender1:armhf (1:0.9.12-1) ... 189s Setting up libdatrie1:armhf (0.2.14-1) ... 189s Setting up libxcb-render0:armhf (1.17.0-2ubuntu1) ... 189s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 189s Setting up python3-mypy-extensions (1.1.0-1) ... 189s Setting up python3-docker (7.1.0-2ubuntu1) ... 189s Setting up python3-ruamel.yaml.clib (0.2.15+ds-1) ... 189s Setting up libdeflate0:armhf (1.23-2) ... 189s Setting up libxcb-shm0:armhf (1.17.0-2ubuntu1) ... 189s Setting up libgomp1:armhf (15.2.0-12ubuntu1) ... 189s Setting up python3-networkx (3.2.1-4ubuntu2) ... 191s Setting up libjbig0:armhf (2.1-6.1ubuntu3) ... 191s Setting up python3-psutil (7.1.0-1ubuntu1) ... 191s Setting up python3-prefixed (0.7.0-1build1) ... 191s Setting up python3-wcwidth (0.2.14+dfsg1-1build1) ... 192s Setting up python3-humanfriendly (10.0-6build1) ... 192s Setting up libfreetype6:armhf (2.14.1+dfsg-2) ... 192s Setting up python3-spython (0.3.13-2build1) ... 192s Setting up libpathplan4:armhf (14.1.1-2ubuntu2) ... 192s Setting up python3-dill (0.4.0-1) ... 192s Setting up libimagequant0:armhf (2.18.0-1build1) ... 192s Setting up fonts-dejavu-mono (2.37-8build1) ... 192s Setting up fonts-dejavu-core (2.37-8build1) ... 192s Setting up libjpeg-turbo8:armhf (2.1.5-4ubuntu2) ... 192s Setting up libltdl7:armhf (2.5.4-9) ... 192s Setting up libcgraph8:armhf (14.1.1-2ubuntu2) ... 192s Setting up libwebp7:armhf (1.5.0-0.1build1) ... 192s Setting up python3-ruamel.yaml (0.18.10+ds-1build1) ... 193s Setting up python3-pubsub (4.0.3-7build1) ... 193s Setting up libgvpr2:armhf (14.1.1-2ubuntu2) ... 193s Setting up python3-rich-argparse (1.6.0-2) ... 193s Setting up python3-rdflib (7.4.0-1) ... 194s Setting up libxslt1.1:armhf (1.1.43-0.3) ... 194s Setting up libharfbuzz0b:armhf (12.3.1-1) ... 194s Setting up libthai-data (0.1.30-1) ... 194s Setting up python3-msgpack (1.1.2-1) ... 194s Setting up python3-cachecontrol (0.14.3-1) ... 194s Setting up libde265-0:armhf (1.0.16-1build1) ... 194s Setting up python3-argcomplete (3.6.3-1) ... 194s Setting up python3-coloredlogs (15.0.1-1build1) ... 194s Setting up python3-mistune (3.1.4-1) ... 195s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 195s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 195s Setting up python3-prompt-toolkit (3.0.52-2) ... 195s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 196s Setting up python3-blessed (1.21.0-1) ... 196s Setting up python3-schema-salad (8.9.20251102115403-1) ... 196s Setting up libthai0:armhf (0.1.30-1) ... 196s Setting up python3-enlighten (1.11.2-1build1) ... 196s Setting up cwl-upgrader (1.2.14-1) ... 197s Setting up libgvc7:armhf (14.1.1-2ubuntu2) ... 197s Setting up python3-lxml:armhf (6.0.2-1) ... 197s Setting up libtiff6:armhf (4.7.0-3ubuntu3) ... 197s Setting up libfontconfig1:armhf (2.17.1-3ubuntu1) ... 197s Setting up fontconfig (2.17.1-3ubuntu1) ... 199s Regenerating fonts cache... done. 199s Setting up libpango-1.0-0:armhf (1.57.0-1) ... 199s Setting up python3-cwl-utils (0.40-1) ... 205s Setting up libcairo2:armhf (1.18.4-3) ... 205s Setting up libpangoft2-1.0-0:armhf (1.57.0-1) ... 205s Setting up libpangocairo-1.0-0:armhf (1.57.0-1) ... 205s Setting up libgvplugin-pango8:armhf (14.1.1-2ubuntu2) ... 205s Setting up libheif-plugin-aomdec:armhf (1.21.2-1) ... 205s Setting up libheif-plugin-libde265:armhf (1.21.2-1) ... 205s Setting up libheif1:armhf (1.21.2-1) ... 205s Setting up libgd3:armhf (2.3.3-13ubuntu1) ... 205s Setting up libgvplugin-gd8:armhf (14.1.1-2ubuntu2) ... 205s Setting up graphviz (14.1.1-2ubuntu2) ... 205s Setting up python3-pydot (4.0.1-1) ... 205s Setting up python3-prov (2.1.1-1) ... 205s Setting up cwltool (3.1.20251031082601-1) ... 206s Setting up toil (9.1.0-1) ... 207s Processing triggers for libc-bin (2.42-2ubuntu4) ... 207s Processing triggers for man-db (2.13.1-1) ... 218s autopkgtest [05:46:26]: test smoke-test: [----------------------- 221s Usage: toil COMMAND ... 221s toil --help 221s toil COMMAND --help 221s 221s Where COMMAND is one of the following: 221s 221s clean - Delete a job store used by a previous Toil workflow invocation. 221s config - Create a config file with all default Toil options. 221s debug-file - Debug tool for copying files contained in a toil jobStore. 221s debug-job - Debug tool for running a toil job locally. 221s destroy-cluster - Terminates the specified cluster and associated resources. 221s kill - Kills rogue toil processes. 221s launch-cluster - Launches a toil leader instance with the specified provisioner. 221s rsync-cluster - Rsyncs into the toil appliance container running on the leader of the cluster. 221s server - CLI entry for the Toil servers. 221s ssh-cluster - SSH into the toil appliance container running on the leader of the cluster. 221s stats - Reports statistical data about a given Toil workflow. 221s status - Tool for reporting on job status. 221s 221s 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: 221s 221s pip install cwltool==3.1.20250110105449 221s 222s usage: toil-cwl-runner [options] WORKFLOW [INFILE] [WF_OPTIONS...] 222s 222s positional arguments: 222s 222s WORKFLOW CWL file to run. 222s 222s INFILE YAML or JSON file of workflow inputs. 222s 222s WF_OPTIONS Additional inputs to the workflow as command-line 222s flags. If CWL workflow takes an input, the name of the 222s input can be used as an option. For example: 222s 222s toil-cwl-runner workflow.cwl --file1 file 222s 222s If an input has the same name as a Toil option, pass 222s '--' before it. 222s 222s options: 222s -h, --help show this help message and exit 222s --not-strict 222s --enable-dev Enable loading and running development versions of CWL 222s --enable-ext Enable loading and running 'cwltool:' extensions to 222s the CWL standards. 222s --quiet 222s --basedir BASEDIR 222s --outdir OUTDIR 222s --version show program's version number and exit 222s --log-dir LOG_DIR Log your tools stdout/stderr to this location outside 222s of container 222s --user-space-docker-cmd USER_SPACE_DOCKER_CMD 222s (Linux/OS X only) Specify a user space docker command 222s (like udocker or dx-docker) that will be used to call 222s 'pull' and 'run' 222s --singularity Use Singularity runtime for running containers. 222s Requires Singularity v2.6.1+ and Linux with kernel 222s version v3.18+ or with overlayfs support backported. 222s --podman Use Podman runtime for running containers. 222s --no-container Do not execute jobs in a Docker container, even when 222s `DockerRequirement` is specified under `hints`. 222s --leave-container Do not delete Docker container used by jobs after they 222s exit 222s --custom-net CUSTOM_NET 222s Specify docker network name to pass to docker run 222s command 222s --no-prepull Do not prepull the container prior to running the 222s workflow 222s --preserve-environment VAR1 VAR2 [VAR1 VAR2 ...] 222s Preserve specified environment variables when running 222s CommandLineTools 222s --preserve-entire-environment 222s Preserve all environment variable when running 222s CommandLineTools. 222s --beta-dependency-resolvers-configuration BETA_DEPENDENCY_RESOLVERS_CONFIGURATION 222s --beta-dependencies-directory BETA_DEPENDENCIES_DIRECTORY 222s --beta-use-biocontainers 222s --beta-conda-dependencies 222s --tmpdir-prefix TMPDIR_PREFIX 222s Path prefix for temporary directories 222s --tmp-outdir-prefix TMP_OUTDIR_PREFIX 222s Path prefix for intermediate output directories 222s --force-docker-pull Pull latest docker image even if it is locally present 222s --no-match-user Disable passing the current uid to `docker run --user` 222s --no-read-only Do not set root directory in the container as read- 222s only 222s --strict-memory-limit 222s When running with software containers and the Docker 222s engine, pass either the calculated memory allocation 222s from ResourceRequirements or the default of 1 gigabyte 222s to Docker's --memory option. 222s --strict-cpu-limit When running with software containers and the Docker 222s engine, pass either the calculated cpu allocation from 222s ResourceRequirements or the default of 1 core to 222s Docker's --cpu option. Requires docker version >= 222s v1.13. 222s --relax-path-checks Relax requirements on path names to permit spaces and 222s hash characters. 222s --default-container DEFAULT_CONTAINER 222s Specify a default docker container that will be used 222s if the workflow fails to specify one. 222s --compute-checksum Compute checksum of contents while collecting outputs 222s --no-compute-checksum 222s Do not compute checksum of contents while collecting 222s outputs 222s --eval-timeout EVAL_TIMEOUT 222s Time to wait for a Javascript expression to evaluate 222s before giving an error, default 20s. 222s --overrides OVERRIDES 222s Read process requirement overrides from file. 222s --mpi-config-file MPI_CONFIG_FILE 222s Platform specific configuration for MPI (parallel 222s launcher, its flag etc). See the cwltool README 222s section 'Running MPI-based tools' for details of the 222s format: https://github.com/common-workflow- 222s language/cwltool#running-mpi-based-tools-that-need-to- 222s be-launched 222s --bypass-file-store Do not use Toil's file store and assume all paths are 222s accessible in place from all nodes. 222s --reference-inputs Do not copy remote inputs into Toil's file store and 222s assume they are accessible in place from all nodes. 222s --disable-streaming Disable file streaming for files that have 222s 'streamable' flag True. 222s --cwl-default-ram Apply CWL specification default ramMin. 222s --no-cwl-default-ram Do not apply CWL specification default ramMin, so that 222s Toil --defaultMemory applies. This can help jobs get 222s to Slurm with no memory limit assigned. 222s --cwl-min-ram CWL_MIN_RAM 222s Specify a minimum memory allocation for all tasks .If 222s --no-cwl-default-ram is passed, this does not apply to 222s tools that do not specify a memory requirement; 222s --defaultMemory is used for those toolsin that case. 222s --destBucket DESTBUCKET 222s Specify a cloud bucket endpoint for output files. 222s --cachedir CACHEDIR Directory to cache intermediate workflow outputs to 222s avoid recomputing steps. Can be very helpful in the 222s development and troubleshooting of CWL documents. This 222s automatically bypasses the file store. Not to be 222s confused with --caching. 222s --runImportsOnWorkers, --run-imports-on-workers 222s Run the file imports on a worker instead of the 222s leader. This is useful if the leader is not optimized 222s for high network performance. If set to true, the 222s argument --importWorkersDisk must also be set. 222s --importWorkersBatchSize, --import-workers-batch-size IMPORT_WORKERS_BATCHSIZE 222s Specify the target total file size for file import 222s batches. As many files as can fit will go into each 222s batch import job. This should be set in conjunction 222s with the argument --runImportsOnWorkers. 222s --importWorkersDisk, --import-workers-disk IMPORT_WORKERS_DISK 222s Specify the disk size each import worker will get. 222s This usually will not need to be set as Toil will 222s attempt to use file streaming when downloading files. 222s If not possible, for example, when downloading from 222s AWS to a GCE job store, this should be set to the 222s largest file size of all files to import. This should 222s be set in conjunction with the arguments 222s --runImportsOnWorkers and --importWorkersBatchSize. 222s 222s --config PATH Get options from a config file. 222s 222s Logging Options: 222s --logCritical Set logging level to Critical. Default: INFO. 222s --logError Set logging level to Error. Default: INFO. 222s --logWarning Set logging level to Warning. Default: INFO. 222s --logInfo Set logging level to Info. Default: INFO. 222s --logDebug Set logging level to Debug. Default: INFO. 222s --logTrace Set logging level to Trace. Default: INFO. 222s --logOff Same as --logCritical. 222s --logLevel {Critical,Error,Warning,Info,Debug,Trace,critical,error,warning,info,debug,trace,CRITICAL,ERROR,WARNING,INFO,DEBUG,TRACE} 222s Set the log level. Default: INFO. Options: 222s ['Critical', 'Error', 'Warning', 'Info', 'Debug', 222s 'Trace', 'critical', 'error', 'warning', 'info', 222s 'debug', 'trace', 'CRITICAL', 'ERROR', 'WARNING', 222s 'INFO', 'DEBUG', 'TRACE']. 222s --logFile LOGFILE File to log in. 222s --rotatingLogging Turn on rotating logging, which prevents log files 222s from getting too big. 222s --logColors BOOL Enable or disable colored logging. Default: True 222s 222s Toil core options: 222s Options to specify the location of the Toil workflow and turn on stats collation about the performance of jobs. 222s 222s --jobstore, --jobStore JOBSTORE 222s The location of the job store for the workflow. A job 222s store holds persistent information about the jobs, 222s stats, and files in a workflow. If the workflow is run 222s with a distributed batch system, the job store must be 222s accessible by all worker nodes. Depending on the 222s desired job store implementation, the location should 222s be formatted according to one of the following 222s schemes: file: where points to a 222s directory on the file system aws:: 222s where is the name of an AWS region like us- 222s west-2 and will be prepended to the names of 222s any top-level AWS resources in use by job store, e.g. 222s S3 buckets. google:: TODO: explain 222s For backwards compatibility, you may also specify 222s ./foo (equivalent to file:./foo or just file:foo) or 222s /bar (equivalent to file:/bar). 222s --workDir PATH Absolute path to directory where temporary files 222s generated during the Toil run should be placed. 222s Standard output and error from batch system jobs 222s (unless --noStdOutErr is set) will be placed in this 222s directory. A cache directory may be placed in this 222s directory. Temp files and folders will be placed in a 222s directory toil- within workDir. The 222s workflowID is generated by Toil and will be reported 222s in the workflow logs. Default is determined by the 222s variables (TMPDIR, TEMP, TMP) via mkdtemp. This 222s directory needs to exist on all machines running jobs; 222s if capturing standard output and error from batch 222s system jobs is desired, it will generally need to be 222s on a shared file system. When sharing a cache between 222s containers on a host, this directory must be shared 222s between the containers. [env var: TOIL_WORKDIR] 222s --coordinationDir PATH 222s Absolute path to directory where Toil will keep state 222s and lock files. When sharing a cache between 222s containers on a host, this directory must be shared 222s between the containers. [env var: 222s TOIL_COORDINATION_DIR] 222s --noStdOutErr Do not capture standard output and error from batch 222s system jobs. 222s --stats Keep statistics about the toil workflow to be used by 222s 'toil stats'. 222s --clean {always,onError,never,onSuccess} 222s Determines the deletion of the jobStore upon 222s completion of the program. Choices: ['always', 222s 'onError', 'never', 'onSuccess']. The --stats option 222s requires information from the jobStore upon completion 222s so the jobStore will never be deleted with that flag. 222s If you wish to be able to restart the run, choose 222s 'never' or 'onSuccess'. Default is 'never' if stats is 222s enabled, and 'onSuccess' otherwise. 222s --cleanWorkDir {always,onError,never,onSuccess} 222s Determines deletion of temporary worker directory upon 222s completion of a job. Choices: ['always', 'onError', 222s 'never', 'onSuccess']. Default = always. WARNING: This 222s option should be changed for debugging only. Running a 222s full pipeline with this option could fill your disk 222s with excessive intermediate data. 222s --clusterStats [OPT_PATH] 222s If enabled, writes out JSON resource usage statistics 222s to a file. The default location for this file is the 222s current working directory, but an absolute path can 222s also be passed to specify where this file should be 222s written. This options only applies when using scalable 222s batch systems. 222s 222s Toil options for restarting an existing workflow: 222s Allows the restart of an existing workflow 222s 222s --restart If --restart is specified then will attempt to restart 222s existing workflow at the location pointed to by the 222s --jobStore option. Will raise an exception if the 222s workflow does not exist 222s 222s Toil options for specifying the batch system: 222s Allows the specification of the batch system. 222s 222s --batchSystem {aws_batch,single_machine,grid_engine,lsf,mesos,slurm,torque,htcondor,kubernetes} 222s The type of batch system to run the job(s) with, 222s currently can be one of aws_batch, single_machine, 222s grid_engine, lsf, mesos, slurm, torque, htcondor, 222s kubernetes. Default = single_machine 222s --disableHotDeployment 222s Hot-deployment was renamed to auto-deployment. Option 222s now redirects to --disableAutoDeployment. Left in for 222s backwards compatibility. 222s --disableAutoDeployment DISABLEAUTODEPLOYMENT 222s Should auto-deployment of Toil Python workflows be 222s deactivated? If True, the workflow's Python code 222s should be present at the same location on all workers. 222s Default = False. 222s --maxJobs MAX_JOBS Specifies the maximum number of jobs to submit to the 222s backing scheduler at once. Not supported on Mesos or 222s AWS Batch. Use 0 for unlimited. Defaults to unlimited. 222s --maxLocalJobs MAX_LOCAL_JOBS 222s Specifies the maximum number of housekeeping jobs to 222s run sumultaneously on the local system. Use 0 for 222s unlimited. Defaults to the number of local cores (8). 222s --manualMemArgs Do not add the default arguments: 'hv=MEMORY' & 222s 'h_vmem=MEMORY' to the qsub call, and instead rely on 222s TOIL_GRIDGENGINE_ARGS to supply alternative arguments. 222s Requires that TOIL_GRIDGENGINE_ARGS be set. 222s --runLocalJobsOnWorkers, --runCwlInternalJobsOnWorkers 222s Whether to run jobs marked as local (e.g. CWLScatter) 222s on the worker nodes instead of the leader node. If 222s false (default), then all such jobs are run on the 222s leader node. Setting this to true can speed up CWL 222s pipelines for very large workflows with many sub- 222s workflows and/or scatters, provided that the worker 222s pool is large enough. 222s --coalesceStatusCalls 222s Ask for job statuses from the batch system in a batch. 222s Deprecated; now always enabled where supported. 222s --statePollingWait STATEPOLLINGWAIT 222s Time, in seconds, to wait before doing a scheduler 222s query for job state. Return cached results if within 222s the waiting period. Only works for grid engine batch 222s systems such as gridengine, htcondor, torque, slurm, 222s and lsf. 222s --statePollingTimeout STATE_POLLING_TIMEOUT 222s Time, in seconds, to retry against a broken scheduler. 222s Only works for grid engine batch systems such as 222s gridengine, htcondor, torque, slurm, and lsf. 222s --batchLogsDir BATCH_LOGS_DIR 222s Directory to tell the backing batch system to log 222s into. Should be available on both the leader and the 222s workers, if the backing batch system writes logs to 222s the worker machines' filesystems, as many HPC 222s schedulers do. If unset, the Toil work directory will 222s be used. Only works for grid engine batch systems such 222s as gridengine, htcondor, torque, slurm, and lsf. [env 222s var: TOIL_BATCH_LOGS_DIR] 222s --memoryIsProduct If the batch system understands requested memory as a 222s product of the requested memory and the numberof 222s cores, set this flag to properly allocate memory. 222s --awsBatchRegion AWS_BATCH_REGION 222s The AWS region containing the AWS Batch queue to 222s submit to. [env var: TOIL_AWS_REGION] 222s --awsBatchQueue AWS_BATCH_QUEUE 222s The name or ARN of the AWS Batch queue to submit to. 222s [env var: TOIL_AWS_BATCH_QUEUE] 222s --awsBatchJobRoleArn AWS_BATCH_JOB_ROLE_ARN 222s The ARN of an IAM role to run AWS Batch jobs as, so 222s they can e.g. access a job store. Must be assumable by 222s ecs-tasks.amazonaws.com. [env var: 222s TOIL_AWS_BATCH_JOB_ROLE_ARN] 222s --scale SCALE A scaling factor to change the value of all submitted 222s tasks's submitted cores. Used in the single_machine 222s batch system. Useful for running workflows on smaller 222s machines than they were designed for, by setting a 222s value less than 1. (default: 1) 222s --slurmAllocateMem SLURM_ALLOCATE_MEM 222s If False, do not use --mem. Used as a workaround for 222s Slurm clusters that reject jobs with memory 222s allocations. [env var: TOIL_SLURM_ALLOCATE_MEM] 222s --slurmDefaultAllMem SLURM_DEFAULT_ALL_MEM 222s If True, assign Toil jobs without their own memory 222s requirements all available memory on a Slurm node (via 222s Slurm --mem=0). [env var: TOIL_SLURM_DEFAULT_ALL_MEM] 222s --slurmTime SLURM_TIME 222s Slurm job time limit, in [DD-]HH:MM:SS format. [env 222s var: TOIL_SLURM_TIME] 222s --slurmPartition SLURM_PARTITION 222s Partition to send Slurm jobs to. [env var: 222s TOIL_SLURM_PARTITION] 222s --slurmGPUPartition SLURM_GPU_PARTITION 222s Partition to send Slurm jobs to if they ask for GPUs. 222s [env var: TOIL_SLURM_GPU_PARTITION] 222s --slurmPE SLURM_PE Special partition to send Slurm jobs to if they ask 222s for more than 1 CPU. [env var: TOIL_SLURM_PE] 222s --slurmArgs SLURM_ARGS 222s Extra arguments to pass to Slurm. [env var: 222s TOIL_SLURM_ARGS] 222s 222s Toil options for configuring storage: 222s Allows configuring Toil's data storage. 222s 222s --symlinkImports BOOL 222s When using a filesystem based job store, CWL input 222s files are by default symlinked in. Setting this option 222s to True instead copies the files into the job store, 222s which may protect them from being modified externally. 222s When set to False, as long as caching is enabled, Toil 222s will protect the file automatically by changing the 222s permissions to read-only. default=True 222s --moveOutputs BOOL When using a filesystem based job store, output files 222s are by default moved to the output directory, and a 222s symlink to the moved exported file is created at the 222s initial location. Setting this option to True instead 222s copies the files into the output directory. Applies to 222s filesystem-based job stores only. default=False 222s --caching BOOL Enable or disable worker level file caching for your 222s workflow, specifying this overrides default from batch 222s system. Does not affect CWL or WDL task caching. 222s --symlinkJobStoreReads BOOL 222s Allow reads and container mounts from a JobStore's 222s shared filesystem directly via symlink. default=True 222s 222s Toil options for autoscaling the cluster of worker nodes: 222s 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. 222s 222s --provisioner, -p {aws,gce,None} 222s The provisioner for cluster auto-scaling. This is the 222s main Toil '--provisioner' option, and defaults to None 222s for running on single machine and non-auto-scaling 222s batch systems. The currently supported choices are 222s ['aws', 'gce', None]. The default is None. 222s --nodeTypes NODETYPES 222s Specifies a list of comma-separated node types, each 222s of which is composed of slash-separated instance 222s types, and an optional spot bid set off by a colon, 222s making the node type preemptible. Instance types may 222s appear in multiple node types, and the same node type 222s may appear as both preemptible and non-preemptible. 222s Valid argument specifying two node types: 222s c5.4xlarge/c5a.4xlarge:0.42,t2.large Node types: 222s c5.4xlarge/c5a.4xlarge:0.42 and t2.large Instance 222s types: c5.4xlarge, c5a.4xlarge, and t2.large 222s Semantics: Bid $0.42/hour for either c5.4xlarge or 222s c5a.4xlarge instances, treated interchangeably, while 222s they are available at that price, and buy t2.large 222s instances at full price. default=[] 222s --maxNodes INT[,INT...] 222s Maximum number of nodes of each type in the cluster, 222s if using autoscaling, provided as a comma-separated 222s list. The first value is used as a default if the list 222s length is less than the number of nodeTypes. 222s default=[10] 222s --minNodes INT[,INT...] 222s Mininum number of nodes of each type in the cluster, 222s if using auto-scaling. This should be provided as a 222s comma-separated list of the same length as the list of 222s node types. default=[0] 222s --targetTime INT Sets how rapidly you aim to complete jobs in seconds. 222s Shorter times mean more aggressive parallelization. 222s The autoscaler attempts to scale up/down so that it 222s expects all queued jobs will complete within 222s targetTime seconds. default=1800 222s --betaInertia FLOAT A smoothing parameter to prevent unnecessary 222s oscillations in the number of provisioned nodes. This 222s controls an exponentially weighted moving average of 222s the estimated number of nodes. A value of 0.0 disables 222s any smoothing, and a value of 0.9 will smooth so much 222s that few changes will ever be made. Must be between 222s 0.0 and 0.9. default=0.1 222s --scaleInterval INT The interval (seconds) between assessing if the scale 222s of the cluster needs to change. default=60 222s --preemptibleCompensation, --preemptableCompensation FLOAT 222s The preference of the autoscaler to replace 222s preemptible nodes with non-preemptible nodes, when 222s preemptible nodes cannot be started for some reason. 222s This value must be between 0.0 and 1.0, inclusive. A 222s value of 0.0 disables such compensation, a value of 222s 0.5 compensates two missing preemptible nodes with a 222s non-preemptible one. A value of 1.0 replaces every 222s missing pre-emptable node with a non-preemptible one. 222s default=0.0 222s --nodeStorage INT Specify the size of the root volume of worker nodes 222s when they are launched in gigabytes. You may want to 222s set this if your jobs require a lot of disk space. 222s (default=50). 222s --nodeStorageOverrides NODETYPE:NODESTORAGE[,NODETYPE:NODESTORAGE...] 222s Comma-separated list of nodeType:nodeStorage that are 222s used to override the default value from --nodeStorage 222s for the specified nodeType(s). This is useful for 222s heterogeneous jobs where some tasks require much more 222s disk than others. 222s --metrics BOOL Enable the prometheus/grafana dashboard for monitoring 222s CPU/RAM usage, queue size, and issued jobs. 222s --assumeZeroOverhead BOOL 222s Ignore scheduler and OS overhead and assume jobs can 222s use every last byte of memory and disk on a node when 222s autoscaling. 222s 222s Toil options for cores/memory requirements: 222s 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. 222s 222s --defaultMemory DEFAULTMEMORY 222s The default amount of memory to request for a job. 222s Only applicable to jobs that do not specify an 222s explicit value for this requirement. Standard suffixes 222s like K, Ki, M, Mi, G or Gi are supported. Default is 222s 2.0 Gi. 222s --defaultCores FLOAT The default amount of cpu to request for a job. Only 222s applicable to jobs that do not specify an explicit 222s value for this requirement. Fractions of a core (for 222s example 0.1) are supported on some batch systems 222s [mesos, single_machine]. Default is 1. 222s --defaultDisk INT The default amount of disk to request for a job. Only 222s applicable to jobs that do not specify an explicit 222s value for this requirement. Standard suffixes like K, 222s Ki, M, Mi, G or Gi are supported. Default is 2.0 Gi. 222s --defaultAccelerators ACCELERATOR[,ACCELERATOR...] 222s The default amount of accelerators to request for a 222s job. Only applicable to jobs that do not specify an 222s explicit value for this requirement. Each accelerator 222s specification can have a type (gpu [default], nvidia, 222s amd, cuda, rocm, opencl, or a specific model like 222s nvidia-tesla-k80), and a count [default: 1]. If both a 222s type and a count are used, they must be separated by a 222s colon. If multiple types of accelerators are used, the 222s specifications are separated by commas. Default is []. 222s --defaultPreemptible, --defaultPreemptable [BOOL] 222s Make all jobs able to run on preemptible (spot) nodes 222s by default. 222s --maxCores INT The max amount of cpu to request for a job. Only 222s applicable to jobs that do not specify an explicit 222s value for this requirement. Fractions of a core (for 222s example 0.1) are supported on some batch systems 222s [mesos, single_machine]. Default is 222s 9223372036854775807. 222s --maxMemory INT The max amount of memory to request for a job. Only 222s applicable to jobs that do not specify an explicit 222s value for this requirement. Standard suffixes like K, 222s Ki, M, Mi, G or Gi are supported. Default is 8.0 Ei. 222s --maxDisk INT The max amount of disk to request for a job. Only 222s applicable to jobs that do not specify an explicit 222s value for this requirement. Standard suffixes like K, 222s Ki, M, Mi, G or Gi are supported. Default is 8.0 Ei. 222s 222s Toil options for rescuing/killing/restarting jobs: 222s The options for jobs that either run too long/fail or get lost (some batch systems have issues!). 222s 222s --retryCount INT Number of times to retry a failing job before giving 222s up and labeling job failed. default=1 222s --stopOnFirstFailure BOOL 222s Stop the workflow at the first complete job failure. 222s --enableUnlimitedPreemptibleRetries, --enableUnlimitedPreemptableRetries BOOL 222s If set, preemptible failures (or any failure due to an 222s instance getting unexpectedly terminated) will not 222s count towards job failures and --retryCount. 222s --doubleMem BOOL If set, batch jobs which die to reaching memory limit 222s on batch schedulers will have their memory doubled and 222s they will be retried. The remaining retry count will 222s be reduced by 1. Currently supported by LSF. 222s --maxJobDuration INT Maximum runtime of a job (in seconds) before we kill 222s it (this is a lower bound, and the actual time before 222s killing the job may be longer). 222s default=9223372036854775807 222s --rescueJobsFrequency INT 222s Period of time to wait (in seconds) between checking 222s for missing/overlong jobs, that is jobs which get lost 222s by the batch system. Expert parameter. default=60 222s --jobStoreTimeout FLOAT 222s Maximum time (in seconds) to wait for a job's update 222s to the job store before declaring it failed. 222s default=30 222s 222s Toil log management options: 222s Options for how Toil should manage its logs. 222s 222s --maxLogFileSize MAXLOGFILESIZE 222s The maximum size of a job log file to keep (in bytes), 222s log files larger than this will be truncated to the 222s last X bytes. Setting this option to zero will prevent 222s any truncation. Setting this option to a negative 222s value will truncate from the beginning. Default=100.0 222s Mi 222s --writeLogs [OPT_PATH] 222s Write worker logs received by the leader into their 222s own files at the specified path. Any non-empty 222s standard output and error from failed batch system 222s jobs will also be written into files at this path. The 222s current working directory will be used if a path is 222s not specified explicitly. Note: By default only the 222s logs of failed jobs are returned to leader. Set log 222s level to 'debug' or enable '--writeLogsFromAllJobs' to 222s get logs back from successful jobs, and adjust 222s 'maxLogFileSize' to control the truncation limit for 222s worker logs. 222s --writeLogsGzip [OPT_PATH] 222s Identical to --writeLogs except the logs files are 222s gzipped on the leader. 222s --writeLogsFromAllJobs BOOL 222s Whether to write logs from all jobs (including the 222s successful ones) without necessarily setting the log 222s level to 'debug'. Ensure that either --writeLogs or 222s --writeLogsGzip is set if enabling this option. 222s --writeMessages PATH File to send messages from the leader's message bus 222s to. 222s --realTimeLogging BOOL 222s Enable real-time logging from workers to leader 222s 222s Toil miscellaneous options: 222s Everything else. 222s 222s --disableChaining BOOL 222s Disables chaining of jobs (chaining uses one job's 222s resource allocation for its successor job if 222s possible). 222s --disableJobStoreChecksumVerification BOOL 222s Disables checksum verification for files transferred 222s to/from the job store. Checksum verification is a 222s safety check to ensure the data is not corrupted 222s during transfer. Currently only supported for non- 222s streaming AWS files. 222s --sseKey PATH Path to file containing 32 character key to be used 222s for server-side encryption on awsJobStore or 222s googleJobStore. SSE will not be used if this flag is 222s not passed. 222s --setEnv, -e NAME=VALUE or NAME 222s Set an environment variable early on in the worker. If 222s VALUE is null, it will be looked up in the current 222s environment. Independently of this option, the worker 222s will try to emulate the leader's environment before 222s running a job, except for some variables known to vary 222s across systems. Using this option, a variable can be 222s injected into the worker process itself before it is 222s started. 222s --servicePollingInterval FLOAT 222s Interval of time service jobs wait between polling for 222s the existence of the keep-alive flag. Default: 60.0 222s --forceDockerAppliance BOOL 222s Disables sanity checking the existence of the docker 222s image specified by TOIL_APPLIANCE_SELF, which Toil 222s uses to provision mesos for autoscaling. 222s --statusWait INT Seconds to wait between reports of running jobs. 222s --disableProgress Disables the progress bar shown when standard error is 222s a terminal. 222s --publishWorkflowMetrics {all,current,no} 222s Whether to publish workflow metrics reports (including 222s unique workflow and task run IDs, job names, and 222s version and Toil feature use information) to Dockstore 222s when a workflow completes. Selecting "current" will 222s publish metrics for the current workflow. Selecting 222s "all" will also publish prior workflow runs from the 222s Toil history database, even if they themselves were 222s run with "no". Note that once published, workflow 222s metrics CANNOT be deleted or un-published; they will 222s stay published forever! 222s 222s Toil debug options: 222s Debug options for finding problems or helping with testing. 222s 222s --debugWorker Experimental no forking mode for local debugging. 222s Specifically, workers are not forked and stderr/stdout 222s are not redirected to the log. 222s --disableWorkerOutputCapture 222s Let worker output go to worker's standard out/error 222s instead of per-job logs. 222s --badWorker FLOAT For testing purposes randomly kill --badWorker 222s proportion of jobs using SIGKILL. default=0.0 222s --badWorkerFailInterval FLOAT 222s When killing the job pick uniformly within the 222s interval from 0.0 to --badWorkerFailInterval seconds 222s after the worker starts. default=0.01 222s 222s Options for recording the Docker container identifier into a file.: 222s --cidfile-dir CIDFILE_DIR 222s Store the Docker container ID into a file in the 222s specified directory. 222s --cidfile-prefix CIDFILE_PREFIX 222s Specify a prefix to the container ID filename. Final 222s file name will be followed by a timestamp. The default 222s is no prefix. 222s 222s Options for recording provenance information of the execution: 222s --provenance PROVENANCE 222s Save provenance to specified folder as a Research 222s Object that captures and aggregates workflow execution 222s and data products. 222s --enable-user-provenance 222s Record user account info as part of provenance. 222s --disable-user-provenance 222s Do not record user account info in provenance. 222s --enable-host-provenance 222s Record host info as part of provenance. 222s --disable-host-provenance 222s Do not record host info in provenance. 222s --orcid ORCID Record user ORCID identifier as part of provenance, 222s e.g. https://orcid.org/0000-0002-1825-0097 or 222s 0000-0002-1825-0097. Alternatively the environment 222s variable ORCID may be set. 222s --full-name CWL_FULL_NAME 222s Record full name of user as part of provenance, e.g. 222s Josiah Carberry. You may need to use shell quotes to 222s preserve spaces. Alternatively the environment 222s variable CWL_FULL_NAME may be set. 222s 222s Args that start with '--' can also be set in a config file 222s (/home/ubuntu/.toil/default.yaml or specified via --config). The config file 222s uses YAML syntax and must represent a YAML 'mapping' (for details, see 222s http://learn.getgrav.org/advanced/yaml). In general, command-line values 222s override environment variables which override config file values which 222s override defaults. 222s autopkgtest [05:46:30]: test smoke-test: -----------------------] 227s autopkgtest [05:46:35]: test smoke-test: - - - - - - - - - - results - - - - - - - - - - 227s smoke-test PASS (superficial) 231s autopkgtest [05:46:39]: @@@@@@@@@@@@@@@@@@@@ summary 231s pybuild-autopkgtest SKIP Test declares architecture as not supported: armhf 231s pybuild-autopkgtest SKIP Test declares architecture as not supported: armhf 231s smoke-test PASS (superficial)