I: pbuilder: network access will be disabled during build I: Current time: Fri Apr 3 23:01:37 -12 2026 I: pbuilder-time-stamp: 1775300497 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [toil_6.1.0-4.dsc] I: copying [./toil_6.1.0.orig.tar.gz] I: copying [./toil_6.1.0-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./toil_6.1.0-4.dsc: unsupported subcommand dpkg-source: info: extracting toil in toil-6.1.0 dpkg-source: info: unpacking toil_6.1.0.orig.tar.gz dpkg-source: info: unpacking toil_6.1.0-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying soften-configargparser-deps dpkg-source: info: applying intersphinx dpkg-source: info: applying setting_version.patch dpkg-source: info: applying no_galaxy_lib dpkg-source: info: applying debianize_docs dpkg-source: info: applying soften-mesos-deps dpkg-source: info: applying atomic_copy_as_alternative.patch dpkg-source: info: applying soften-cwltool-dep.patch dpkg-source: info: applying accept_debian_packaged_docker_version.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2971413/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='4ef447f205a8403d90ecc112e40ac857' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2971413' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.uIQMfion/pbuilderrc_oOxs --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.uIQMfion/b1 --logfile b1/build.log toil_6.1.0-4.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2971413/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all:any, python3-setuptools, python3-configargparse, python3-docker, python3-dill, cwltool (>= 3.1.20240112164112), python3-schema-salad (>= 8.4.20230128170514), python3-enlighten, python3-wdlparse, python3-pytest, python3-pytest-xdist, python3-boto3 (>= 1.17), python3-stubserver, rsync, python3-yaml, docker.io, python3-urllib3, python3-sphinx, python3-sphinx-autoapi, python3-sphinx-autodoc-typehints, python3-sphinxcontrib.autoprogram, python3-pubsub, python3-doc, python3-tz dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19892 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all:any. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-configargparse; however: Package python3-configargparse is not installed. pbuilder-satisfydepends-dummy depends on python3-docker; however: Package python3-docker is not installed. pbuilder-satisfydepends-dummy depends on python3-dill; however: Package python3-dill is not installed. pbuilder-satisfydepends-dummy depends on cwltool (>= 3.1.20240112164112); however: Package cwltool is not installed. pbuilder-satisfydepends-dummy depends on python3-schema-salad (>= 8.4.20230128170514); however: Package python3-schema-salad is not installed. pbuilder-satisfydepends-dummy depends on python3-enlighten; however: Package python3-enlighten is not installed. pbuilder-satisfydepends-dummy depends on python3-wdlparse; however: Package python3-wdlparse is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however: Package python3-pytest-xdist is not installed. pbuilder-satisfydepends-dummy depends on python3-boto3 (>= 1.17); however: Package python3-boto3 is not installed. pbuilder-satisfydepends-dummy depends on python3-stubserver; however: Package python3-stubserver is not installed. pbuilder-satisfydepends-dummy depends on rsync; however: Package rsync is not installed. pbuilder-satisfydepends-dummy depends on python3-yaml; however: Package python3-yaml is not installed. pbuilder-satisfydepends-dummy depends on docker.io; however: Package docker.io is not installed. pbuilder-satisfydepends-dummy depends on python3-urllib3; however: Package python3-urllib3 is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-autoapi; however: Package python3-sphinx-autoapi is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-autodoc-typehints; however: Package python3-sphinx-autodoc-typehints is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.autoprogram; however: Package python3-sphinxcontrib.autoprogram is not installed. pbuilder-satisfydepends-dummy depends on python3-pubsub; however: Package python3-pubsub is not installed. pbuilder-satisfydepends-dummy depends on python3-doc; however: Package python3-doc is not installed. pbuilder-satisfydepends-dummy depends on python3-tz; however: Package python3-tz is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} containerd{a} cwl-upgrader{a} cwltool{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docker.io{a} docutils-common{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-glyphicons-halflings{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} intltool-debian{a} iptables{a} libabsl20230802{a} libann0{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libbrotli1{a} libcairo2{a} libcdt5{a} libcgraph6{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgcrypt20{a} libgd3{a} libglib2.0-0t64{a} libgpg-error0{a} libgraphite2-3{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice6{a} libicu72{a} libimagequant0{a} libip4tc2{a} libip6tc2{a} libjbig0{a} libjpeg62-turbo{a} libjs-bootstrap{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblab-gamut1{a} liblerc4{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmnl0{a} libnetfilter-conntrack3{a} libnfnetlink0{a} libnftnl11{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpathplan4{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpopt0{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} libsharpyuv0{a} libsm6{a} libsvtav1enc2{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxslt1.1{a} libxt6t64{a} libxtables12{a} libyaml-0-2{a} libyuv0{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-all{a} python3-antlr4{a} python3-arcp{a} python3-argcomplete{a} python3-astroid{a} python3-autocommand{a} python3-babel{a} python3-blessed{a} python3-boto3{a} python3-botocore{a} python3-cachecontrol{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-coloredlogs{a} python3-configargparse{a} python3-cwl-utils{a} python3-dateutil{a} python3-defusedxml{a} python3-dill{a} python3-doc{a} python3-docker{a} python3-docutils{a} python3-enlighten{a} python3-execnet{a} python3-filelock{a} python3-humanfriendly{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-jmespath{a} python3-lxml{a} python3-markdown-it{a} python3-markupsafe{a} python3-mdurl{a} python3-minimal{a} python3-mistune{a} python3-more-itertools{a} python3-msgpack{a} python3-mypy-extensions{a} python3-networkx{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-prefixed{a} python3-prov{a} python3-psutil{a} python3-pubsub{a} python3-pydot{a} python3-pygments{a} python3-pyparsing{a} python3-pytest{a} python3-pytest-xdist{a} python3-pytz{a} python3-rdflib{a} python3-requests{a} python3-rich{a} python3-rich-argparse{a} python3-roman{a} python3-ruamel.yaml{a} python3-ruamel.yaml.clib{a} python3-s3transfer{a} python3-schema-salad{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-autoapi{a} python3-sphinx-autodoc-typehints{a} python3-sphinxcontrib.autoprogram{a} python3-spython{a} python3-stubserver{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-urllib3{a} python3-wcwidth{a} python3-wdlparse{a} python3-yaml{a} python3-zipp{a} python3.13{a} python3.13-doc{a} python3.13-minimal{a} readline-common{a} rsync{a} runc{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tini{a} tzdata{a} x11-common{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: apparmor black criu curl dbus-user-session docker-cli fonts-liberation git javascript-common libarchive-cpio-perl libglib2.0-data libgpg-error-l10n libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libjson-xs-perl libltdl-dev libmail-sendmail-perl libpaper-utils lynx needrestart nftables nodejs python3-bs4 python3-cssselect python3-gdal python3-html5lib python3-html5rdf python3-matplotlib python3-numpy python3-orjson python3-pil python3-pygraphviz python3-scipy shared-mime-info wget xdg-user-dirs 0 packages upgraded, 232 newly installed, 0 to remove and 0 not upgraded. Need to get 140 MB of archives. After unpacking 717 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 runc arm64 1.1.15+ds1-2+b1 [2724 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 containerd arm64 1.7.24~ds1-4+b2 [19.2 MB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libip4tc2 arm64 1.8.11-2 [19.6 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libip6tc2 arm64 1.8.11-2 [19.8 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libxtables12 arm64 1.8.11-2 [30.6 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 libmnl0 arm64 1.0.5-3 [11.9 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libnfnetlink0 arm64 1.0.2-3 [13.9 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libnetfilter-conntrack3 arm64 1.1.0-1 [39.7 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libnftnl11 arm64 1.2.8-1 [60.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 iptables arm64 1.8.11-2 [354 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 tini arm64 0.19.0-1+b1 [229 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 docker.io arm64 26.1.5+dfsg1-9 [15.0 MB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.2-1 [853 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.2-1 [1997 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.2-1 [27.1 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 media-types all 12.0.0 [28.9 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025a-2 [259 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.2-1 [1914 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.2-1 [745 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.2-1 [10.0 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.2-1 [28.1 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libpopt0 arm64 1.19+dfsg-2 [42.8 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 rsync arm64 3.3.0+ds1-4 [408 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.4.1-1 [1390 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20241223 [164 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 53 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-ruamel.yaml.clib arm64 0.2.12+ds-1+b1 [117 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-ruamel.yaml all 0.18.10+ds-1 [147 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer arm64 3.4.1-1+b1 [119 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.10-1 [42.0 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-msgpack arm64 1.0.3-3+b5 [77.4 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-cachecontrol all 0.14.2-1 [18.3 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-mistune all 3.0.2-2 [33.2 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-mypy-extensions all 1.0.0-1 [6064 B] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 python3-rdflib all 7.1.1-2 [472 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 python3-filelock all 3.17.0-1 [12.7 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 python3-schema-salad arm64 8.8.20241206093842-2+b1 [1053 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 cwl-upgrader all 1.2.12-1 [15.7 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 python3-argcomplete all 3.5.3-1 [40.4 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 python3-humanfriendly all 10.0-6 [85.6 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 python3-coloredlogs all 15.0.1-1 [47.4 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 python3-cwl-utils all 0.36-1 [125 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libgpg-error0 arm64 1.51-3 [78.5 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libxslt1.1 arm64 1.1.35-1.1+b1 [222 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 python3-lxml arm64 5.3.1-1+b1 [1139 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 87 http://deb.debian.org/debian unstable/main arm64 python3-prov all 2.0.1-1 [95.1 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 python3-psutil arm64 5.9.8-2+b1 [226 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libann0 arm64 1.1.2+doc-9+b2 [24.1 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libcdt5 arm64 2.42.4-2+b4 [39.4 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libcgraph6 arm64 2.42.4-2+b4 [61.4 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libaom3 arm64 3.12.0-1 [1672 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.5.1-1 [252 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libabsl20230802 arm64 20230802.1-4 [432 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libgav1-1 arm64 0.19.0-3 [491 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 librav1e0.7 arm64 0.7.1-9+b1 [661 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libsvtav1enc2 arm64 2.3.0+dfsg-1 [1558 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3.1 [173 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libyuv0 arm64 0.0.1904.20250204-1 [137 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libavif16 arm64 1.1.1-1 [109 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.47-1 [274 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2 [317 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2 [386 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.19.5-1+b1 [11.5 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.15-1+b3 [153 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.19.5-1+b1 [15.4 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.19.5-1+b1 [438 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.83.5-1 [1422 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b3 [53.4 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libgd3 arm64 2.3.3-12+b1 [115 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libgts-0.7-5t64 arm64 0.7.6+darcs121130-5.2+b1 [145 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b4 [27.2 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.5.4-3 [415 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-2 [462 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.56.1-1 [213 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [52.8 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [33.8 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libpathplan4 arm64 2.42.4-2+b4 [41.4 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libgvc6 arm64 2.42.4-2+b4 [628 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libgvpr2 arm64 2.42.4-2+b4 [182 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 liblab-gamut1 arm64 2.42.4-2+b4 [198 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b4 [55.7 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 graphviz arm64 2.42.4-2+b4 [571 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 python3-pydot all 2.0.0-3 [32.6 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 python3-mdurl all 0.1.2-1 [9444 B] Get: 159 http://deb.debian.org/debian unstable/main arm64 python3-markdown-it all 3.0.0-2 [62.5 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 python3-rich all 13.9.4-1 [203 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 python3-rich-argparse all 1.6.0-2 [16.9 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 python3-spython all 0.3.13-2 [55.2 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 python3-arcp all 0.2.1-7 [13.6 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 cwltool all 3.1.20250110105449-3 [514 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-3 [539 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 172 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.8.0-1 [724 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250108 [113 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.13.2-1 [1048 B] Get: 193 http://deb.debian.org/debian unstable/main arm64 python3-antlr4 all 4.9.2-1 [98.1 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 python3-astroid all 3.3.8-2 [213 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.17.0-1 [117 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 python3-six all 1.17.0-1 [16.5 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [24.9 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 python3-blessed all 1.20.0-2 [54.3 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 python3-jmespath all 1.0.1-1 [21.1 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 python3-botocore all 1.36.22+repack-1 [7271 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 python3-s3transfer all 0.11.2-2 [57.3 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 python3-boto3 all 1.36.0+dfsg-1 [330 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 python3-configargparse all 1.7-2 [31.4 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 python3-dill all 0.3.9-1 [83.5 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 python3.13-doc all 3.13.2-1 [15.3 MB] Get: 207 http://deb.debian.org/debian unstable/main arm64 python3-doc all 3.13.2-1 [10.2 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 python3-docker all 7.1.0-2 [89.8 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 python3-roman all 5.0-1 [10.6 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 python3-prefixed all 0.7.0-1 [7984 B] Get: 212 http://deb.debian.org/debian unstable/main arm64 python3-enlighten arm64 1.11.2-1 [41.4 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 python3-execnet all 2.1.1-1 [40.2 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 215 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 216 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1+b4 [14.1 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.5-2 [107 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 python3-pubsub all 4.0.3-7 [46.7 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.4-1 [250 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 python3-pytest-xdist all 3.6.1-1 [44.4 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 python3-pytz all 2025.1-3 [150 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 224 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 8.1.3-5 [617 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 8.1.3-5 [468 kB] Get: 226 http://deb.debian.org/debian unstable/main arm64 python3-yaml arm64 6.0.2-1+b2 [122 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-autoapi all 3.3.3-1 [108 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-autodoc-typehints all 2.3.0-2 [25.3 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 python3-sphinxcontrib.autoprogram all 0.1.9-1 [10.6 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 python3-stubserver all 1.1-4 [7764 B] Get: 231 http://deb.debian.org/debian unstable/main arm64 python3-tz all 2025.1-3 [4004 B] Get: 232 http://deb.debian.org/debian unstable/main arm64 python3-wdlparse all 0.1.0-3 [66.1 kB] Fetched 140 MB in 2s (70.2 MB/s) Preconfiguring packages ... Selecting previously unselected package runc. (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 ... 19892 files and directories currently installed.) Preparing to unpack .../00-runc_1.1.15+ds1-2+b1_arm64.deb ... Unpacking runc (1.1.15+ds1-2+b1) ... Selecting previously unselected package containerd. Preparing to unpack .../01-containerd_1.7.24~ds1-4+b2_arm64.deb ... Unpacking containerd (1.7.24~ds1-4+b2) ... Selecting previously unselected package libip4tc2:arm64. 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Preparing to unpack .../14-libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../15-python3.13-minimal_3.13.2-1_arm64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:arm64 (3.13.2-1) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 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Setting up libyaml-0-2:arm64 (0.2.5-2) ... Setting up libip6tc2:arm64 (1.8.11-2) ... Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up liblab-gamut1:arm64 (2.42.4-2+b4) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libdeflate0:arm64 (1.23-1+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libgcrypt20:arm64 (1.11.0-7) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up runc (1.1.15+ds1-2+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up python-babel-localedata (2.17.0-1) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Apr 4 11:02:49 UTC 2026. Universal Time is now: Sat Apr 4 11:02:49 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3.1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libsvtav1enc2:arm64 (2.3.0+dfsg-1) ... Setting up libpathplan4:arm64 (2.42.4-2+b4) ... Setting up libann0 (1.1.2+doc-9+b2) ... Setting up libfribidi0:arm64 (1.0.16-1) ... Setting up libimagequant0:arm64 (2.18.0-1+b2) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.47-1) ... Setting up libmnl0:arm64 (1.0.5-3) ... Setting up tini (0.19.0-1+b1) ... Setting up autopoint (0.23.1-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libxtables12:arm64 (1.8.11-2) ... Setting up libltdl7:arm64 (2.5.4-3) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:arm64 (1.5.0-0.1) ... Setting up libffi8:arm64 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up libdav1d7:arm64 (1.5.1-1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up libnfnetlink0:arm64 (1.0.2-3) ... Setting up librav1e0.7:arm64 (0.7.1-9+b1) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libjson-perl (4.10000-1) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libabsl20230802:arm64 (20230802.1-4) ... Setting up sgml-base (1.31) ... Setting up libcdt5:arm64 (2.42.4-2+b4) ... Setting up libcgraph6:arm64 (2.42.4-2+b4) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libde265-0:arm64 (1.0.15-1+b3) ... Setting up containerd (1.7.24~ds1-4+b2) ... Setting up openssl (3.4.1-1) ... Setting up libyuv0:arm64 (0.0.1904.20250204-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpopt0:arm64 (1.19+dfsg-2) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libice6:arm64 (2:1.1.1-1) ... Setting up gettext (0.23.1-1) ... Setting up libxpm4:arm64 (1:3.5.17-1+b3) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b4) ... Setting up libtool (2.5.4-3) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up libnftnl11:arm64 (1.2.8-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up python3.13-doc (3.13.2-1) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libglib2.0-0t64:arm64 (2.83.5-1) ... No schema files found: doing nothing. Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libgav1-1:arm64 (0.19.0-3) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libgvpr2:arm64 (2.42.4-2+b4) ... Setting up libnetfilter-conntrack3:arm64 (1.1.0-1) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:arm64 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:arm64 (10.2.0-1) ... Setting up libgts-0.7-5t64:arm64 (0.7.6+darcs121130-5.2+b1) ... Setting up libfontconfig1:arm64 (2.15.0-2) ... Setting up libsm6:arm64 (2:1.2.4-1) ... Setting up libpython3.13-stdlib:arm64 (3.13.2-1) ... Setting up python3-doc (3.13.2-1) ... Setting up rsync (3.3.0+ds1-4) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libpython3-stdlib:arm64 (3.13.2-1) ... Setting up fontconfig (2.15.0-2) ... Regenerating fonts cache... done. Setting up libavif16:arm64 (1.1.1-1) ... Setting up python3.13 (3.13.2-1) ... Setting up iptables (1.8.11-2) ... update-alternatives: using /usr/sbin/iptables-legacy to provide /usr/sbin/iptables (iptables) in auto mode update-alternatives: using /usr/sbin/ip6tables-legacy to provide /usr/sbin/ip6tables (ip6tables) in auto mode update-alternatives: using /usr/sbin/iptables-nft to provide /usr/sbin/iptables (iptables) in auto mode update-alternatives: using /usr/sbin/ip6tables-nft to provide /usr/sbin/ip6tables (ip6tables) in auto mode update-alternatives: using /usr/sbin/arptables-nft to provide /usr/sbin/arptables (arptables) in auto mode update-alternatives: using /usr/sbin/ebtables-nft to provide /usr/sbin/ebtables (ebtables) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:arm64 (1.56.1-1) ... Setting up python3 (3.13.2-1) ... Setting up docker.io (26.1.5+dfsg1-9) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (2.1.5-1+b4) ... Setting up libcairo2:arm64 (1.18.2-2) ... Setting up python3-psutil (5.9.8-2+b1) ... Setting up python3-prefixed (0.7.0-1) ... Setting up python3-stubserver (1.1-4) ... Setting up python3-six (1.17.0-1) ... Setting up python3-roman (5.0-1) ... Setting up python3-jinja2 (3.1.5-2) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-wcwidth (0.2.13+dfsg1-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-humanfriendly (10.0-6) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up python3-spython (0.3.13-2) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-jmespath (1.0.1-1) ... Setting up python3-dill (0.3.9-1) ... Setting up libraqm0:arm64 (0.10.2-1) ... Setting up python3-mdurl (0.1.2-1) ... Setting up sphinx-common (8.1.3-5) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Setting up python3-idna (3.10-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-markdown-it (3.0.0-2) ... Setting up python3-pubsub (4.0.3-7) ... Setting up python3-astroid (3.3.8-2) ... Setting up python3-lxml:arm64 (5.3.1-1+b1) ... Setting up python3-rdflib (7.1.1-2) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-msgpack (1.0.3-3+b5) ... Setting up libpangoft2-1.0-0:arm64 (1.56.1-1) ... Setting up python3-argcomplete (3.5.3-1) ... Setting up python3-execnet (2.1.1-1) ... Setting up python3-coloredlogs (15.0.1-1) ... Setting up python3-mistune (3.0.2-2) ... Setting up libpangocairo-1.0-0:arm64 (1.56.1-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-configargparse (1.7-2) ... Setting up python3-arcp (0.2.1-7) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-antlr4 (4.9.2-1) ... Setting up python3-filelock (3.17.0-1) ... Setting up libxmu6:arm64 (2:1.1.3-3+b4) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-babel (2.17.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-rich (13.9.4-1) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.1-1+b1) ... Setting up python3-pytest (8.3.4-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-mypy-extensions (1.0.0-1) ... Setting up python3-blessed (1.20.0-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up python3-ruamel.yaml.clib (0.2.12+ds-1+b1) ... Setting up python3-all (3.13.2-1) ... Setting up python3-yaml (6.0.2-1+b2) ... Setting up debhelper (13.24.1) ... Setting up python3-pytz (2025.1-3) ... Setting up libxaw7:arm64 (2:1.0.16-1) ... Setting up python3-tz (2025.1-3) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-enlighten (1.11.2-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-requests (2.32.3+dfsg-4) ... Setting up python3-ruamel.yaml (0.18.10+ds-1) ... Setting up python3-rich-argparse (1.6.0-2) ... Setting up python3-cachecontrol (0.14.2-1) ... Setting up python3-wdlparse (0.1.0-3) ... Setting up python3-pkg-resources (75.8.0-1) ... Setting up python3-setuptools (75.8.0-1) ... Setting up python3-pytest-xdist (3.6.1-1) ... Setting up python3-docker (7.1.0-2) ... Setting up python3-schema-salad (8.8.20241206093842-2+b1) ... Setting up python3-networkx (3.2.1-5) ... Setting up python3-prov (2.0.1-1) ... Setting up cwl-upgrader (1.2.12-1) ... Setting up python3-botocore (1.36.22+repack-1) ... Setting up dh-python (6.20250108) ... Setting up python3-s3transfer (0.11.2-2) ... Setting up python3-cwl-utils (0.36-1) ... Setting up python3-boto3 (1.36.0+dfsg-1) ... Setting up libheif-plugin-libde265:arm64 (1.19.5-1+b1) ... Setting up libheif1:arm64 (1.19.5-1+b1) ... Setting up libgd3:arm64 (2.3.3-12+b1) ... Setting up libgvc6 (2.42.4-2+b4) ... Setting up libheif-plugin-dav1d:arm64 (1.19.5-1+b1) ... Setting up graphviz (2.42.4-2+b4) ... Setting up python3-pydot (2.0.0-3) ... Setting up cwltool (3.1.20250110105449-3) ... Processing triggers for libc-bin (2.41-3) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-5) ... Setting up python3-sphinx-autodoc-typehints (2.3.0-2) ... Setting up python3-sphinx-autoapi (3.3.3-1) ... Setting up python3-sphinxcontrib.autoprogram (0.1.9-1) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/toil-6.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../toil_6.1.0-4_source.changes dpkg-buildpackage: info: source package toil dpkg-buildpackage: info: source version 6.1.0-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from toil-6.1.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/toil-6.1.0' rm -rf .pybuild rm -rf docs/_build find . -name "*.pyc" -delete make[1]: Leaving directory '/build/reproducible-path/toil-6.1.0' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/toil-6.1.0' dh_auto_build I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil copying src/toil/version.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil copying src/toil/worker.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil copying src/toil/toilState.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil copying src/toil/statsAndLogging.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil copying src/toil/serviceManager.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil copying src/toil/resource.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil copying src/toil/realtimeLogger.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil copying src/toil/leader.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil copying src/toil/job.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil copying src/toil/exceptions.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil copying src/toil/deferred.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil copying src/toil/common.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil copying src/toil/bus.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil copying src/toil/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/wdl copying src/toil/wdl/wdltoil.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/wdl copying src/toil/wdl/utils.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/wdl copying src/toil/wdl/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/wdl creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/toilUpdateEC2Instances.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/toilStatus.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/toilStats.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/toilSshCluster.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/toilServer.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/toilRsyncCluster.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/toilMain.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/toilLaunchCluster.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/toilKill.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/toilDestroyCluster.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/toilDebugJob.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/toilDebugFile.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/toilConfig.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/toilClean.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils copying src/toil/utils/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test copying src/toil/test/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server copying src/toil/server/wsgi_app.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server copying src/toil/server/utils.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server copying src/toil/server/celery_app.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server copying src/toil/server/app.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server copying src/toil/server/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/provisioners copying src/toil/provisioners/node.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/provisioners copying src/toil/provisioners/gceProvisioner.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/provisioners copying src/toil/provisioners/clusterScaler.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/provisioners copying src/toil/provisioners/abstractProvisioner.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/provisioners copying src/toil/provisioners/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/provisioners creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/options copying src/toil/options/wdl.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/options copying src/toil/options/cwl.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/options copying src/toil/options/common.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/options copying src/toil/options/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/options creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/throttle.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/threading.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/retry.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/resources.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/objects.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/misc.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/memoize.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/iterables.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/io.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/humanize.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/generatedEC2Lists.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/expando.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/exceptions.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/ec2nodes.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/ec2.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/docker.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/conversions.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/compatibility.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/bioio.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/accelerators.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib copying src/toil/lib/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/jobStores copying src/toil/jobStores/fileJobStore.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/jobStores copying src/toil/jobStores/utils.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/jobStores copying src/toil/jobStores/googleJobStore.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/jobStores copying src/toil/jobStores/conftest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/jobStores copying src/toil/jobStores/abstractJobStore.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/jobStores copying src/toil/jobStores/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/jobStores creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/fileStores copying src/toil/fileStores/nonCachingFileStore.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/fileStores copying src/toil/fileStores/cachingFileStore.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/fileStores copying src/toil/fileStores/abstractFileStore.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/fileStores copying src/toil/fileStores/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/fileStores creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/cwl copying src/toil/cwl/utils.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/cwl copying src/toil/cwl/cwltoil.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/cwl copying src/toil/cwl/conftest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/cwl copying src/toil/cwl/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/cwl creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/torque.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/slurm.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/singleMachine.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/registry.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/options.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/lsfHelper.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/lsf.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/local_support.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/kubernetes.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/htcondor.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/gridengine.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/contained_executor.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/cleanup_support.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/awsBatch.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/abstractGridEngineBatchSystem.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/abstractBatchSystem.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems copying src/toil/batchSystems/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/wdl copying src/toil/test/wdl/wdltoil_test.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/wdl copying src/toil/test/wdl/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/wdl creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/utils copying src/toil/test/utils/utilsTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/utils copying src/toil/test/utils/toilKillTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/utils copying src/toil/test/utils/toilDebugTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/utils copying src/toil/test/utils/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/utils creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/workerTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/userDefinedJobArgTypeTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/toilContextManagerTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/threadingTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/systemTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/retainTempDirTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/resumabilityTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/restartDAGTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/resourceTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/regularLogTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/realtimeLoggerTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/promisesTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/promisedRequirementTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/miscTests.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/jobTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/jobServiceTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/jobFileStoreTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/jobEncapsulationTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/jobDescriptionTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/importExportFileTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/helloWorldTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/fileStoreTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/dockerCheckTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/deferredFunctionTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/checkpointTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/busTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/autoDeploymentTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src copying src/toil/test/src/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/src creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/sort copying src/toil/test/sort/sortTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/sort copying src/toil/test/sort/sort.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/sort copying src/toil/test/sort/restart_sort.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/sort copying src/toil/test/sort/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/sort creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/server copying src/toil/test/server/serverTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/server copying src/toil/test/server/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/server creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/provisioners copying src/toil/test/provisioners/restartScript.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/provisioners copying src/toil/test/provisioners/provisionerTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/provisioners copying src/toil/test/provisioners/gceProvisionerTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/provisioners copying src/toil/test/provisioners/clusterTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/provisioners copying src/toil/test/provisioners/clusterScalerTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/provisioners copying src/toil/test/provisioners/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/provisioners creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/options copying src/toil/test/options/options.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/options copying src/toil/test/options/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/options creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/mesos copying src/toil/test/mesos/stress.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/mesos copying src/toil/test/mesos/helloWorld.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/mesos copying src/toil/test/mesos/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/mesos copying src/toil/test/mesos/MesosDataStructuresTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/mesos creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/lib copying src/toil/test/lib/test_misc.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/lib copying src/toil/test/lib/test_ec2.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/lib copying src/toil/test/lib/test_conversions.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/lib copying src/toil/test/lib/dockerTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/lib copying src/toil/test/lib/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/lib creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/jobStores copying src/toil/test/jobStores/jobStoreTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/jobStores copying src/toil/test/jobStores/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/jobStores creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/docs copying src/toil/test/docs/scriptsTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/docs copying src/toil/test/docs/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/docs creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/cwlTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/conftest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cactus copying src/toil/test/cactus/test_cactus_integration.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cactus copying src/toil/test/cactus/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cactus creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/batchSystems copying src/toil/test/batchSystems/test_slurm.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/batchSystems copying src/toil/test/batchSystems/test_lsf_helper.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/batchSystems copying src/toil/test/batchSystems/batchSystemTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/batchSystems copying src/toil/test/batchSystems/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/batchSystems creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/provisioners/aws copying src/toil/test/provisioners/aws/awsProvisionerTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/provisioners/aws copying src/toil/test/provisioners/aws/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/provisioners/aws creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/lib/aws copying src/toil/test/lib/aws/test_utils.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/lib/aws copying src/toil/test/lib/aws/test_s3.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/lib/aws copying src/toil/test/lib/aws/test_iam.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/lib/aws copying src/toil/test/lib/aws/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/lib/aws creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server/wes copying src/toil/server/wes/toil_backend.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server/wes copying src/toil/server/wes/tasks.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server/wes copying src/toil/server/wes/amazon_wes_utils.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server/wes copying src/toil/server/wes/abstract_backend.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server/wes copying src/toil/server/wes/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server/wes creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server/cli copying src/toil/server/cli/wes_cwl_runner.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server/cli copying src/toil/server/cli/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server/cli creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server/api_spec copying src/toil/server/api_spec/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server/api_spec creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/provisioners/aws copying src/toil/provisioners/aws/awsProvisioner.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/provisioners/aws copying src/toil/provisioners/aws/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/provisioners/aws creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib/encryption copying src/toil/lib/encryption/conftest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib/encryption copying src/toil/lib/encryption/_nacl.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib/encryption copying src/toil/lib/encryption/_dummy.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib/encryption copying src/toil/lib/encryption/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib/encryption creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib/aws copying src/toil/lib/aws/utils.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib/aws copying src/toil/lib/aws/session.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib/aws copying src/toil/lib/aws/iam.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib/aws copying src/toil/lib/aws/ami.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib/aws copying src/toil/lib/aws/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib/aws creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/jobStores/aws copying src/toil/jobStores/aws/utils.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/jobStores/aws copying src/toil/jobStores/aws/jobStore.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/jobStores/aws copying src/toil/jobStores/aws/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/jobStores/aws creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems/mesos copying src/toil/batchSystems/mesos/executor.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems/mesos copying src/toil/batchSystems/mesos/conftest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems/mesos copying src/toil/batchSystems/mesos/batchSystem.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems/mesos copying src/toil/batchSystems/mesos/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems/mesos creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems/mesos/test copying src/toil/batchSystems/mesos/test/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems/mesos/test copying src/toil/test/cwl/conditional_wf.yaml -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/colon_test_output_job.yaml -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/test_filename_conflict_resolution.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/test_filename_conflict_detection_at_root.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/test_filename_conflict_detection.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/stream.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/sorttool.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/seqtk_seq.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/s3_secondary_file.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/revtool2.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/revtool.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/revsort2.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/revsort.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/preemptible_expression.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/preemptible.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/nvidia_smi.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/mpi_simple.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/load_contents.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/glob_dir.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/file_from_directory.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/echo_string_scatter_capture_stdout.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/echo_string.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/echo.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/echo-stdout-log-dir.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/echo-stderr.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/download_subdirectory.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/download_directory.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/download.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/directory_from_directory.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/conditional_wf.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/colon_test_output.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/test/cwl/alwaysfails.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/cwl copying src/toil/server/api_spec/workflow_execution_service.swagger.yaml -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server/api_spec PYTHONPATH=/build/reproducible-path/toil-6.1.0/src /usr/bin/make -C docs man SPHINXOPTS="" make[2]: Entering directory '/build/reproducible-path/toil-6.1.0/docs' Running Sphinx v8.1.3 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. 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WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://cwltool.readthedocs.io/en/latest/objects.inv' not fetchable due to : HTTPSConnectionPool(host='cwltool.readthedocs.io', port=443): Max retries exceeded with url: /en/latest/objects.inv (Caused by NameResolutionError(": Failed to resolve 'cwltool.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) building [mo]: targets for 0 po files that are out of date writing output... building [man]: all manpages updating environment: [new config] 237 added, 0 changed, 0 removed reading sources... [ 0%] appendices/architecture reading sources... [ 1%] appendices/aws_min_permissions reading sources... [ 1%] appendices/deploy reading sources... [ 2%] appendices/environment_vars reading sources... [ 2%] autoapi/index reading sources... [ 3%] autoapi/toil/batchSystems/abstractBatchSystem/index reading sources... 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[100%] wdl/running WARNING: Failed guarded type import with ModuleNotFoundError("No module named 'pipes'") looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/toil-6.1.0/docs/gettingStarted/install.rst: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying assets: done writing... toil.1 { gettingStarted/quickStart cwl/introduction cwl/running wdl/introduction wdl/running wdl/developing wdl/conformance running/introduction running/cliOptions running/utils running/debugging running/cloud/cloud running/cloud/clusterUtils running/cloud/kubernetes running/cloud/amazon running/cloud/gce running/hpcEnvironments running/server/wes python/developing python/toilAPI python/toilAPIJobstore python/toilAPIJobFunctions python/toilAPIMethods python/toilAPIRunner python/toilAPIFilestore python/toilAPIBatchsystem python/toilAPIService python/toilAPIExceptions contributing/contributing contributing/checklists appendices/architecture appendices/aws_min_permissions appendices/deploy appendices/environment_vars autoapi/index autoapi/toil/index autoapi/toil/batchSystems/index autoapi/toil/batchSystems/abstractBatchSystem/index autoapi/toil/batchSystems/abstractGridEngineBatchSystem/index autoapi/toil/batchSystems/awsBatch/index autoapi/toil/batchSystems/cleanup_support/index autoapi/toil/batchSystems/contained_executor/index autoapi/toil/batchSystems/gridengine/index autoapi/toil/batchSystems/htcondor/index autoapi/toil/batchSystems/kubernetes/index autoapi/toil/batchSystems/local_support/index autoapi/toil/batchSystems/lsf/index autoapi/toil/batchSystems/lsfHelper/index autoapi/toil/batchSystems/mesos/index autoapi/toil/batchSystems/mesos/batchSystem/index autoapi/toil/batchSystems/mesos/conftest/index autoapi/toil/batchSystems/mesos/executor/index autoapi/toil/batchSystems/mesos/test/index autoapi/toil/batchSystems/options/index 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autoapi/toil/provisioners/index autoapi/toil/provisioners/abstractProvisioner/index autoapi/toil/provisioners/aws/index autoapi/toil/provisioners/aws/awsProvisioner/index autoapi/toil/provisioners/clusterScaler/index autoapi/toil/provisioners/gceProvisioner/index autoapi/toil/provisioners/node/index autoapi/toil/realtimeLogger/index autoapi/toil/resource/index autoapi/toil/server/index autoapi/toil/server/api_spec/index autoapi/toil/server/app/index autoapi/toil/server/celery_app/index autoapi/toil/server/cli/index autoapi/toil/server/cli/wes_cwl_runner/index autoapi/toil/server/utils/index autoapi/toil/server/wes/index autoapi/toil/server/wes/abstract_backend/index autoapi/toil/server/wes/amazon_wes_utils/index autoapi/toil/server/wes/tasks/index autoapi/toil/server/wes/toil_backend/index autoapi/toil/server/wsgi_app/index autoapi/toil/serviceManager/index autoapi/toil/statsAndLogging/index autoapi/toil/test/index autoapi/toil/test/batchSystems/index autoapi/toil/test/batchSystems/batchSystemTest/index autoapi/toil/test/batchSystems/test_lsf_helper/index autoapi/toil/test/batchSystems/test_slurm/index autoapi/toil/test/cactus/index autoapi/toil/test/cactus/test_cactus_integration/index autoapi/toil/test/cwl/index autoapi/toil/test/cwl/conftest/index autoapi/toil/test/cwl/cwlTest/index autoapi/toil/test/docs/index autoapi/toil/test/docs/scriptsTest/index autoapi/toil/test/jobStores/index autoapi/toil/test/jobStores/jobStoreTest/index autoapi/toil/test/lib/index autoapi/toil/test/lib/aws/index autoapi/toil/test/lib/aws/test_iam/index autoapi/toil/test/lib/aws/test_s3/index autoapi/toil/test/lib/aws/test_utils/index autoapi/toil/test/lib/dockerTest/index autoapi/toil/test/lib/test_conversions/index autoapi/toil/test/lib/test_ec2/index autoapi/toil/test/lib/test_misc/index autoapi/toil/test/mesos/index autoapi/toil/test/mesos/MesosDataStructuresTest/index autoapi/toil/test/mesos/helloWorld/index autoapi/toil/test/mesos/stress/index autoapi/toil/test/options/index autoapi/toil/test/options/options/index autoapi/toil/test/provisioners/index autoapi/toil/test/provisioners/aws/index autoapi/toil/test/provisioners/aws/awsProvisionerTest/index autoapi/toil/test/provisioners/clusterScalerTest/index autoapi/toil/test/provisioners/clusterTest/index autoapi/toil/test/provisioners/gceProvisionerTest/index autoapi/toil/test/provisioners/provisionerTest/index autoapi/toil/test/provisioners/restartScript/index autoapi/toil/test/server/index autoapi/toil/test/server/serverTest/index autoapi/toil/test/sort/index autoapi/toil/test/sort/restart_sort/index autoapi/toil/test/sort/sort/index autoapi/toil/test/sort/sortTest/index autoapi/toil/test/src/index autoapi/toil/test/src/autoDeploymentTest/index autoapi/toil/test/src/busTest/index autoapi/toil/test/src/checkpointTest/index autoapi/toil/test/src/deferredFunctionTest/index autoapi/toil/test/src/dockerCheckTest/index autoapi/toil/test/src/fileStoreTest/index autoapi/toil/test/src/helloWorldTest/index autoapi/toil/test/src/importExportFileTest/index autoapi/toil/test/src/jobDescriptionTest/index autoapi/toil/test/src/jobEncapsulationTest/index autoapi/toil/test/src/jobFileStoreTest/index autoapi/toil/test/src/jobServiceTest/index autoapi/toil/test/src/jobTest/index autoapi/toil/test/src/miscTests/index autoapi/toil/test/src/promisedRequirementTest/index autoapi/toil/test/src/promisesTest/index autoapi/toil/test/src/realtimeLoggerTest/index autoapi/toil/test/src/regularLogTest/index autoapi/toil/test/src/resourceTest/index autoapi/toil/test/src/restartDAGTest/index autoapi/toil/test/src/resumabilityTest/index autoapi/toil/test/src/retainTempDirTest/index autoapi/toil/test/src/systemTest/index autoapi/toil/test/src/threadingTest/index autoapi/toil/test/src/toilContextManagerTest/index autoapi/toil/test/src/userDefinedJobArgTypeTest/index autoapi/toil/test/src/workerTest/index autoapi/toil/test/utils/index autoapi/toil/test/utils/toilDebugTest/index autoapi/toil/test/utils/toilKillTest/index autoapi/toil/test/utils/utilsTest/index autoapi/toil/test/wdl/index autoapi/toil/test/wdl/wdltoil_test/index autoapi/toil/toilState/index autoapi/toil/utils/index autoapi/toil/utils/toilClean/index autoapi/toil/utils/toilConfig/index autoapi/toil/utils/toilDebugFile/index autoapi/toil/utils/toilDebugJob/index autoapi/toil/utils/toilDestroyCluster/index autoapi/toil/utils/toilKill/index autoapi/toil/utils/toilLaunchCluster/index autoapi/toil/utils/toilMain/index autoapi/toil/utils/toilRsyncCluster/index autoapi/toil/utils/toilServer/index autoapi/toil/utils/toilSshCluster/index autoapi/toil/utils/toilStats/index autoapi/toil/utils/toilStatus/index autoapi/toil/utils/toilUpdateEC2Instances/index autoapi/toil/version/index autoapi/toil/wdl/index autoapi/toil/wdl/utils/index autoapi/toil/wdl/wdltoil/index autoapi/toil/worker/index } /build/reproducible-path/toil-6.1.0/docs/gettingStarted/quickStart.rst:506: WARNING: "table row spanning" not supported [docutils] done build succeeded, 4 warnings. The manual pages are in _build/man. make[2]: Leaving directory '/build/reproducible-path/toil-6.1.0/docs' make[1]: Leaving directory '/build/reproducible-path/toil-6.1.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/toil-6.1.0' PYBUILD_SYSTEM=custom \ PYBUILD_TEST_ARGS='HOME={home_dir} {interpreter} setup.py develop --user && PYTHONPATH={dir}/src:$PYTHONPATH PATH={home_dir}/.local/bin/:$PATH TOIL_TEST_QUICK=True TOIL_SKIP_DOCKER=True {interpreter} -m pytest -n auto --dist loadscope -vv -W ignore --ignore src/toil/test/lib/aws/test_s3.py --ignore src/toil/test/provisioners/aws/awsProvisionerTest.py --ignore src/toil/test/wdl/wdltoil_test.py --ignore src/toil/test/cwl/cwlTest.py --ignore src/toil/test/src/promisedRequirementTest.py --ignore src/toil/test/lib/test_ec2.py --ignore src/toil/test/batchSystems/batchSystemTest.py --ignore src/toil/test/lib/aws/test_iam.py -k "not (test_bioconda or test_run_conformance or testImportFtpFile or ToilWdlIntegrationTest or SortTest or testCwlexample or testVirtualEnv or ToilDocumentationTest or test_cwl_toil_kill or testImportReadFileCompatibility or CleanWorkDirTest or DeferredFunctionTest or WdlToilTest or test_cactus_integration)" {dir}/src/toil/test' \ dh_auto_test I: pybuild base:311: HOME=/build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil python3.13 setup.py develop --user && PYTHONPATH=/build/reproducible-path/toil-6.1.0/src:$PYTHONPATH PATH=/build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/.local/bin/:$PATH TOIL_TEST_QUICK=True TOIL_SKIP_DOCKER=True python3.13 -m pytest -n auto --dist loadscope -vv -W ignore --ignore src/toil/test/lib/aws/test_s3.py --ignore src/toil/test/provisioners/aws/awsProvisionerTest.py --ignore src/toil/test/wdl/wdltoil_test.py --ignore src/toil/test/cwl/cwlTest.py --ignore src/toil/test/src/promisedRequirementTest.py --ignore src/toil/test/lib/test_ec2.py --ignore src/toil/test/batchSystems/batchSystemTest.py --ignore src/toil/test/lib/aws/test_iam.py -k "not (test_bioconda or test_run_conformance or testImportFtpFile or ToilWdlIntegrationTest or SortTest or testCwlexample or testVirtualEnv or ToilDocumentationTest or test_cwl_toil_kill or testImportReadFileCompatibility or CleanWorkDirTest or DeferredFunctionTest or WdlToilTest or test_cactus_integration)" /build/reproducible-path/toil-6.1.0/src/toil/test running develop /usr/lib/python3/dist-packages/setuptools/command/develop.py:41: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! easy_install.initialize_options(self) /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:79: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running egg_info creating src/toil.egg-info writing src/toil.egg-info/PKG-INFO writing dependency_links to src/toil.egg-info/dependency_links.txt writing entry points to src/toil.egg-info/entry_points.txt writing requirements to src/toil.egg-info/requires.txt writing top-level names to src/toil.egg-info/top_level.txt writing manifest file 'src/toil.egg-info/SOURCES.txt' reading manifest file 'src/toil.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'src/toil.egg-info/SOURCES.txt' running build_ext Creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/.local/lib/python3.13/site-packages/toil.egg-link (link to src) Adding toil 6.1.0 to easy-install.pth file Installing _toil_contained_executor script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/.local/bin Installing _toil_mesos_executor script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/.local/bin Installing _toil_worker script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/.local/bin Installing cwltoil script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/.local/bin Installing toil script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/.local/bin Installing toil-cwl-runner script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/.local/bin Installing toil-wdl-runner script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/.local/bin Installing toil-wes-cwl-runner script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/.local/bin Installed /build/reproducible-path/toil-6.1.0/src Processing dependencies for toil==6.1.0 Searching for urllib3==2.3.0 Best match: urllib3 2.3.0 Adding urllib3 2.3.0 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for typing-extensions==4.12.2 Best match: typing-extensions 4.12.2 Adding typing-extensions 4.12.2 to easy-install.pth file Using /usr/lib/python3/dist-packages/setuptools/_vendor Searching for ruamel.yaml==0.18.10 Best match: ruamel.yaml 0.18.10 Adding ruamel.yaml 0.18.10 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for requests==2.32.3 Best match: requests 2.32.3 Adding requests 2.32.3 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for PyYAML==6.0.2 Best match: PyYAML 6.0.2 Adding PyYAML 6.0.2 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for pytz==2025.1 Best match: pytz 2025.1 Adding pytz 2025.1 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for python-dateutil==2.9.0 Best match: python-dateutil 2.9.0 Adding python-dateutil 2.9.0 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for psutil==5.9.8 Best match: psutil 5.9.8 Adding psutil 5.9.8 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for enlighten==1.11.2 Best match: enlighten 1.11.2 Adding enlighten 1.11.2 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for docker==7.1.0 Best match: docker 7.1.0 Adding docker 7.1.0 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for dill==0.3.9 Best match: dill 0.3.9 Adding dill 0.3.9 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for ConfigArgParse==1.7 Best match: ConfigArgParse 1.7 Adding ConfigArgParse 1.7 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for Pypubsub==4.0.3 Best match: Pypubsub 4.0.3 Adding Pypubsub 4.0.3 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for certifi==2025.1.31 Best match: certifi 2025.1.31 Adding certifi 2025.1.31 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for idna==3.10 Best match: idna 3.10 Adding idna 3.10 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for charset-normalizer==3.4.1 Best match: charset-normalizer 3.4.1 Adding charset-normalizer 3.4.1 to easy-install.pth file Installing normalizer script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/.local/bin Using /usr/lib/python3/dist-packages Finished processing dependencies for toil==6.1.0 ============================= test session starts ============================== platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3.13 cachedir: .pytest_cache rootdir: /build/reproducible-path/toil-6.1.0 configfile: setup.cfg plugins: xdist-3.6.1, typeguard-4.4.2 created: 12/12 workers 12 workers [469 items] scheduling tests via LoadScopeScheduling src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testAsyncWriteWithCaching [gw6] [ 0%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testAsyncWriteWithCaching src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionFailCase [gw6] [ 0%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionFailCase src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testAsyncWriteWithCaching src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testBatchCreate [gw0] [ 0%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testBatchCreate src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testChildLoadingEquality [gw0] [ 0%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testChildLoadingEquality src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testAsyncWriteWithCaching [gw7] [ 1%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testAsyncWriteWithCaching src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionFailCase [gw7] [ 1%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionFailCase src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_many_all_exist src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean [gw4] [ 1%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CRx_FORGO [gw4] [ 1%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CRx_FORGO src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CRx_None [gw4] [ 1%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CRx_None 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src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testCleanCache [gw3] [ 3%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testCleanCache src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality [gw3] [ 3%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence [gw3] [ 3%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionOfCorruptedJobStore [gw3] [ 3%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionOfCorruptedJobStore src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionPartialEvict [gw7] [ 4%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionPartialEvict src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionTotalEvict [gw7] [ 4%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionTotalEvict src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testControlledFailedWorkerRetry src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testApplianceParser [gw10] [ 4%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testApplianceParser src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo [gw10] [ 4%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo [gw5] [ 4%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testAsyncWriteWithCaching src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testCacheEvictionFailCase 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src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testExtremeCacheSetup src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreExportFile src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testCleanCache [gw0] [ 7%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testCleanCache src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testConfigEquality [gw0] [ 7%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testConfigEquality src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testDestructionIdempotence [gw0] [ 7%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testDestructionIdempotence src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testDestructionOfCorruptedJobStore [gw0] [ 7%] SKIPPED 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src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip [gw9] [ 12%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url [gw7] [ 12%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreExportFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreLogging [gw7] [ 12%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreLogging src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreOperations [gw7] [ 13%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreOperations src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testMultipleJobsReadSameCacheHitGlobalFile [gw7] [ 13%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testMultipleJobsReadSameCacheHitGlobalFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testMultipleJobsReadSameCacheMissGlobalFile [gw0] [ 13%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testFileDeletion src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testGrowingAndShrinkingJob [gw0] [ 13%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testGrowingAndShrinkingJob src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testImportHttpFile [gw0] [ 13%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testImportHttpFile src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testInitialState [gw0] [ 14%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testInitialState src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testInlinedFiles [gw0] [ 14%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testInlinedFiles src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobCreation [gw0] [ 14%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobCreation src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobDeletions [gw1] [ 14%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testEmptyFileStoreIDIsReadable src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testFileDeletion [gw1] [ 14%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testFileDeletion src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testGrowingAndShrinkingJob [gw1] [ 15%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testGrowingAndShrinkingJob src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile [gw1] [ 15%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo [gw10] [ 15%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo [gw10] [ 15%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionPartialEvict [gw6] [ 15%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionPartialEvict src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionTotalEvict [gw6] [ 16%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionTotalEvict src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testControlledFailedWorkerRetry [gw6] [ 16%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testControlledFailedWorkerRetry src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testDeleteLocalFile [gw6] [ 16%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testDeleteLocalFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testExtremeCacheSetup [gw6] [ 16%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testExtremeCacheSetup src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreExportFile [gw6] [ 17%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreExportFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreLogging [gw6] [ 17%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreLogging src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreOperations [gw6] [ 17%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreOperations src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testMultipleJobsReadSameCacheHitGlobalFile [gw6] [ 17%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testMultipleJobsReadSameCacheHitGlobalFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testMultipleJobsReadSameCacheMissGlobalFile [gw6] [ 17%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testMultipleJobsReadSameCacheMissGlobalFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCachHitFileFromJobStore [gw6] [ 18%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCachHitFileFromJobStore src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile [gw6] [ 18%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile [gw6] [ 18%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode [gw6] [ 18%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testRemoveLocalImmutablyReadFile [gw6] [ 18%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testRemoveLocalImmutablyReadFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testRemoveLocalMutablyReadFile [gw6] [ 19%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testRemoveLocalMutablyReadFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReturnFileSizes [gw6] [ 19%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReturnFileSizes src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReturnFileSizesWithBadWorker [gw0] [ 19%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobDeletions src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobLoadEquality [gw0] [ 19%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobLoadEquality src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testLargeFile [gw0] [ 20%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testLargeFile src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testMultiThreadImportFile [gw7] [ 20%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testMultipleJobsReadSameCacheMissGlobalFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCachHitFileFromJobStore [gw7] [ 20%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCachHitFileFromJobStore src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile [gw7] [ 20%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile [gw7] [ 20%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState [gw1] [ 21%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testInlinedFiles [gw1] [ 21%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testInlinedFiles [gw3] [ 21%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobCreation src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions [gw3] [ 21%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality [gw3] [ 21%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testLargeFile [gw3] [ 22%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testLargeFile src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testMultipartUploads [gw3] [ 22%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testMultipartUploads src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream [gw3] [ 22%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testPerJobFiles [gw3] [ 22%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testPerJobFiles src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete [gw3] [ 23%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete [gw9] [ 23%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails [gw9] [ 23%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails [gw6] [ 23%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReturnFileSizesWithBadWorker src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testSimultaneousReadsUncachedStream [gw6] [ 23%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testSimultaneousReadsUncachedStream src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testToilIsNotBroken src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation [gw1] [ 24%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions [gw1] [ 24%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions [gw6] [ 24%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testToilIsNotBroken src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility [gw6] [ 24%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteLocalFileToJobStore [gw6] [ 24%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteLocalFileToJobStore src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteNonLocalFileToJobStore [gw6] [ 25%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteNonLocalFileToJobStore src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows [gw11] [ 25%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url [gw11] [ 25%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_https_url src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip [gw11] [ 25%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip 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src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url [gw11] [ 26%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails [gw11] [ 27%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails [gw4] [ 27%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CRx_STOP src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_FORGO [gw4] [ 27%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_FORGO src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_None [gw4] [ 27%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_None src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_RM [gw4] [ 27%] SKIPPED 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src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPartialReadFromStream [gw0] [ 30%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPartialReadFromStream src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPerJobFiles [gw0] [ 30%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPerJobFiles src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPersistantFilesToDelete [gw0] [ 30%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPersistantFilesToDelete src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testReadWriteFileStreamTextMode [gw0] [ 31%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testReadWriteFileStreamTextMode src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testReadWriteSharedFilesTextMode [gw0] [ 31%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testReadWriteSharedFilesTextMode src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testSDBDomainsDeletedOnFailedJobstoreBucketCreation [gw0] [ 31%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testSDBDomainsDeletedOnFailedJobstoreBucketCreation src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testSharedFiles src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode [gw7] [ 31%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testRemoveLocalImmutablyReadFile [gw7] [ 31%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testRemoveLocalImmutablyReadFile 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src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken [gw7] [ 33%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility [gw7] [ 33%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteLocalFileToJobStore [gw7] [ 33%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteLocalFileToJobStore src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteNonLocalFileToJobStore [gw7] [ 33%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteNonLocalFileToJobStore src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality [gw1] [ 33%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testLargeFile [gw1] [ 34%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testLargeFile src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile [gw1] [ 34%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testMultipartUploads [gw1] [ 34%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testMultipartUploads src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob [gw0] [ 34%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testSharedFiles src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testStatsAndLogging [gw0] [ 34%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testStatsAndLogging src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testUpdateBehavior [gw0] [ 35%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testUpdateBehavior src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testWriteLogFiles [gw0] [ 35%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testWriteLogFiles src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testZeroLengthFiles [gw0] [ 35%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testZeroLengthFiles src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode [gw3] [ 35%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode [gw3] [ 36%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles [gw3] [ 36%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging [gw3] [ 36%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior [gw3] [ 36%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles [gw3] [ 36%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles [gw3] [ 37%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py [gw3] [ 37%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py [gw3] [ 37%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py [gw0] [ 37%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py [gw0] [ 37%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py [gw0] [ 38%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py [gw0] [ 38%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py [gw0] [ 38%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py [gw4] [ 38%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_STOP src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_FORGO [gw4] [ 39%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_FORGO src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_None [gw4] [ 39%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_None src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_RM [gw4] [ 39%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_RM src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_STOP [gw4] [ 39%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_STOP src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_FORGO [gw4] [ 39%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_FORGO src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_None [gw4] [ 40%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_None src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_RM [gw4] [ 40%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_RM [gw1] [ 40%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream [gw1] [ 40%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles [gw1] [ 40%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete [gw1] [ 41%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode [gw1] [ 41%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode [gw0] [ 41%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py [gw0] [ 41%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py [gw3] [ 42%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py [gw3] [ 42%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py [gw3] [ 42%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py [gw3] [ 42%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py [gw3] [ 42%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py [gw0] [ 43%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py [gw0] [ 43%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py [gw0] [ 43%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py [gw0] [ 43%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py [gw0] [ 43%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py [gw1] [ 44%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testSDBDomainsDeletedOnFailedJobstoreBucketCreation [gw1] [ 44%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testSDBDomainsDeletedOnFailedJobstoreBucketCreation src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles [gw1] [ 44%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging [gw8] [ 44%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_many_all_exist src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_exists src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_STOP [gw4] [ 44%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_STOP src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs [gw4] [ 45%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Demux [gw4] [ 45%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Demux src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Demux_Stream [gw4] [ 45%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Demux_Stream src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Stream [gw4] [ 45%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Stream src/toil/test/lib/dockerTest.py::DockerTest::testDockerPipeChain [gw4] [ 46%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerPipeChain src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py [gw3] [ 46%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py [gw3] [ 46%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py [gw3] [ 46%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py [gw3] [ 46%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo [gw10] [ 47%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows [gw10] [ 47%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url [gw10] [ 47%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_https_url src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip [gw1] [ 47%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior [gw1] [ 47%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior [gw3] [ 48%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py [gw10] [ 48%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_inputs_zip src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip [gw10] [ 48%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_and_inputs_zip src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip [gw10] [ 48%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_manifest_zip src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles [gw1] [ 49%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles [gw1] [ 49%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles src/toil/test/lib/dockerTest.py::DockerTest::testDockerPipeChainErrorDetection [gw4] [ 49%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerPipeChainErrorDetection src/toil/test/lib/dockerTest.py::DockerTest::testNonCachingDockerChain [gw4] [ 49%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testNonCachingDockerChain src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py [gw1] [ 49%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py [gw1] [ 50%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py [gw1] [ 50%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py [gw1] [ 50%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py [gw8] [ 50%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_exists src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_not_exists src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip [gw9] [ 50%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip src/toil/test/src/jobTest.py::JobTest::testDAGConsistency src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions [gw6] [ 51%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions src/toil/test/src/miscTests.py::MiscTests::testGetSizeOfDirectoryWorks [gw6] [ 51%] SKIPPED src/toil/test/src/miscTests.py::MiscTests::testGetSizeOfDirectoryWorks src/toil/test/src/miscTests.py::MiscTests::testIDStability [gw1] [ 51%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py [gw1] [ 51%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py [gw10] [ 52%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_multi_file_zip src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip [gw10] [ 52%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_no_params_zip src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url [gw10] [ 52%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails [gw10] [ 52%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip [gw11] [ 52%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testFileStoreLogging [gw11] [ 53%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testFileStoreLogging src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testFileStoreOperations [gw11] [ 53%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testFileStoreOperations src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode [gw6] [ 53%] PASSED src/toil/test/src/miscTests.py::MiscTests::testIDStability src/toil/test/src/miscTests.py::MiscTests::test_atomic_context_error [gw6] [ 53%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_atomic_context_error src/toil/test/src/miscTests.py::MiscTests::test_atomic_context_ok [gw6] [ 53%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_atomic_context_ok src/toil/test/src/miscTests.py::MiscTests::test_atomic_install [gw6] [ 54%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_atomic_install src/toil/test/src/miscTests.py::MiscTests::test_atomic_install_dev [gw6] [ 54%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_atomic_install_dev src/toil/test/src/miscTests.py::MiscTests::test_call_command_err src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions [gw7] [ 54%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testFileStoreLogging [gw7] [ 54%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testFileStoreLogging src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testFileStoreOperations [gw7] [ 55%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testFileStoreOperations src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode [gw7] [ 55%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken [gw7] [ 55%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken [gw8] [ 55%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_not_exists src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_exists [gw1] [ 55%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py [gw1] [ 56%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py [gw1] [ 56%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py [gw1] [ 56%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py [gw1] [ 56%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py [gw6] [ 56%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_call_command_err src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility [gw7] [ 57%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility [gw8] [ 57%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_exists src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_not_exists [gw1] [ 57%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py [gw0] [ 57%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testFileStoreLogging [gw0] [ 57%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testFileStoreLogging src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testFileStoreOperations [gw0] [ 58%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testFileStoreOperations src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode [gw0] [ 58%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py [gw3] [ 58%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_build_tag [gw3] [ 58%] PASSED src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_build_tag src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags [gw3] [ 59%] PASSED src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags [gw3] [ 59%] PASSED src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken [gw0] [ 59%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility [gw0] [ 59%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility src/toil/test/lib/dockerTest.py::DockerTest::testNonCachingDockerChainErrorDetection [gw4] [ 59%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testNonCachingDockerChainErrorDetection src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testDeferralWithConcurrentEncapsulation [gw8] [ 60%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_not_exists src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_some_exists src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji [gw3] [ 60%] PASSED src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji [gw4] [ 60%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testDeferralWithConcurrentEncapsulation src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testDeferralWithFailureAndEncapsulation [gw4] [ 60%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testDeferralWithFailureAndEncapsulation src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testRestart [gw4] [ 60%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testRestart src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testSplitRootPackages [gw4] [ 61%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testSplitRootPackages src/toil/test/src/miscTests.py::MiscTests::test_call_command_ok src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip [gw10] [ 61%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip src/toil/test/src/regularLogTest.py::RegularLogTest::testLogToMaster [gw2] [ 61%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality [gw10] [ 61%] SKIPPED src/toil/test/src/regularLogTest.py::RegularLogTest::testLogToMaster src/toil/test/src/regularLogTest.py::RegularLogTest::testMultipleLogToMaster [gw10] [ 62%] SKIPPED src/toil/test/src/regularLogTest.py::RegularLogTest::testMultipleLogToMaster src/toil/test/src/regularLogTest.py::RegularLogTest::testRegularLog [gw6] [ 62%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_call_command_ok src/toil/test/src/resourceTest.py::ResourceTest::testBuiltIn src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions [gw7] [ 62%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions src/toil/test/src/miscTests.py::TestPanic::test_nested_panic [gw7] [ 62%] PASSED src/toil/test/src/miscTests.py::TestPanic::test_nested_panic src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py [gw1] [ 62%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore [gw2] [ 63%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testCleanCache [gw2] [ 63%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testCleanCache src/toil/test/src/miscTests.py::TestPanic::test_panic [gw7] [ 63%] PASSED src/toil/test/src/miscTests.py::TestPanic::test_panic src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions [gw0] [ 63%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClass [gw0] [ 63%] SKIPPED src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClass src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain [gw8] [ 64%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_some_exists src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_all_exist src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object [gw3] [ 64%] PASSED src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object src/toil/test/lib/test_conversions.py::ConversionTest::test_convert src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testUserTypesInJobFunctionArgs [gw4] [ 64%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testUserTypesInJobFunctionArgs src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_get_service_info [gw4] [ 64%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_get_service_info src/toil/test/src/miscTests.py::TestPanic::test_panic_by_hand [gw7] [ 65%] PASSED src/toil/test/src/miscTests.py::TestPanic::test_panic_by_hand src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality [gw3] [ 65%] PASSED src/toil/test/lib/test_conversions.py::ConversionTest::test_convert src/toil/test/lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds [gw3] [ 65%] PASSED src/toil/test/lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_health [gw4] [ 65%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_health [gw8] [ 65%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_all_exist src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_none_exist src/toil/test/src/miscTests.py::TestPanic::test_panic_with_secondary [gw7] [ 66%] PASSED src/toil/test/src/miscTests.py::TestPanic::test_panic_with_secondary src/toil/test/src/busTest.py::MessageBusTest::test_cross_thread_messaging src/toil/test/lib/test_conversions.py::ConversionTest::test_human2bytes [gw3] [ 66%] PASSED src/toil/test/lib/test_conversions.py::ConversionTest::test_human2bytes src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_home [gw4] [ 66%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_home src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_basic_import_export [gw2] [ 66%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence [gw9] [ 66%] FAILED src/toil/test/src/jobTest.py::JobTest::testDAGConsistency [gw8] [ 67%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_none_exist src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_some_exist src/toil/test/src/jobTest.py::JobTest::testDeadlockDetection [gw8] [ 67%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_some_exist src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_exists [gw2] [ 67%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionOfCorruptedJobStore [gw2] [ 67%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionOfCorruptedJobStore src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable [gw8] [ 68%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_exists src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_not_exists [gw2] [ 68%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testFileDeletion [gw2] [ 68%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testFileDeletion src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob [gw8] [ 68%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_one_not_exists src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_all_exist [gw7] [ 68%] PASSED src/toil/test/src/busTest.py::MessageBusTest::test_cross_thread_messaging src/toil/test/src/busTest.py::MessageBusTest::test_enum_ints_in_file [gw7] [ 69%] PASSED src/toil/test/src/busTest.py::MessageBusTest::test_enum_ints_in_file src/toil/test/src/busTest.py::MessageBusTest::test_restart_without_bus_path [gw2] [ 69%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile [gw8] [ 69%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_all_exist src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_none_exist [gw1] [ 69%] FAILED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore [gw8] [ 69%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_none_exist [gw4] [ 70%] PASSED src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_basic_import_export src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_import_export_restart_false [gw8] [ 70%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist [gw3] [ 70%] FAILED src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointRetriedOnce [gw3] [ 70%] SKIPPED src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointRetriedOnce src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_exists src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointedRestartSucceeds [gw3] [ 71%] SKIPPED src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointedRestartSucceeds src/toil/test/options/options.py::OptionsTest::test_caching_option_priority [gw7] [ 71%] FAILED src/toil/test/src/busTest.py::MessageBusTest::test_restart_without_bus_path src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testContextManger [gw7] [ 71%] SKIPPED src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testContextManger src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testExportAfterFailedExport [gw8] [ 71%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_exists src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_not_exists [gw7] [ 71%] SKIPPED src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testExportAfterFailedExport src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testNoContextManger [gw7] [ 72%] SKIPPED src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testNoContextManger src/toil/test/provisioners/gceProvisionerTest.py::GCEStaticAutoscaleTest::testAutoScale [gw7] [ 72%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEStaticAutoscaleTest::testAutoScale src/toil/test/provisioners/gceProvisionerTest.py::GCEStaticAutoscaleTest::testSpotAutoScale [gw7] [ 72%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEStaticAutoscaleTest::testSpotAutoScale src/toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store [gw7] [ 72%] SKIPPED src/toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store src/toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store_paths [gw7] [ 72%] SKIPPED src/toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store_paths src/toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription [gw8] [ 73%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_not_exists src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_exists [gw3] [ 73%] PASSED src/toil/test/options/options.py::OptionsTest::test_caching_option_priority src/toil/test/options/options.py::OptionsTest::test_default_caching_slurm [gw4] [ 73%] FAILED src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_import_export_restart_false src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_import_export_restart_true [gw4] [ 73%] SKIPPED src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_import_export_restart_true src/toil/test/__init__.py::toil.test.make_tests [gw4] [ 73%] PASSED src/toil/test/__init__.py::toil.test.make_tests src/toil/test/__init__.py::toil.test.timeLimit [gw7] [ 74%] PASSED src/toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription src/toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing [gw8] [ 74%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_exists src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_not_exists [gw6] [ 74%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testBuiltIn src/toil/test/src/resourceTest.py::ResourceTest::testNonPyStandAlone [gw8] [ 74%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_job_not_exists src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_exists [gw7] [ 75%] PASSED src/toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing src/toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testAddChildEncapsulate [gw3] [ 75%] PASSED src/toil/test/options/options.py::OptionsTest::test_default_caching_slurm src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTest::testAutoScale [gw3] [ 75%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTest::testAutoScale [gw7] [ 75%] PASSED src/toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testAddChildEncapsulate src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTest::testSpotAutoScale [gw3] [ 75%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTest::testSpotAutoScale src/toil/test/utils/toilDebugTest.py::testJobStoreContents [gw3] [ 76%] SKIPPED src/toil/test/utils/toilDebugTest.py::testJobStoreContents src/toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testEncapsulation src/toil/test/utils/toilDebugTest.py::testFetchJobStoreFiles [gw8] [ 76%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_exists src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_not_exists [gw3] [ 76%] FAILED src/toil/test/utils/toilDebugTest.py::testFetchJobStoreFiles src/toil/test/utils/toilDebugTest.py::DebugJobTest::test_print_job_info [gw5] [ 76%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testExtremeCacheSetup [gw5] [ 76%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testExtremeCacheSetup src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreExportFile [gw5] [ 77%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreExportFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreLogging [gw5] [ 77%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreLogging [gw8] [ 77%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_not_exists src/toil/test/src/resumabilityTest.py::ResumabilityTest::test [gw8] [ 77%] SKIPPED src/toil/test/src/resumabilityTest.py::ResumabilityTest::test src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreOperations [gw5] [ 78%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreOperations src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testMultipleJobsReadSameCacheHitGlobalFile [gw5] [ 78%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testMultipleJobsReadSameCacheHitGlobalFile [gw3] [ 78%] FAILED src/toil/test/utils/toilDebugTest.py::DebugJobTest::test_print_job_info src/toil/test/utils/toilDebugTest.py::DebugJobTest::test_run_job [gw7] [ 78%] FAILED src/toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testEncapsulation [gw3] [ 78%] FAILED src/toil/test/utils/toilDebugTest.py::DebugJobTest::test_run_job [gw11] [ 79%] FAILED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken src/toil/test/src/resumabilityTest.py::ResumabilityTest::test_chaining src/toil/test/batchSystems/test_lsf_helper.py::LSFHelperTest::test_parse_mem_and_cmd_from_output [gw3] [ 79%] PASSED src/toil/test/batchSystems/test_lsf_helper.py::LSFHelperTest::test_parse_mem_and_cmd_from_output src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testMultipleJobsReadSameCacheMissGlobalFile [gw5] [ 79%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testMultipleJobsReadSameCacheMissGlobalFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore src/toil/test/src/threadingTest.py::ThreadingTest::testGlobalMutexOrdering src/toil/test/lib/test_misc.py::UserNameAvailableTest::test_get_user_name [gw3] [ 79%] PASSED src/toil/test/lib/test_misc.py::UserNameAvailableTest::test_get_user_name src/toil/test/lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name [gw3] [ 79%] PASSED src/toil/test/lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name src/toil/test/mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue [gw3] [ 80%] FAILED src/toil/test/mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue src/toil/test/provisioners/gceProvisionerTest.py::GCERestartTest::testAutoScaledCluster [gw3] [ 80%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCERestartTest::testAutoScaledCluster src/toil/test/provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing [gw3] [ 80%] PASSED src/toil/test/provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing src/toil/test/server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery [gw3] [ 80%] SKIPPED src/toil/test/server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery src/toil/test/server/serverTest.py::FileStateStoreTest::test_state_store [gw3] [ 81%] SKIPPED src/toil/test/server/serverTest.py::FileStateStoreTest::test_state_store src/toil/test/server/serverTest.py::FileStateStoreURLTest::test_state_store [gw3] [ 81%] SKIPPED src/toil/test/server/serverTest.py::FileStateStoreURLTest::test_state_store src/toil/test/src/helloWorldTest.py::HelloWorldTest::testHelloWorld [gw8] [ 81%] FAILED src/toil/test/src/resumabilityTest.py::ResumabilityTest::test_chaining src/toil/test/jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName [gw8] [ 81%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName src/toil/test/lib/test_misc.py::UserNameUnvailableTest::test_get_user_name [gw8] [ 81%] PASSED src/toil/test/lib/test_misc.py::UserNameUnvailableTest::test_get_user_name src/toil/test/src/promisesTest.py::PathIndexingPromiseTest::test [gw3] [ 82%] FAILED src/toil/test/src/helloWorldTest.py::HelloWorldTest::testHelloWorld src/toil/test/src/promisesTest.py::CachedUnpicklingJobStoreTest::test [gw8] [ 82%] FAILED src/toil/test/src/promisesTest.py::PathIndexingPromiseTest::test src/toil/test/src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger [gw2] [ 82%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState [gw3] [ 82%] FAILED src/toil/test/src/promisesTest.py::CachedUnpicklingJobStoreTest::test src/toil/test/src/promisesTest.py::ChainedIndexedPromisesTest::test [gw3] [ 82%] FAILED src/toil/test/src/promisesTest.py::ChainedIndexedPromisesTest::test src/toil/test/src/workerTest.py::WorkerTests::testNextChainable [gw3] [ 83%] PASSED src/toil/test/src/workerTest.py::WorkerTests::testNextChainable [gw11] [ 83%] FAILED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility [gw5] [ 83%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile [gw0] [ 83%] PASSED src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction [gw8] [ 84%] FAILED src/toil/test/src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger src/toil/test/src/systemTest.py::SystemTest::testAtomicityOfNonEmptyDirectoryRenames [gw10] [ 84%] FAILED src/toil/test/src/regularLogTest.py::RegularLogTest::testRegularLog src/toil/test/src/regularLogTest.py::RegularLogTest::testWriteGzipLogs [gw10] [ 84%] SKIPPED src/toil/test/src/regularLogTest.py::RegularLogTest::testWriteGzipLogs src/toil/test/src/regularLogTest.py::RegularLogTest::testWriteLogs [gw0] [ 84%] FAILED src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain [gw6] [ 84%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testNonPyStandAlone src/toil/test/src/resourceTest.py::ResourceTest::testPackage [gw11] [ 85%] FAILED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions [gw6] [ 85%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testPackage src/toil/test/src/resourceTest.py::ResourceTest::testStandAlone [gw6] [ 85%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testStandAlone src/toil/test/src/resourceTest.py::ResourceTest::testStandAloneInPackage [gw6] [ 85%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testStandAloneInPackage [gw5] [ 85%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile [gw9] [ 86%] PASSED src/toil/test/src/jobTest.py::JobTest::testDeadlockDetection src/toil/test/src/jobTest.py::JobTest::testEvaluatingRandomDAG [gw9] [ 86%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testEvaluatingRandomDAG src/toil/test/src/jobTest.py::JobTest::testNewCheckpointIsLeafVertexNonRootCase [gw9] [ 86%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testNewCheckpointIsLeafVertexNonRootCase src/toil/test/src/jobTest.py::JobTest::testNewCheckpointIsLeafVertexRootCase [gw9] [ 86%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testNewCheckpointIsLeafVertexRootCase src/toil/test/src/jobTest.py::JobTest::testSiblingDAGConsistency [gw9] [ 86%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testSiblingDAGConsistency src/toil/test/src/jobTest.py::JobTest::testStatic [gw9] [ 87%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testStatic src/toil/test/src/jobTest.py::JobTest::testStatic2 [gw9] [ 87%] FAILED src/toil/test/src/jobTest.py::JobTest::testStatic2 src/toil/test/src/jobTest.py::JobTest::testTrivialDAGConsistency [gw9] [ 87%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testTrivialDAGConsistency [gw4] [ 87%] PASSED src/toil/test/__init__.py::toil.test.timeLimit src/toil/test/src/restartDAGTest.py::RestartDAGTest::testRestartedWorkflowSchedulesCorrectJobsOnFailedParent [gw4] [ 88%] SKIPPED src/toil/test/src/restartDAGTest.py::RestartDAGTest::testRestartedWorkflowSchedulesCorrectJobsOnFailedParent [gw11] [ 88%] FAILED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions src/toil/test/src/restartDAGTest.py::RestartDAGTest::testRestartedWorkflowSchedulesCorrectJobsOnKilledParent [gw4] [ 88%] SKIPPED src/toil/test/src/restartDAGTest.py::RestartDAGTest::testRestartedWorkflowSchedulesCorrectJobsOnKilledParent [gw0] [ 88%] PASSED src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain [gw5] [ 88%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode [gw10] [ 89%] FAILED src/toil/test/src/regularLogTest.py::RegularLogTest::testWriteLogs [gw5] [ 89%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testRemoveLocalImmutablyReadFile [gw5] [ 89%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testRemoveLocalImmutablyReadFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testRemoveLocalMutablyReadFile [gw5] [ 89%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testRemoveLocalMutablyReadFile src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReturnFileSizes [gw5] [ 89%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReturnFileSizes src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReturnFileSizesWithBadWorker [gw5] [ 90%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReturnFileSizesWithBadWorker src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream [gw1] [ 90%] FAILED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStoreWithBadWorker [gw1] [ 90%] SKIPPED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStoreWithBadWorker src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore [gw1] [ 90%] FAILED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore [gw5] [ 91%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken [gw5] [ 91%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility [gw5] [ 91%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore [gw5] [ 91%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore [gw5] [ 91%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions [gw5] [ 92%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions [gw7] [ 92%] PASSED src/toil/test/src/threadingTest.py::ThreadingTest::testGlobalMutexOrdering src/toil/test/src/threadingTest.py::ThreadingTest::testLastProcessStanding [gw7] [ 92%] PASSED src/toil/test/src/threadingTest.py::ThreadingTest::testLastProcessStanding src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTestMultipleNodeTypes::testAutoScale [gw7] [ 92%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTestMultipleNodeTypes::testAutoScale [gw8] [ 92%] PASSED src/toil/test/src/systemTest.py::SystemTest::testAtomicityOfNonEmptyDirectoryRenames [gw2] [ 93%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation [gw2] [ 93%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions [gw2] [ 93%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality [gw2] [ 93%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testLargeFile [gw2] [ 94%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testLargeFile src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testMultipartUploads [gw2] [ 94%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testMultipartUploads src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream [gw2] [ 94%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles [gw2] [ 94%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete [gw2] [ 94%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName [gw2] [ 95%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode [gw2] [ 95%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode [gw2] [ 95%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles [gw2] [ 95%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging [gw2] [ 95%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior [gw2] [ 96%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles [gw2] [ 96%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles [gw2] [ 96%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports [gw2] [ 96%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_does_not_leak_symlinks [gw2] [ 97%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_does_not_leak_symlinks src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_init_preserves_symlink_path [gw2] [ 97%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_jobstore_init_preserves_symlink_path src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py [gw2] [ 97%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py [gw2] [ 97%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py [gw2] [ 97%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py [gw2] [ 98%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py [gw2] [ 98%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py [gw2] [ 98%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py [gw2] [ 98%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py [gw2] [ 98%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py [gw2] [ 99%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py [gw2] [ 99%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py [gw2] [ 99%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py [gw2] [ 99%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py [gw2] [100%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py ==================================== ERRORS ==================================== _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/cactus/test_cactus_integration.py", line 14, in __init__ super().__init__(methodName=methodName) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/cactus/test_cactus_integration.py", line 14, in __init__ super().__init__(methodName=methodName) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/provisioners/clusterScalerTest.py _______ ImportError while importing test module '/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterScalerTest.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: /usr/lib/python3/dist-packages/_pytest/python.py:493: in importtestmodule mod = import_path( /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path importlib.import_module(module_name) /usr/lib/python3.13/importlib/__init__.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) :1387: in _gcd_import ??? :1360: in _find_and_load ??? :1331: in _find_and_load_unlocked ??? :935: in _load_unlocked ??? :1026: in exec_module ??? :488: in _call_with_frames_removed ??? src/toil/test/provisioners/clusterScalerTest.py:34: in from toil.provisioners.abstractProvisioner import AbstractProvisioner, Shape src/toil/provisioners/abstractProvisioner.py:29: in from toil.provisioners.node import Node src/toil/provisioners/node.py:16: in import pipes E ModuleNotFoundError: No module named 'pipes' __________ ERROR collecting src/toil/test/provisioners/clusterTest.py __________ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/cactus/test_cactus_integration.py", line 14, in __init__ super().__init__(methodName=methodName) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______________ ERROR collecting src/toil/test/sort/sortTest.py ________________ ImportError while importing test module '/build/reproducible-path/toil-6.1.0/src/toil/test/sort/sortTest.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: /usr/lib/python3/dist-packages/_pytest/python.py:493: in importtestmodule mod = import_path( /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path importlib.import_module(module_name) /usr/lib/python3.13/importlib/__init__.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) :1387: in _gcd_import ??? :1360: in _find_and_load ??? :1331: in _find_and_load_unlocked ??? :935: in _load_unlocked ??? :1026: in exec_module ??? :488: in _call_with_frames_removed ??? src/toil/test/sort/sortTest.py:24: in from toil.batchSystems.mesos.test import MesosTestSupport src/toil/batchSystems/mesos/__init__.py:20: in from toil.provisioners.abstractProvisioner import Shape src/toil/provisioners/abstractProvisioner.py:29: in from toil.provisioners.node import Node src/toil/provisioners/node.py:16: in import pipes E ModuleNotFoundError: No module named 'pipes' __________ ERROR collecting src/toil/test/provisioners/clusterTest.py __________ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/cactus/test_cactus_integration.py", line 14, in __init__ super().__init__(methodName=methodName) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/cactus/test_cactus_integration.py", line 14, in __init__ super().__init__(methodName=methodName) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _____________ ERROR collecting src/toil/test/src/jobServiceTest.py _____________ ImportError while importing test module '/build/reproducible-path/toil-6.1.0/src/toil/test/src/jobServiceTest.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: /usr/lib/python3/dist-packages/_pytest/python.py:493: in importtestmodule mod = import_path( /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path importlib.import_module(module_name) /usr/lib/python3.13/importlib/__init__.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) :1387: in _gcd_import ??? :1360: in _find_and_load ??? :1331: in _find_and_load_unlocked ??? :935: in _load_unlocked ??? :1026: in exec_module ??? :488: in _call_with_frames_removed ??? src/toil/test/src/jobServiceTest.py:29: in from toil.leader import DeadlockException src/toil/leader.py:51: in from toil.provisioners.abstractProvisioner import AbstractProvisioner src/toil/provisioners/abstractProvisioner.py:29: in from toil.provisioners.node import Node src/toil/provisioners/node.py:16: in import pipes E ModuleNotFoundError: No module named 'pipes' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/cactus/test_cactus_integration.py", line 14, in __init__ super().__init__(methodName=methodName) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _____________ ERROR collecting src/toil/test/utils/toilKillTest.py _____________ Traceback (most recent call last): File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 365, in generate_locator from toil.jobStores.aws.jobStore import AWSJobStore # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/aws/jobStore.py", line 29, in import boto.s3.connection ModuleNotFoundError: No module named 'boto' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilKillTest.py", line 96, in __init__ self.job_store = generate_locator("aws", decoration="testkill") ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 387, in generate_locator raise JobStoreUnavailableException(f"libraries for {job_store_type} job store are not installed") toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/cactus/test_cactus_integration.py", line 14, in __init__ super().__init__(methodName=methodName) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' ______________ ERROR collecting src/toil/test/utils/utilsTest.py _______________ ImportError while importing test module '/build/reproducible-path/toil-6.1.0/src/toil/test/utils/utilsTest.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: /usr/lib/python3/dist-packages/_pytest/python.py:493: in importtestmodule mod = import_path( /usr/lib/python3/dist-packages/_pytest/pathlib.py:587: in import_path importlib.import_module(module_name) /usr/lib/python3.13/importlib/__init__.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) :1387: in _gcd_import ??? :1360: in _find_and_load ??? :1331: in _find_and_load_unlocked ??? :935: in _load_unlocked ??? :1026: in exec_module ??? :488: in _call_with_frames_removed ??? src/toil/test/utils/utilsTest.py:41: in from toil.test.sort.sortTest import makeFileToSort src/toil/test/sort/sortTest.py:24: in from toil.batchSystems.mesos.test import MesosTestSupport src/toil/batchSystems/mesos/__init__.py:20: in from toil.provisioners.abstractProvisioner import Shape src/toil/provisioners/abstractProvisioner.py:29: in from toil.provisioners.node import Node src/toil/provisioners/node.py:16: in import pipes E ModuleNotFoundError: No module named 'pipes' __________ ERROR collecting src/toil/test/provisioners/clusterTest.py __________ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' __________ ERROR collecting src/toil/test/provisioners/clusterTest.py __________ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' __________ ERROR collecting src/toil/test/provisioners/clusterTest.py __________ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/cactus/test_cactus_integration.py", line 14, in __init__ super().__init__(methodName=methodName) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/cactus/test_cactus_integration.py", line 14, in __init__ super().__init__(methodName=methodName) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/cactus/test_cactus_integration.py", line 14, in __init__ super().__init__(methodName=methodName) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' __________ ERROR collecting src/toil/test/provisioners/clusterTest.py __________ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' __________ ERROR collecting src/toil/test/provisioners/clusterTest.py __________ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _____________ ERROR collecting src/toil/test/utils/toilKillTest.py _____________ Traceback (most recent call last): File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 365, in generate_locator from toil.jobStores.aws.jobStore import AWSJobStore # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/aws/jobStore.py", line 29, in import boto.s3.connection ModuleNotFoundError: No module named 'boto' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilKillTest.py", line 96, in __init__ self.job_store = generate_locator("aws", decoration="testkill") ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 387, in generate_locator raise JobStoreUnavailableException(f"libraries for {job_store_type} job store are not installed") toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed __________ ERROR collecting src/toil/test/provisioners/clusterTest.py __________ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/cactus/test_cactus_integration.py", line 14, in __init__ super().__init__(methodName=methodName) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' __________ ERROR collecting src/toil/test/provisioners/clusterTest.py __________ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _____________ ERROR collecting src/toil/test/utils/toilKillTest.py _____________ Traceback (most recent call last): File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 365, in generate_locator from toil.jobStores.aws.jobStore import AWSJobStore # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/aws/jobStore.py", line 29, in import boto.s3.connection ModuleNotFoundError: No module named 'boto' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilKillTest.py", line 96, in __init__ self.job_store = generate_locator("aws", decoration="testkill") ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 387, in generate_locator raise JobStoreUnavailableException(f"libraries for {job_store_type} job store are not installed") toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _______ ERROR collecting src/toil/test/cactus/test_cactus_integration.py _______ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/cactus/test_cactus_integration.py", line 14, in __init__ super().__init__(methodName=methodName) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _____________ ERROR collecting src/toil/test/utils/toilKillTest.py _____________ Traceback (most recent call last): File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 365, in generate_locator from toil.jobStores.aws.jobStore import AWSJobStore # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/aws/jobStore.py", line 29, in import boto.s3.connection ModuleNotFoundError: No module named 'boto' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilKillTest.py", line 96, in __init__ self.job_store = generate_locator("aws", decoration="testkill") ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 387, in generate_locator raise JobStoreUnavailableException(f"libraries for {job_store_type} job store are not installed") toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed __________ ERROR collecting src/toil/test/provisioners/clusterTest.py __________ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _____________ ERROR collecting src/toil/test/utils/toilKillTest.py _____________ Traceback (most recent call last): File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 365, in generate_locator from toil.jobStores.aws.jobStore import AWSJobStore # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/aws/jobStore.py", line 29, in import boto.s3.connection ModuleNotFoundError: No module named 'boto' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilKillTest.py", line 96, in __init__ self.job_store = generate_locator("aws", decoration="testkill") ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 387, in generate_locator raise JobStoreUnavailableException(f"libraries for {job_store_type} job store are not installed") toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed _____________ ERROR collecting src/toil/test/utils/toilKillTest.py _____________ Traceback (most recent call last): File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 365, in generate_locator from toil.jobStores.aws.jobStore import AWSJobStore # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/aws/jobStore.py", line 29, in import boto.s3.connection ModuleNotFoundError: No module named 'boto' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilKillTest.py", line 96, in __init__ self.job_store = generate_locator("aws", decoration="testkill") ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 387, in generate_locator raise JobStoreUnavailableException(f"libraries for {job_store_type} job store are not installed") toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed _____________ ERROR collecting src/toil/test/utils/toilKillTest.py _____________ Traceback (most recent call last): File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 365, in generate_locator from toil.jobStores.aws.jobStore import AWSJobStore # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/aws/jobStore.py", line 29, in import boto.s3.connection ModuleNotFoundError: No module named 'boto' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilKillTest.py", line 96, in __init__ self.job_store = generate_locator("aws", decoration="testkill") ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 387, in generate_locator raise JobStoreUnavailableException(f"libraries for {job_store_type} job store are not installed") toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed _____________ ERROR collecting src/toil/test/utils/toilKillTest.py _____________ Traceback (most recent call last): File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 365, in generate_locator from toil.jobStores.aws.jobStore import AWSJobStore # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/aws/jobStore.py", line 29, in import boto.s3.connection ModuleNotFoundError: No module named 'boto' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilKillTest.py", line 96, in __init__ self.job_store = generate_locator("aws", decoration="testkill") ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 387, in generate_locator raise JobStoreUnavailableException(f"libraries for {job_store_type} job store are not installed") toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed __________ ERROR collecting src/toil/test/provisioners/clusterTest.py __________ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' __________ ERROR collecting src/toil/test/provisioners/clusterTest.py __________ Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/provisioners/clusterTest.py", line 34, in __init__ self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'strip' _____________ ERROR collecting src/toil/test/utils/toilKillTest.py _____________ Traceback (most recent call last): File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 365, in generate_locator from toil.jobStores.aws.jobStore import AWSJobStore # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/aws/jobStore.py", line 29, in import boto.s3.connection ModuleNotFoundError: No module named 'boto' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilKillTest.py", line 96, in __init__ self.job_store = generate_locator("aws", decoration="testkill") ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 387, in generate_locator raise JobStoreUnavailableException(f"libraries for {job_store_type} job store are not installed") toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed _____________ ERROR collecting src/toil/test/utils/toilKillTest.py _____________ Traceback (most recent call last): File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 365, in generate_locator from toil.jobStores.aws.jobStore import AWSJobStore # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/aws/jobStore.py", line 29, in import boto.s3.connection ModuleNotFoundError: No module named 'boto' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilKillTest.py", line 96, in __init__ self.job_store = generate_locator("aws", decoration="testkill") ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 387, in generate_locator raise JobStoreUnavailableException(f"libraries for {job_store_type} job store are not installed") toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed _____________ ERROR collecting src/toil/test/utils/toilKillTest.py _____________ Traceback (most recent call last): File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 365, in generate_locator from toil.jobStores.aws.jobStore import AWSJobStore # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/aws/jobStore.py", line 29, in import boto.s3.connection ModuleNotFoundError: No module named 'boto' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilKillTest.py", line 96, in __init__ self.job_store = generate_locator("aws", decoration="testkill") ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 387, in generate_locator raise JobStoreUnavailableException(f"libraries for {job_store_type} job store are not installed") toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed _____________ ERROR collecting src/toil/test/utils/toilKillTest.py _____________ Traceback (most recent call last): File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 365, in generate_locator from toil.jobStores.aws.jobStore import AWSJobStore # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/aws/jobStore.py", line 29, in import boto.s3.connection ModuleNotFoundError: No module named 'boto' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389, in collect return list(collector.collect()) File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 97, in collect self.session._fixturemanager.parsefactories(self.newinstance(), self.nodeid) ~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 82, in newinstance return self.obj("runTest") ~~~~~~~~^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilKillTest.py", line 96, in __init__ self.job_store = generate_locator("aws", decoration="testkill") ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/utils.py", line 387, in generate_locator raise JobStoreUnavailableException(f"libraries for {job_store_type} job store are not installed") toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed =================================== FAILURES =================================== __________________________ JobTest.testDAGConsistency __________________________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/jobTest.py", line 145, in testDAGConsistency toil.start(i) ~~~~~~~~~~^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.jobTest.JobTest:testDAGConsistency (Apr 03 2026 23:05:44:708484 PDT) ------------------------------ Captured log call ------------------------------- DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'concurrent', 'debugWorkflow', 'botocore', 'requests', 'asyncio', 'urllib3', 'charset_normalizer', 'dill', 'bcdocs', 'boto3', 'docker', 'boto'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'debug', 'logFile': None, 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.jobTest.JobTest-testDAGConsistency-yyf4uqoa/jobStore', 'workDir': None, 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.jobTest.JobTest-testDAGConsistency-yyf4uqoa/jobStore'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '7109090b-57d5-4002-b231-afdd991c2195' DEBUG toil.common:common.py:740 Obtained node ID a1dca538-3ebd-4126-8036-4b3775a5c79e from file /proc/sys/kernel/random/boot_id DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toilwf-7f1527e022ae523aa483a22b6c9798e0 DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281472888703024. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281472888703024 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.jobTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-cdfb2834605c4459a5f8c1f10d863466/stream for result of 'parent' TemporaryID(0dec03fe-b516-4ea6-9c8a-a1d9eec43463) v0 DEBUG toil.job:job.py:2624 Saving graph of 1 jobs, 1 non-service, 1 new DEBUG toil.job:job.py:2644 Processing job 'parent' kind-parent/instance-gx9agc5r v0 DEBUG toil.job:job.py:1299 New job version: 'parent' kind-parent/instance-gx9agc5r v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '7109090b-57d5-4002-b231-afdd991c2195', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.jobTest.JobTest-testDAGConsistency-yyf4uqoa/jobStore', 'workDir': None, 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} DEBUG toil.realtimeLogger:realtimeLogger.py:162 Real-time logging disabled DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281472888703024... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281472888703024 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-7f1527e022ae523aa483a22b6c9798e0/deferred/funcber4eoaw DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-7f1527e022ae523aa483a22b6c9798e0/deferred/funcber4eoaw DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toilwf-7f1527e022ae523aa483a22b6c9798e0 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-7f1527e022ae523aa483a22b6c9798e0 DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.007382392883300781 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.jobTest.JobTest-testDAGConsistency-yyf4uqoa/jobStore) INFO toil.test:__init__.py:120 Tore down toil.test.src.jobTest.JobTest.testDAGConsistency ____________________ JobFileStoreTest.testCachingFileStore _____________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/jobFileStoreTest.py", line 38, in testCachingFileStore workflow.start(Job.wrapJobFn(simpleFileStoreJob)) ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.jobFileStoreTest.JobFileStoreTest:testCachingFileStore (Apr 03 2026 23:05:44:816757 PDT) ------------------------------ Captured log call ------------------------------- INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. INFO toil.test:__init__.py:120 Tore down toil.test.src.jobFileStoreTest.JobFileStoreTest.testCachingFileStore ___________________ CheckpointTest.testCheckpointNotRetried ____________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/checkpointTest.py", line 33, in testCheckpointNotRetried Job.Runner.startToil(CheckRetryCount(numFailuresBeforeSuccess=1), options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.checkpointTest.CheckpointTest:testCheckpointNotRetried (Apr 03 2026 23:05:44:856548 PDT) ------------------------------ Captured log call ------------------------------- INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. INFO toil.test:__init__.py:120 Tore down toil.test.src.checkpointTest.CheckpointTest.testCheckpointNotRetried _________________ MessageBusTest.test_restart_without_bus_path _________________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/busTest.py", line 127, in test_restart_without_bus_path toil.start(root) ~~~~~~~~~~^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.busTest.MessageBusTest:test_restart_without_bus_path (Apr 03 2026 23:05:44:986025 PDT) ------------------------------ Captured log call ------------------------------- DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'dill', 'concurrent', 'bcdocs', 'boto3', 'docker', 'boto', 'urllib3', 'debugWorkflow', 'botocore', 'charset_normalizer', 'asyncio', 'requests'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': None, 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.busTest.MessageBusTest-jobstore-0u5qmva3', 'workDir': None, 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'never', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 0, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/toil-test-src.busTest.MessageBusTest-test_restart_without_bus_path-tempDir-u9vn0cte/bus_holder/messagebus.txt', 'realTimeLogging': False, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.busTest.MessageBusTest-jobstore-0u5qmva3'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '8ed47b74-ba3d-4e68-a4dc-472a9104f341' DEBUG toil.common:common.py:740 Obtained node ID a1dca538-3ebd-4126-8036-4b3775a5c79e from file /proc/sys/kernel/random/boot_id DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toilwf-7384668feffa547ab47f82c0854ce0b0 DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281472735048576. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281472735048576 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.busTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-83f81dffdcee47a2a82f5d5d637f70d1/stream for result of 'failing_job_fn' TemporaryID(3d2f35b6-1e91-43ef-ac7e-b9229cb627e2) v0 DEBUG toil.job:job.py:2624 Saving graph of 1 jobs, 1 non-service, 1 new DEBUG toil.job:job.py:2644 Processing job 'failing_job_fn' kind-failing_job_fn/instance-ep1d2nn2 v0 DEBUG toil.job:job.py:1299 New job version: 'failing_job_fn' kind-failing_job_fn/instance-ep1d2nn2 v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '8ed47b74-ba3d-4e68-a4dc-472a9104f341', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.busTest.MessageBusTest-jobstore-0u5qmva3', 'workDir': None, 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'never', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 0, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': '/tmp/toil-test-src.busTest.MessageBusTest-test_restart_without_bus_path-tempDir-u9vn0cte/bus_holder/messagebus.txt', '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', 'workflowAttemptNumber': 0} DEBUG toil.realtimeLogger:realtimeLogger.py:162 Real-time logging disabled DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281472735048576... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281472735048576 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-7384668feffa547ab47f82c0854ce0b0/deferred/funcciqo7n6b DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-7384668feffa547ab47f82c0854ce0b0/deferred/funcciqo7n6b DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toilwf-7384668feffa547ab47f82c0854ce0b0 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-7384668feffa547ab47f82c0854ce0b0 DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.013093233108520508 seconds. INFO toil.test:__init__.py:120 Tore down toil.test.src.busTest.MessageBusTest.test_restart_without_bus_path ____________ ImportExportFileTest.test_import_export_restart_false _____________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/importExportFileTest.py", line 89, in test_import_export_restart_false self._run_import_export_workflow(restart=False) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/importExportFileTest.py", line 82, in _run_import_export_workflow self._import_export_workflow(options, fail=False) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/importExportFileTest.py", line 58, in _import_export_workflow workflow_final_output_file_id = toil.start( RestartingJob(msg_portion_file_id, self.trigger_file_id, self.message_portion_2)) File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.importExportFileTest.ImportExportFileTest:test_import_export_restart_false (Apr 03 2026 23:05:45:077785 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.importExportFileTest.ImportExportFileTest.test_import_export_restart_false ... INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. INFO toil.test:__init__.py:120 Tore down toil.test.src.importExportFileTest.ImportExportFileTest.test_import_export_restart_false ____________________________ testFetchJobStoreFiles ____________________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call result: TResult | None = func() ~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec return self._inner_hookexec(hook_name, methods, kwargs, firstresult) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall raise exception.with_traceback(exception.__traceback__) File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 122, in _multicall teardown.throw(exception) # type: ignore[union-attr] ~~~~~~~~~~~~~~^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call yield from thread_exception_runtest_hook() File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook yield File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 122, in _multicall teardown.throw(exception) # type: ignore[union-attr] ~~~~~~~~~~~~~~^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call yield from unraisable_exception_runtest_hook() File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook yield File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 122, in _multicall teardown.throw(exception) # type: ignore[union-attr] ~~~~~~~~~~~~~~^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call yield from self._runtest_for(item, "call") File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for yield File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 122, in _multicall teardown.throw(exception) # type: ignore[union-attr] ~~~~~~~~~~~~~~^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 880, in pytest_runtest_call return (yield) ^^^^^ File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 122, in _multicall teardown.throw(exception) # type: ignore[union-attr] ~~~~~~~~~~~~~~^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call return (yield) ^^^^^ File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall res = hook_impl.function(*args) File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call item.runtest() ~~~~~~~~~~~~^^ File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest self.ihook.pytest_pyfunc_call(pyfuncitem=self) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec return self._inner_hookexec(hook_name, methods, kwargs, firstresult) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall raise exception.with_traceback(exception.__traceback__) File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall res = hook_impl.function(*args) File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call result = testfunction(**testargs) File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilDebugTest.py", line 118, in testFetchJobStoreFiles job_store_dir = workflow_debug_jobstore() File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilDebugTest.py", line 32, in workflow_debug_jobstore subprocess.check_call( ~~~~~~~~~~~~~~~~~~~~~^ [ ^ ...<3 lines>... ] ^ ) ^ File "/usr/lib/python3.13/subprocess.py", line 416, in check_call retcode = call(*popenargs, **kwargs) File "/usr/lib/python3.13/subprocess.py", line 397, in call with Popen(*popenargs, **kwargs) as p: ~~~~~^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.13/subprocess.py", line 1038, in __init__ self._execute_child(args, executable, preexec_fn, close_fds, ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ pass_fds, cwd, env, ^^^^^^^^^^^^^^^^^^^ ...<5 lines>... gid, gids, uid, umask, ^^^^^^^^^^^^^^^^^^^^^^ start_new_session, process_group) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.13/subprocess.py", line 1974, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'python3.11' ___________ CachingFileStoreTestWithFileJobStore.testDeleteLocalFile ___________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 1229, in testDeleteLocalFile Job.Runner.startToil(A, self.options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testDeleteLocalFile (Apr 03 2026 23:05:44:559980 PDT) ------------------------------ Captured log call ------------------------------- DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testDeleteLocalFile-g0s8i7ul/logFile'. DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testDeleteLocalFile-g0s8i7ul/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-rha9u_rc', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testDeleteLocalFile-g0s8i7ul', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 0, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-rha9u_rc'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'c2c7e4c8-6b53-4cd9-8744-71672fb29a68' DEBUG toil.common:common.py:740 Obtained node ID a1dca538-3ebd-4126-8036-4b3775a5c79e from file /proc/sys/kernel/random/boot_id DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testDeleteLocalFile-g0s8i7ul/toilwf-0c56c06ea8885b82a6f06fb8768c4959 DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281472851459584. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281472851459584 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-1dbffa420f34455eb84fce2bd9d2cd2e/stream for result of '_deleteLocalFileFn' TemporaryID(b9349a75-5276-4eaa-82de-982b6a12e890) v0 DEBUG toil.job:job.py:2624 Saving graph of 1 jobs, 1 non-service, 1 new DEBUG toil.job:job.py:2644 Processing job '_deleteLocalFileFn' kind-_deleteLocalFileFn/instance-1ghff6l9 v0 DEBUG toil.job:job.py:1299 New job version: '_deleteLocalFileFn' kind-_deleteLocalFileFn/instance-1ghff6l9 v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'c2c7e4c8-6b53-4cd9-8744-71672fb29a68', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-rha9u_rc', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testDeleteLocalFile-g0s8i7ul', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 0, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281472851459584... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281472851459584 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-0c56c06ea8885b82a6f06fb8768c4959/deferred/funcd7dael4t DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-0c56c06ea8885b82a6f06fb8768c4959/deferred/funcd7dael4t DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testDeleteLocalFile-g0s8i7ul/toilwf-0c56c06ea8885b82a6f06fb8768c4959 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-0c56c06ea8885b82a6f06fb8768c4959 DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.008116483688354492 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-rha9u_rc) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testDeleteLocalFile _______________________ DebugJobTest.test_print_job_info _______________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilDebugTest.py", line 187, in test_print_job_info job_store, job_id = self._get_job_store_and_job_id() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilDebugTest.py", line 140, in _get_job_store_and_job_id subprocess.check_call([ ~~~~~~~~~~~~~~~~~~~~~^^ python, ^^^^^^^ ...<4 lines>... job_store ^^^^^^^^^ ], stderr=subprocess.DEVNULL) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.13/subprocess.py", line 416, in check_call retcode = call(*popenargs, **kwargs) File "/usr/lib/python3.13/subprocess.py", line 397, in call with Popen(*popenargs, **kwargs) as p: ~~~~~^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.13/subprocess.py", line 1038, in __init__ self._execute_child(args, executable, preexec_fn, close_fds, ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ pass_fds, cwd, env, ^^^^^^^^^^^^^^^^^^^ ...<5 lines>... gid, gids, uid, umask, ^^^^^^^^^^^^^^^^^^^^^^ start_new_session, process_group) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.13/subprocess.py", line 1974, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'python3.11' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.utils.toilDebugTest.DebugJobTest:test_print_job_info (Apr 03 2026 23:05:45:356865 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.utils.toilDebugTest.DebugJobTest.test_print_job_info ... INFO toil.test.utils.toilDebugTest:toilDebugTest.py:137 Running workflow that always fails INFO toil.test:__init__.py:120 Tore down toil.test.utils.toilDebugTest.DebugJobTest.test_print_job_info ____________________ JobEncapsulationTest.testEncapsulation ____________________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/jobEncapsulationTest.py", line 43, in testEncapsulation Job.Runner.startToil(a, options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.jobEncapsulationTest.JobEncapsulationTest:testEncapsulation (Apr 03 2026 23:05:45:318046 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.jobEncapsulationTest.JobEncapsulationTest.testEncapsulation ... INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. INFO toil.test:__init__.py:120 Tore down toil.test.src.jobEncapsulationTest.JobEncapsulationTest.testEncapsulation __________________________ DebugJobTest.test_run_job ___________________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilDebugTest.py", line 165, in test_run_job job_store, job_id = self._get_job_store_and_job_id() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/toilDebugTest.py", line 140, in _get_job_store_and_job_id subprocess.check_call([ ~~~~~~~~~~~~~~~~~~~~~^^ python, ^^^^^^^ ...<4 lines>... job_store ^^^^^^^^^ ], stderr=subprocess.DEVNULL) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.13/subprocess.py", line 416, in check_call retcode = call(*popenargs, **kwargs) File "/usr/lib/python3.13/subprocess.py", line 397, in call with Popen(*popenargs, **kwargs) as p: ~~~~~^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.13/subprocess.py", line 1038, in __init__ self._execute_child(args, executable, preexec_fn, close_fds, ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ pass_fds, cwd, env, ^^^^^^^^^^^^^^^^^^^ ...<5 lines>... gid, gids, uid, umask, ^^^^^^^^^^^^^^^^^^^^^^ start_new_session, process_group) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.13/subprocess.py", line 1974, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'python3.11' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.utils.toilDebugTest.DebugJobTest:test_run_job (Apr 03 2026 23:05:45:394041 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.utils.toilDebugTest.DebugJobTest.test_run_job ... INFO toil.test.utils.toilDebugTest:toilDebugTest.py:137 Running workflow that always fails INFO toil.test:__init__.py:120 Tore down toil.test.utils.toilDebugTest.DebugJobTest.test_run_job ___ NonCachingFileStoreTestWithFileJobStore.testReadWriteFileStreamTextMode ____ [gw11] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 351, in testReadWriteFileStreamTextMode toil.start(A) ~~~~~~~~~~^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore:testReadWriteFileStreamTextMode (Apr 03 2026 23:05:44:716327 PDT) ------------------------------ Captured log call ------------------------------- DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'urllib3', 'concurrent', 'docker', 'requests', 'dill', 'boto3', 'debugWorkflow', 'charset_normalizer', 'botocore', 'bcdocs', 'boto', 'asyncio'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-k9vvlpzp/logFile'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-k9vvlpzp/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-faj0p6er', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-k9vvlpzp', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-faj0p6er'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '11c5b25e-27b7-4283-89fe-ad78362d73d7' DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.common:common.py:740 Obtained node ID a1dca538-3ebd-4126-8036-4b3775a5c79e from file /proc/sys/kernel/random/boot_id DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-k9vvlpzp/toilwf-202d45249e5156219b441118feba42d8 DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281473752841056. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281473752841056 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-0123fecdd38045b5b53a2951d4ba4e8d/stream for result of '_testReadWriteFileStreamTextMode' TemporaryID(8fff4e91-c94a-4bf4-ae1c-6044904963d7) v0 DEBUG toil.job:job.py:2624 Saving graph of 1 jobs, 1 non-service, 1 new DEBUG toil.job:job.py:2644 Processing job '_testReadWriteFileStreamTextMode' kind-_testReadWriteFileStreamTextMode/instance-k0flldyr v0 DEBUG toil.job:job.py:1299 New job version: '_testReadWriteFileStreamTextMode' kind-_testReadWriteFileStreamTextMode/instance-k0flldyr v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '11c5b25e-27b7-4283-89fe-ad78362d73d7', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-faj0p6er', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-k9vvlpzp', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281473752841056... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281473752841056 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-202d45249e5156219b441118feba42d8/deferred/funczlf9i_xq DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-202d45249e5156219b441118feba42d8/deferred/funczlf9i_xq DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-k9vvlpzp/toilwf-202d45249e5156219b441118feba42d8 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-202d45249e5156219b441118feba42d8 DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.0058171749114990234 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-faj0p6er) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore.testReadWriteFileStreamTextMode _______________________ DataStructuresTest.testJobQueue ________________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/mesos/MesosDataStructuresTest.py", line 41, in testJobQueue from toil.batchSystems.mesos import JobQueue File "/build/reproducible-path/toil-6.1.0/src/toil/batchSystems/mesos/__init__.py", line 20, in from toil.provisioners.abstractProvisioner import Shape File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.mesos.MesosDataStructuresTest.DataStructuresTest:testJobQueue (Apr 03 2026 23:05:45:430962 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.mesos.MesosDataStructuresTest.DataStructuresTest.testJobQueue ... INFO toil.test:__init__.py:120 Tore down toil.test.mesos.MesosDataStructuresTest.DataStructuresTest.testJobQueue ________________________ ResumabilityTest.test_chaining ________________________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/resumabilityTest.py", line 71, in test_chaining Job.Runner.startToil(root, options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.resumabilityTest.ResumabilityTest:test_chaining (Apr 03 2026 23:05:45:398587 PDT) ------------------------------ Captured log call ------------------------------- DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'botocore', 'concurrent', 'dill', 'boto', 'charset_normalizer', 'requests', 'docker', 'debugWorkflow', 'asyncio', 'urllib3', 'bcdocs', 'boto3'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.resumabilityTest.ResumabilityTest-test_chaining-e5xfbah3/log.txt'. DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'botocore', 'concurrent', 'dill', 'boto', 'charset_normalizer', 'requests', 'docker', 'debugWorkflow', 'asyncio', 'urllib3', 'bcdocs', 'boto3'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.resumabilityTest.ResumabilityTest-test_chaining-e5xfbah3/log.txt', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.resumabilityTest.ResumabilityTest-jobstore-rf8_5u0o', 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 0, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.resumabilityTest.ResumabilityTest-jobstore-rf8_5u0o'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '9992753b-0b72-4755-b1f1-237b137c180e' DEBUG toil.common:common.py:740 Obtained node ID a1dca538-3ebd-4126-8036-4b3775a5c79e from file /proc/sys/kernel/random/boot_id DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toilwf-fa444e702503572fb8dde6e44494c211 DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281473214619264. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281473214619264 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.resumabilityTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-78424485356f4e75bf05baff7b3bef3b/stream for result of 'chaining_parent' TemporaryID(7b01f6c8-7af0-45e3-9dce-f10823fd2851) v0 DEBUG toil.job:job.py:2624 Saving graph of 1 jobs, 1 non-service, 1 new DEBUG toil.job:job.py:2644 Processing job 'chaining_parent' kind-chaining_parent/instance-gwez67xe v0 DEBUG toil.job:job.py:1299 New job version: 'chaining_parent' kind-chaining_parent/instance-gwez67xe v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '9992753b-0b72-4755-b1f1-237b137c180e', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.resumabilityTest.ResumabilityTest-jobstore-rf8_5u0o', 'workDir': None, 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 0, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} DEBUG toil.realtimeLogger:realtimeLogger.py:162 Real-time logging disabled DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281473214619264... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281473214619264 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-fa444e702503572fb8dde6e44494c211/deferred/funcyob1w8uy DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-fa444e702503572fb8dde6e44494c211/deferred/funcyob1w8uy DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toilwf-fa444e702503572fb8dde6e44494c211 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-fa444e702503572fb8dde6e44494c211 DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.009510278701782227 seconds. INFO toil.test:__init__.py:120 Tore down toil.test.src.resumabilityTest.ResumabilityTest.test_chaining ________________________ HelloWorldTest.testHelloWorld _________________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/helloWorldTest.py", line 23, in testHelloWorld Job.Runner.startToil(HelloWorld(), options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.helloWorldTest.HelloWorldTest:testHelloWorld (Apr 03 2026 23:05:45:463897 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.helloWorldTest.HelloWorldTest.testHelloWorld ... INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. INFO toil.test:__init__.py:120 Tore down toil.test.src.helloWorldTest.HelloWorldTest.testHelloWorld _________________________ PathIndexingPromiseTest.test _________________________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/promisesTest.py", line 69, in test self.assertEqual(Job.Runner.startToil(root, options), ('b', 43, 3)) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.promisesTest.PathIndexingPromiseTest:test (Apr 03 2026 23:05:45:512673 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.promisesTest.PathIndexingPromiseTest.test ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. INFO toil.test:__init__.py:120 Tore down toil.test.src.promisesTest.PathIndexingPromiseTest.test ______________________ CachedUnpicklingJobStoreTest.test _______________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/promisesTest.py", line 28, in test Job.Runner.startToil(root, options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.promisesTest.CachedUnpicklingJobStoreTest:test (Apr 03 2026 23:05:45:562086 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.promisesTest.CachedUnpicklingJobStoreTest.test ... INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. INFO toil.test:__init__.py:120 Tore down toil.test.src.promisesTest.CachedUnpicklingJobStoreTest.test _______________________ ChainedIndexedPromisesTest.test ________________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/promisesTest.py", line 45, in test self.assertEqual(Job.Runner.startToil(root, options), 42) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.promisesTest.ChainedIndexedPromisesTest:test (Apr 03 2026 23:05:45:665988 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.promisesTest.ChainedIndexedPromisesTest.test ... INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. INFO toil.test:__init__.py:120 Tore down toil.test.src.promisesTest.ChainedIndexedPromisesTest.test _________ NonCachingFileStoreTestWithFileJobStore.testToilIsNotBroken __________ [gw11] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 120, in testToilIsNotBroken Job.Runner.startToil(A, self.options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore:testToilIsNotBroken (Apr 03 2026 23:05:45:400545 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore.testToilIsNotBroken ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'urllib3', 'concurrent', 'docker', 'requests', 'dill', 'boto3', 'debugWorkflow', 'charset_normalizer', 'botocore', 'bcdocs', 'boto', 'asyncio'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testToilIsNotBroken-vf61985k/logFile'. DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'urllib3', 'concurrent', 'docker', 'requests', 'dill', 'boto3', 'debugWorkflow', 'charset_normalizer', 'botocore', 'bcdocs', 'boto', 'asyncio'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testToilIsNotBroken-vf61985k/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-x23e0u7b', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testToilIsNotBroken-vf61985k', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-x23e0u7b'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '1d287344-ec48-49c5-b531-f95c7f4f1531' DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testToilIsNotBroken-vf61985k/toilwf-58e11a6bf00a58cc952ed4dd7a38718c DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281473755044816. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281473755044816 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-2ec6c495c1944d5ba31e0694403479ce/stream for result of '_uselessFunc' TemporaryID(1899c77e-5b73-49e9-be13-a13ba364b750) v0 DEBUG toil.job:job.py:2624 Saving graph of 4 jobs, 4 non-service, 4 new DEBUG toil.job:job.py:2644 Processing job '_uselessFunc' kind-_uselessFunc/instance-tqjrfy6r v0 DEBUG toil.job:job.py:2644 Processing job '_uselessFunc' kind-_uselessFunc/instance-7m5_5078 v0 DEBUG toil.job:job.py:2644 Processing job '_uselessFunc' kind-_uselessFunc/instance-syfn9l7t v0 DEBUG toil.job:job.py:2644 Processing job '_uselessFunc' kind-_uselessFunc/instance-9i6l6thu v0 DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-tqjrfy6r v1 DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-7m5_5078 v1 DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-syfn9l7t v1 DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-9i6l6thu v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '1d287344-ec48-49c5-b531-f95c7f4f1531', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-x23e0u7b', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testToilIsNotBroken-vf61985k', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281473755044816... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281473755044816 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-58e11a6bf00a58cc952ed4dd7a38718c/deferred/funcoabuv1d5 DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-58e11a6bf00a58cc952ed4dd7a38718c/deferred/funcoabuv1d5 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testToilIsNotBroken-vf61985k/toilwf-58e11a6bf00a58cc952ed4dd7a38718c DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-58e11a6bf00a58cc952ed4dd7a38718c DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.009715795516967773 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-x23e0u7b) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore.testToilIsNotBroken _____ CachingFileStoreTestWithFileJobStore.testReadCachHitFileFromJobStore _____ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 805, in testReadCachHitFileFromJobStore Job.Runner.startToil(A, self.options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testReadCachHitFileFromJobStore (Apr 03 2026 23:05:45:400211 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testReadCachHitFileFromJobStore ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCachHitFileFromJobStore-eab34o_z/logFile'. DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCachHitFileFromJobStore-eab34o_z/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-oijduiyr', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCachHitFileFromJobStore-eab34o_z', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-oijduiyr'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '788dcc1c-3bb3-40a5-bb6d-6da9698d9b94' DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCachHitFileFromJobStore-eab34o_z/toilwf-833f0504f1825567b808737e126afd27 DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281472859387088. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281472859387088 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-7d75852d610b4b469e3e36a56972cf4b/stream for result of '_writeFileToJobStoreWithAsserts' TemporaryID(20a9fd05-4f1c-4d32-9830-1dae5884c150) v0 DEBUG toil.job:job.py:2624 Saving graph of 2 jobs, 2 non-service, 2 new DEBUG toil.job:job.py:2644 Processing job '_readFromJobStore' kind-_readFromJobStore/instance-4keyjpfw v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-bd913402d4624303ab0d86226e61b506/stream for result of '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-bkvvlv0b v0 DEBUG toil.job:job.py:2644 Processing job '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-bkvvlv0b v0 DEBUG toil.job:job.py:1299 New job version: '_readFromJobStore' kind-_readFromJobStore/instance-4keyjpfw v1 DEBUG toil.job:job.py:1299 New job version: '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-bkvvlv0b v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '788dcc1c-3bb3-40a5-bb6d-6da9698d9b94', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-oijduiyr', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCachHitFileFromJobStore-eab34o_z', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281472859387088... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281472859387088 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-833f0504f1825567b808737e126afd27/deferred/funccurjnbv5 DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-833f0504f1825567b808737e126afd27/deferred/funccurjnbv5 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCachHitFileFromJobStore-eab34o_z/toilwf-833f0504f1825567b808737e126afd27 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-833f0504f1825567b808737e126afd27 DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.008910179138183594 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-oijduiyr) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testReadCachHitFileFromJobStore ____________________ RealtimeLoggerTest.testRealtimeLogger _____________________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/realtimeLoggerTest.py", line 33, in testRealtimeLogger Job.Runner.startToil(LogTest(), options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.realtimeLoggerTest.RealtimeLoggerTest:testRealtimeLogger (Apr 03 2026 23:05:45:599184 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.realtimeLoggerTest.RealtimeLoggerTest.testRealtimeLogger ... INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. INFO toil.test:__init__.py:120 Tore down toil.test.src.realtimeLoggerTest.RealtimeLoggerTest.testRealtimeLogger ________________________ RegularLogTest.testRegularLog _________________________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/regularLogTest.py", line 94, in testRegularLog toilOutput = subprocess.check_output([sys.executable, '-m', helloWorld.__name__, ...<2 lines>... '--batchSystem=single_machine', '--logLevel=debug'], stderr=subprocess.STDOUT) File "/usr/lib/python3.13/subprocess.py", line 474, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, ~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ **kwargs).stdout ^^^^^^^^^ File "/usr/lib/python3.13/subprocess.py", line 579, in run raise CalledProcessError(retcode, process.args, output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['/usr/bin/python3.13', '-m', 'toil.test.mesos.helloWorld', './toilTest', '--clean=always', '--batchSystem=single_machine', '--logLevel=debug']' returned non-zero exit status 1. ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.regularLogTest.RegularLogTest:testRegularLog (Apr 03 2026 23:05:44:812269 PDT) __________________ UserDefinedJobArgTypeTest.testJobFunction ___________________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/userDefinedJobArgTypeTest.py", line 39, in testJobFunction Job.Runner.startToil(Job.wrapJobFn(jobFunction, 0, Foo()), self.options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.userDefinedJobArgTypeTest.UserDefinedJobArgTypeTest:testJobFunction (Apr 03 2026 23:05:46:198763 PDT) ------------------------------ Captured log call ------------------------------- INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. INFO toil.test:__init__.py:120 Tore down toil.test.src.userDefinedJobArgTypeTest.UserDefinedJobArgTypeTest.testJobFunction ___ NonCachingFileStoreTestWithFileJobStore.testWriteExportFileCompatibility ___ [gw11] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 300, in testWriteExportFileCompatibility initialPermissions, fileID = toil.start(export_file_job) ~~~~~~~~~~^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore:testWriteExportFileCompatibility (Apr 03 2026 23:05:46:033559 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore.testWriteExportFileCompatibility ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'urllib3', 'concurrent', 'docker', 'requests', 'dill', 'boto3', 'debugWorkflow', 'charset_normalizer', 'botocore', 'bcdocs', 'boto', 'asyncio'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-qufyqw5i/logFile'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-qufyqw5i/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-twsbaj7v', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-qufyqw5i', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-twsbaj7v'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '210e5929-9760-4353-9f2b-2c86af5d12f6' DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-qufyqw5i/toilwf-a2fb5d0ddfc2533b92ada5d62fe3ad63 DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281473755047056. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281473755047056 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-affd40424e1f414296e8a424afcb8036/stream for result of '_testWriteExportFileCompatibility' TemporaryID(9a4f97b0-1130-4f39-b6ef-ce39edbaca79) v0 DEBUG toil.job:job.py:2624 Saving graph of 1 jobs, 1 non-service, 1 new DEBUG toil.job:job.py:2644 Processing job '_testWriteExportFileCompatibility' kind-_testWriteExportFileCompatibility/instance-b10ve0_w v0 DEBUG toil.job:job.py:1299 New job version: '_testWriteExportFileCompatibility' kind-_testWriteExportFileCompatibility/instance-b10ve0_w v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '210e5929-9760-4353-9f2b-2c86af5d12f6', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-twsbaj7v', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-qufyqw5i', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281473755047056... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281473755047056 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-a2fb5d0ddfc2533b92ada5d62fe3ad63/deferred/funcieg1qah9 DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-a2fb5d0ddfc2533b92ada5d62fe3ad63/deferred/funcieg1qah9 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-qufyqw5i/toilwf-a2fb5d0ddfc2533b92ada5d62fe3ad63 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-a2fb5d0ddfc2533b92ada5d62fe3ad63 DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.009018421173095703 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-twsbaj7v) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore.testWriteExportFileCompatibility _ CachingFileStoreTestWithFileJobStore.testReadCacheMissFileFromJobStoreWithCachingReadFile _ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 735, in testReadCacheMissFileFromJobStoreWithCachingReadFile self._testCacheMissFunction(cacheReadFile=True) ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 749, in _testCacheMissFunction Job.Runner.startToil(A, self.options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testReadCacheMissFileFromJobStoreWithCachingReadFile (Apr 03 2026 23:05:46:054980 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testReadCacheMissFileFromJobStoreWithCachingReadFile ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithCachingReadFile-1bhgvwn9/logFile'. DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithCachingReadFile-1bhgvwn9/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-fd5c5y19', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithCachingReadFile-1bhgvwn9', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-fd5c5y19'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'e1c5d84a-eb0c-4101-93bd-0f16b53573a4' DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithCachingReadFile-1bhgvwn9/toilwf-9d6cb57408cf575490c9c535ac478a8e DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281472851699152. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281472851699152 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-8146fc2de20042b3be9c82dbfed4a170/stream for result of '_writeFileToJobStoreWithAsserts' TemporaryID(db03e515-8747-461e-b78f-65baf03e8f24) v0 DEBUG toil.job:job.py:2624 Saving graph of 2 jobs, 2 non-service, 2 new DEBUG toil.job:job.py:2644 Processing job '_readFromJobStore' kind-_readFromJobStore/instance-shturzj6 v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-0eb52560c70c43548b7ec2afc3786036/stream for result of '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-alvvk8j8 v0 DEBUG toil.job:job.py:2644 Processing job '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-alvvk8j8 v0 DEBUG toil.job:job.py:1299 New job version: '_readFromJobStore' kind-_readFromJobStore/instance-shturzj6 v1 DEBUG toil.job:job.py:1299 New job version: '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-alvvk8j8 v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'e1c5d84a-eb0c-4101-93bd-0f16b53573a4', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-fd5c5y19', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithCachingReadFile-1bhgvwn9', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281472851699152... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281472851699152 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-9d6cb57408cf575490c9c535ac478a8e/deferred/funcw3gjumru DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-9d6cb57408cf575490c9c535ac478a8e/deferred/funcw3gjumru DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithCachingReadFile-1bhgvwn9/toilwf-9d6cb57408cf575490c9c535ac478a8e DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-9d6cb57408cf575490c9c535ac478a8e DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.016834259033203125 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-fd5c5y19) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testReadCacheMissFileFromJobStoreWithCachingReadFile _____________________________ JobTest.testStatic2 ______________________________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/jobTest.py", line 115, in testStatic2 Job.Runner.startToil(A, options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.jobTest.JobTest:testStatic2 (Apr 03 2026 23:05:47:128553 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.jobTest.JobTest.testStatic2 ... DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. INFO toil.test:__init__.py:120 Tore down toil.test.src.jobTest.JobTest.testStatic2 __ NonCachingFileStoreTestWithFileJobStore.testWriteReadGlobalFilePermissions __ [gw11] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 269, in testWriteReadGlobalFilePermissions Job.Runner.startToil(read_write_job, self.options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore:testWriteReadGlobalFilePermissions (Apr 03 2026 23:05:46:655099 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore.testWriteReadGlobalFilePermissions ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'urllib3', 'concurrent', 'docker', 'requests', 'dill', 'boto3', 'debugWorkflow', 'charset_normalizer', 'botocore', 'bcdocs', 'boto', 'asyncio'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-6h06pxqy/logFile'. DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'urllib3', 'concurrent', 'docker', 'requests', 'dill', 'boto3', 'debugWorkflow', 'charset_normalizer', 'botocore', 'bcdocs', 'boto', 'asyncio'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-6h06pxqy/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-wzbkmyba', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-6h06pxqy', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-wzbkmyba'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '32a6f1dd-1580-47eb-bdd4-b06c30fa97b3' DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-6h06pxqy/toilwf-42d60fb8b8d6592c95f6beeef90fc983 DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281473754692832. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281473754692832 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-120719d7c31e4f25b6a15fd2d2e609e1/stream for result of '_testWriteReadGlobalFilePermissions' TemporaryID(07999322-c82b-48dc-a480-c72c3f4f6f36) v0 DEBUG toil.job:job.py:2624 Saving graph of 1 jobs, 1 non-service, 1 new DEBUG toil.job:job.py:2644 Processing job '_testWriteReadGlobalFilePermissions' kind-_testWriteReadGlobalFilePermissions/instance-rz9m_aqk v0 DEBUG toil.job:job.py:1299 New job version: '_testWriteReadGlobalFilePermissions' kind-_testWriteReadGlobalFilePermissions/instance-rz9m_aqk v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '32a6f1dd-1580-47eb-bdd4-b06c30fa97b3', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-wzbkmyba', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-6h06pxqy', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281473754692832... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281473754692832 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-42d60fb8b8d6592c95f6beeef90fc983/deferred/funchd14b3vm DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-42d60fb8b8d6592c95f6beeef90fc983/deferred/funchd14b3vm DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-6h06pxqy/toilwf-42d60fb8b8d6592c95f6beeef90fc983 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-42d60fb8b8d6592c95f6beeef90fc983 DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.008817434310913086 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-wzbkmyba) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore.testWriteReadGlobalFilePermissions _ CachingFileStoreTestWithFileJobStore.testReadCacheMissFileFromJobStoreWithoutCachingReadFile _ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 728, in testReadCacheMissFileFromJobStoreWithoutCachingReadFile self._testCacheMissFunction(cacheReadFile=False) ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 749, in _testCacheMissFunction Job.Runner.startToil(A, self.options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testReadCacheMissFileFromJobStoreWithoutCachingReadFile (Apr 03 2026 23:05:46:714647 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testReadCacheMissFileFromJobStoreWithoutCachingReadFile ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithoutCachingReadFile-fu3emx0c/logFile'. DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithoutCachingReadFile-fu3emx0c/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-jdnw_evo', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithoutCachingReadFile-fu3emx0c', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-jdnw_evo'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '4be018af-23b8-471a-832d-c7c69157df68' DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithoutCachingReadFile-fu3emx0c/toilwf-6d9427701ea159dca47d7678f27738de DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281472854426896. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281472854426896 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-7c00766b9c444c7985a7f2755ad1d30f/stream for result of '_writeFileToJobStoreWithAsserts' TemporaryID(f0e056f7-c204-4980-af98-506cdbd57fb1) v0 DEBUG toil.job:job.py:2624 Saving graph of 2 jobs, 2 non-service, 2 new DEBUG toil.job:job.py:2644 Processing job '_readFromJobStore' kind-_readFromJobStore/instance-yt9gyobl v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-01ee2dd0ffee49cdb2a1fc22b1d4c9de/stream for result of '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-ry7_mtkj v0 DEBUG toil.job:job.py:2644 Processing job '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-ry7_mtkj v0 DEBUG toil.job:job.py:1299 New job version: '_readFromJobStore' kind-_readFromJobStore/instance-yt9gyobl v1 DEBUG toil.job:job.py:1299 New job version: '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-ry7_mtkj v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '4be018af-23b8-471a-832d-c7c69157df68', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-jdnw_evo', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithoutCachingReadFile-fu3emx0c', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281472854426896... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281472854426896 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-6d9427701ea159dca47d7678f27738de/deferred/funcoixdawkn DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-6d9427701ea159dca47d7678f27738de/deferred/funcoixdawkn DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithoutCachingReadFile-fu3emx0c/toilwf-6d9427701ea159dca47d7678f27738de DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-6d9427701ea159dca47d7678f27738de DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.005414485931396484 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-jdnw_evo) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testReadCacheMissFileFromJobStoreWithoutCachingReadFile _________________________ RegularLogTest.testWriteLogs _________________________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/regularLogTest.py", line 66, in testWriteLogs subprocess.check_call([sys.executable, ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ '-m', helloWorld.__name__, ^^^^^^^^^^^^^^^^^^^^^^^^^^ ...<2 lines>... '--logLevel=debug', ^^^^^^^^^^^^^^^^^^^ '--writeLogs=%s' % self.tempDir]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.13/subprocess.py", line 421, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/usr/bin/python3.13', '-m', 'toil.test.mesos.helloWorld', './toilTest', '--clean=always', '--logLevel=debug', '--writeLogs=/tmp/toil-test-src.regularLogTest.RegularLogTest-testWriteLogs-tempDir-711osmhj']' returned non-zero exit status 1. ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.regularLogTest.RegularLogTest:testWriteLogs (Apr 03 2026 23:05:46:244175 PDT) ----------------------------- Captured stderr call ----------------------------- [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'boto', 'urllib3', 'boto3', 'charset_normalizer', 'botocore', 'dill', 'requests', 'docker'} [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.statsAndLogging] Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.common] Initialized default configuration: {"config_version": 1.0} [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.batchSystems.options] Add options for single_machine batch system [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.batchSystems.options] Add options for grid_engine batch system [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.batchSystems.options] Add options for lsf batch system [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.batchSystems.options] Add options for slurm batch system [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.batchSystems.options] Add options for torque batch system [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.common] Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.common] Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'debug', 'logFile': None, 'logRotating': False, 'jobStore': 'file:/build/reproducible-path/toil-6.1.0/toilTest', 'workDir': None, 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': '/tmp/toil-test-src.regularLogTest.RegularLogTest-testWriteLogs-tempDir-711osmhj', '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/build/reproducible-path/toil-6.1.0/toilTest'. [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.jobStores.abstractJobStore] The workflow ID is: 'bf8e416d-0b8d-41b8-9eb4-45d43d4b4178' [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.common] Obtained node ID a1dca538-3ebd-4126-8036-4b3775a5c79e from file /proc/sys/kernel/random/boot_id [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.common] Using the single machine batch system [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.common] Created the workflow directory for this machine at /tmp/toilwf-329e8eb546045ac895a4b5244fe9e961 [2026-04-03T23:05:47-1200] [Thread-1 (daddy)] [D] [toil.batchSystems.singleMachine] Started daddy thread for batch system 281473795810240. [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.batchSystems.singleMachine] Started batch system 281473795810240 in normal mode. [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.common] User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.mesos.helloWorld', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.common] No user script to auto-deploy. [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.common] Written the environment for the jobs to the environment file [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.common] Caching all jobs in job store [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.common] 0 jobs downloaded. [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-3a812c6aa6984a998f3c533c73b5efb2/stream for result of 'hello_world' TemporaryID(8b19e270-7a5d-4409-9b5e-b4ee6f92cbcb) v0 [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 1 new [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.job] Processing job 'hello_world' kind-hello_world/instance-2fqjz4t5 v0 [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.job] New job version: 'hello_world' kind-hello_world/instance-2fqjz4t5 v1 [2026-04-03T23:05:47-1200] [MainThread] [I] [toil] Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. [2026-04-03T23:05:47-1200] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': 'bf8e416d-0b8d-41b8-9eb4-45d43d4b4178', 'kill_polling_interval': 5, 'jobStore': 'file:/build/reproducible-path/toil-6.1.0/toilTest', 'workDir': None, 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': '/tmp/toil-test-src.regularLogTest.RegularLogTest-testWriteLogs-tempDir-711osmhj', 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.realtimeLogger] Real-time logging disabled [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.common] Shutting down batch system ... [2026-04-03T23:05:47-1200] [Thread-1 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread cleaning up 0 remaining children for batch system 281473795810240... [2026-04-03T23:05:47-1200] [Thread-1 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread for batch system 281473795810240 finishing because no children should now exist [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Attempting worker cleanup [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.deferred] Cleaning up deferred functions system [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.deferred] Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-329e8eb546045ac895a4b5244fe9e961/deferred/funcrgw2gmxx [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.deferred] Running orphaned deferred functions [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.deferred] Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-329e8eb546045ac895a4b5244fe9e961/deferred/funcrgw2gmxx [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting workflow directory /tmp/toilwf-329e8eb546045ac895a4b5244fe9e961 [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-329e8eb546045ac895a4b5244fe9e961 [2026-04-03T23:05:47-1200] [MainThread] [D] [toil.common] ... finished shutting down the batch system in 0.010696887969970703 seconds. [2026-04-03T23:05:47-1200] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/build/reproducible-path/toil-6.1.0/toilTest) Traceback (most recent call last): File "", line 198, in _run_module_as_main File "", line 88, in _run_code File "/build/reproducible-path/toil-6.1.0/src/toil/test/mesos/helloWorld.py", line 71, in main() ~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/mesos/helloWorld.py", line 67, in main toil.start(i) ~~~~~~~~~~^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' _____ CachingFileStoreTestWithFileJobStore.testReadWriteFileStreamTextMode _____ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 351, in testReadWriteFileStreamTextMode toil.start(A) ~~~~~~~~~~^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testReadWriteFileStreamTextMode (Apr 03 2026 23:05:47:363177 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testReadWriteFileStreamTextMode ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-loj17ic1/logFile'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-loj17ic1/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-2716gq54', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-loj17ic1', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-2716gq54'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'f4c0a838-4a26-4f4f-9a8f-d562be0a5df0' DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-loj17ic1/toilwf-c17da0986bb25873a04e9c0cfd4844b2 DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281472854425984. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281472854425984 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-e12643d2f7544df881c4d43da673a163/stream for result of '_testReadWriteFileStreamTextMode' TemporaryID(5c0636c9-0acb-4eda-9892-092832b72cc8) v0 DEBUG toil.job:job.py:2624 Saving graph of 1 jobs, 1 non-service, 1 new DEBUG toil.job:job.py:2644 Processing job '_testReadWriteFileStreamTextMode' kind-_testReadWriteFileStreamTextMode/instance-id7r9qfs v0 DEBUG toil.job:job.py:1299 New job version: '_testReadWriteFileStreamTextMode' kind-_testReadWriteFileStreamTextMode/instance-id7r9qfs v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'f4c0a838-4a26-4f4f-9a8f-d562be0a5df0', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-2716gq54', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-loj17ic1', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281472854425984... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281472854425984 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-c17da0986bb25873a04e9c0cfd4844b2/deferred/funcv4v2_3x7 DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-c17da0986bb25873a04e9c0cfd4844b2/deferred/funcv4v2_3x7 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-loj17ic1/toilwf-c17da0986bb25873a04e9c0cfd4844b2 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-c17da0986bb25873a04e9c0cfd4844b2 DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.008961677551269531 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-2716gq54) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testReadWriteFileStreamTextMode ______________________ JobFileStoreTest.testJobFileStore _______________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/jobFileStoreTest.py", line 77, in testJobFileStore self._testJobFileStore(retryCount=0, badWorker=0.0, stringNo=5, stringLength=1000000) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/jobFileStoreTest.py", line 69, in _testJobFileStore Job.Runner.startToil(Job.wrapJobFn(fileTestJob, [], ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ testStrings, chainLength), ^^^^^^^^^^^^^^^^^^^^^^^^^^ options) ^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.jobFileStoreTest.JobFileStoreTest:testJobFileStore (Apr 03 2026 23:05:45:050727 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.jobFileStoreTest.JobFileStoreTest.testJobFileStore ... DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'dill', 'charset_normalizer', 'concurrent', 'boto', 'requests', 'bcdocs', 'urllib3', 'docker', 'boto3', 'asyncio', 'botocore', 'debugWorkflow'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'dill', 'charset_normalizer', 'concurrent', 'boto', 'requests', 'bcdocs', 'urllib3', 'docker', 'boto3', 'asyncio', 'botocore', 'debugWorkflow'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': None, 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.jobFileStoreTest.JobFileStoreTest-jobstore-jdyqzxbm', 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 0, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, 'debugWorker': False, 'disableWorkerOutputCapture': False, 'badWorker': 0.0, 'badWorkerFailInterval': 1.0, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.jobFileStoreTest.JobFileStoreTest-jobstore-jdyqzxbm'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'e84bd45b-5771-45df-83f1-f678b8f6d273' DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toilwf-d59ce7ae1b7b5860b2de8b0491efb147 DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281473073575440. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281473073575440 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.jobFileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-cb79cf6eb6d64b0ca582d8c491312b48/stream for result of 'fileTestJob' TemporaryID(7c8acac4-c996-49a7-9e60-f2deb7e3a02c) v0 DEBUG toil.job:job.py:2624 Saving graph of 1 jobs, 1 non-service, 1 new DEBUG toil.job:job.py:2644 Processing job 'fileTestJob' kind-fileTestJob/instance-d6xa_a63 v0 DEBUG toil.job:job.py:1299 New job version: 'fileTestJob' kind-fileTestJob/instance-d6xa_a63 v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'e84bd45b-5771-45df-83f1-f678b8f6d273', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.jobFileStoreTest.JobFileStoreTest-jobstore-jdyqzxbm', 'workDir': None, 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'onSuccess', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': False, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 0, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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': 1.0, 'logLevel': 'DEBUG', 'workflowAttemptNumber': 0} DEBUG toil.realtimeLogger:realtimeLogger.py:162 Real-time logging disabled DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281473073575440... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281473073575440 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-d59ce7ae1b7b5860b2de8b0491efb147/deferred/functj4gw2yx DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-d59ce7ae1b7b5860b2de8b0491efb147/deferred/functj4gw2yx DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toilwf-d59ce7ae1b7b5860b2de8b0491efb147 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-d59ce7ae1b7b5860b2de8b0491efb147 DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.00641179084777832 seconds. INFO toil.test:__init__.py:120 Tore down toil.test.src.jobFileStoreTest.JobFileStoreTest.testJobFileStore ___________________ JobFileStoreTest.testNonCachingFileStore ___________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/jobFileStoreTest.py", line 44, in testNonCachingFileStore workflow.start(Job.wrapJobFn(simpleFileStoreJob)) ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.jobFileStoreTest.JobFileStoreTest:testNonCachingFileStore (Apr 03 2026 23:05:48:402043 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.jobFileStoreTest.JobFileStoreTest.testNonCachingFileStore ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. INFO toil.test:__init__.py:120 Tore down toil.test.src.jobFileStoreTest.JobFileStoreTest.testNonCachingFileStore ___ CachingFileStoreTestWithFileJobStore.testSimultaneousReadsUncachedStream ___ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 1302, in testSimultaneousReadsUncachedStream Job.Runner.startToil(parent, self.options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testSimultaneousReadsUncachedStream (Apr 03 2026 23:05:47:987594 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testSimultaneousReadsUncachedStream ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testSimultaneousReadsUncachedStream-rbpsbexr/logFile'. DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testSimultaneousReadsUncachedStream-rbpsbexr/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-47ux29da', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testSimultaneousReadsUncachedStream-rbpsbexr', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 0, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': True, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-47ux29da'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'da623dd4-3846-493b-8ab0-66b748e2d402' DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testSimultaneousReadsUncachedStream-rbpsbexr/toilwf-002f9196b27d555d9125d13c8e0c9bf0 DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281472854432672. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281472854432672 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-ca619c9bd80b4ef699a699671cb6b12e/stream for result of '_createUncachedFileStream' TemporaryID(3b4661bc-c37f-445b-aa66-07c7f8536481) v0 DEBUG toil.job:job.py:2624 Saving graph of 31 jobs, 31 non-service, 31 new DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-6ca16zk2 v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-4be2a61c22f74bde90ec6e123d3e8596/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-ipeh0c50 v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-463947e1fb7e47bab83d9a19d11ee142/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-vw_mhc2f v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-bfee78547f654509b4b5a92c9b42f37d/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-xv3cbfh4 v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-787790ca01b24cf9a6af6449cc6c752c/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-zm6kn2_0 v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-8bbda91111c0472581cc6d56b7280966/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-pjzw3iwy v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-84b7269dfa0e43549027819e851ce99d/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-2yvc85lq v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-90167dbaf1d34c649a9f92a41c1929d3/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-g4ktiinb v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-ecfd873039d340e58c52eece72459fc8/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-vrcozb_w v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-acbcc1b5bdf44bffb59fa51a6aef1858/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-d3gnhwwz v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-b25b85e84d2c4393b7dffcc044ed4390/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-q4wwpgvv v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-8868cee8ce0a44c3854f998bdddb767e/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-630j0fjo v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-596351b2e85f4da68933f977635f24e8/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-sy70nx5e v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-9e964baaccab4678966feebdaa1105e6/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-0qmac0_5 v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-1677067e28d646b9a41a161322155af4/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-j78wfots v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-24c199a6bf58401ab4e6ce3cb3929c9a/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-03s5185z v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-8d2c961dda6b436a8ec3905a7fafe89d/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-_pjqhacq v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-bc2eaa87a6f5439584be7a4377febf67/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-o0j2b6nw v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-e5290e7c68b843219a9fa639b5eff6f7/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-soo3efjl v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-ac8d87be3f224aabba96887b03f7aae4/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-zveiu3z7 v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-7293d679a2ab4ef69b144815edaeb462/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-eeew0de4 v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-0ec56f18179d4878bb9763040a8649c8/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-738kq80g v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-40982797f3314382b0394e65c681209e/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-7_znd334 v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-723697bb633f494a9f2c8ff473fee192/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-zlus6_cy v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-862acdeed5254592ae72247f2cafca17/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-ar_0bpvn v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-b55bb3f7f93a4041bea98c8cc7978850/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-eeijn9ow v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-c003472c95c143f9b3e53c1b88b537c6/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-6g7hyd9_ v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-31a8cd5ec99a4ca98f46a0123626935d/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-h_p25lmz v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-cbca27e1b2bd4078aabebdea72683453/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-qgmamgrv v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-63a78c0a32924a3b8934aba7e7ae6686/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-2huy9w5c v0 DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-8eadbd8fd9de4666928852f3458bc793/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:2644 Processing job '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v0 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-6ca16zk2 v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-ipeh0c50 v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-vw_mhc2f v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-xv3cbfh4 v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-zm6kn2_0 v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-pjzw3iwy v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-2yvc85lq v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-g4ktiinb v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-vrcozb_w v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-d3gnhwwz v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-q4wwpgvv v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-630j0fjo v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-sy70nx5e v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-0qmac0_5 v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-j78wfots v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-03s5185z v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-_pjqhacq v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-o0j2b6nw v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-soo3efjl v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-zveiu3z7 v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-eeew0de4 v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-738kq80g v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-7_znd334 v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-zlus6_cy v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-ar_0bpvn v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-eeijn9ow v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-6g7hyd9_ v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-h_p25lmz v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-qgmamgrv v1 DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-2huy9w5c v1 DEBUG toil.job:job.py:1299 New job version: '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f5it690b v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'da623dd4-3846-493b-8ab0-66b748e2d402', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-47ux29da', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testSimultaneousReadsUncachedStream-rbpsbexr', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 0, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'environment': {}, 'disableChaining': True, '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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281472854432672... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281472854432672 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-002f9196b27d555d9125d13c8e0c9bf0/deferred/funchbm7vqeg DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-002f9196b27d555d9125d13c8e0c9bf0/deferred/funchbm7vqeg DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testSimultaneousReadsUncachedStream-rbpsbexr/toilwf-002f9196b27d555d9125d13c8e0c9bf0 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-002f9196b27d555d9125d13c8e0c9bf0 DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.00909566879272461 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-47ux29da) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testSimultaneousReadsUncachedStream ___________ CachingFileStoreTestWithFileJobStore.testToilIsNotBroken ___________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 120, in testToilIsNotBroken Job.Runner.startToil(A, self.options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testToilIsNotBroken (Apr 03 2026 23:05:48:678239 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testToilIsNotBroken ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testToilIsNotBroken-qrl_l8k0/logFile'. DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testToilIsNotBroken-qrl_l8k0/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-lwbczwe9', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testToilIsNotBroken-qrl_l8k0', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-lwbczwe9'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '6f751f75-085a-428a-b826-e22ffd03776a' DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testToilIsNotBroken-qrl_l8k0/toilwf-d1a5287f58ec56a893daa6e3f105167b DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281472854441184. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281472854441184 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-70669f731c394737b16266258609d807/stream for result of '_uselessFunc' TemporaryID(d5c5bf96-3c18-4d0e-bd10-f6d937109b89) v0 DEBUG toil.job:job.py:2624 Saving graph of 4 jobs, 4 non-service, 4 new DEBUG toil.job:job.py:2644 Processing job '_uselessFunc' kind-_uselessFunc/instance-1mbv_toi v0 DEBUG toil.job:job.py:2644 Processing job '_uselessFunc' kind-_uselessFunc/instance-17tc8110 v0 DEBUG toil.job:job.py:2644 Processing job '_uselessFunc' kind-_uselessFunc/instance-8h4fxu5p v0 DEBUG toil.job:job.py:2644 Processing job '_uselessFunc' kind-_uselessFunc/instance-ituthpga v0 DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-1mbv_toi v1 DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-17tc8110 v1 DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-8h4fxu5p v1 DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-ituthpga v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '6f751f75-085a-428a-b826-e22ffd03776a', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-lwbczwe9', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testToilIsNotBroken-qrl_l8k0', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281472854441184... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281472854441184 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-d1a5287f58ec56a893daa6e3f105167b/deferred/funcg53m24h2 DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-d1a5287f58ec56a893daa6e3f105167b/deferred/funcg53m24h2 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testToilIsNotBroken-qrl_l8k0/toilwf-d1a5287f58ec56a893daa6e3f105167b DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-d1a5287f58ec56a893daa6e3f105167b DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.009018659591674805 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-lwbczwe9) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testToilIsNotBroken ____ CachingFileStoreTestWithFileJobStore.testWriteExportFileCompatibility _____ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 300, in testWriteExportFileCompatibility initialPermissions, fileID = toil.start(export_file_job) ~~~~~~~~~~^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testWriteExportFileCompatibility (Apr 03 2026 23:05:49:295011 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testWriteExportFileCompatibility ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-orqyb167/logFile'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-orqyb167/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-pi4f1az2', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-orqyb167', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-pi4f1az2'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'e73f4718-c4a5-46fb-aefc-c118ee09214e' DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-orqyb167/toilwf-fcd95d5efbbe51f3b7b032ffeaa7e49e DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281472854432672. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281472854432672 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-afc0864805f145818d2d5c2ddc0350f3/stream for result of '_testWriteExportFileCompatibility' TemporaryID(6d90347e-3cbf-4aea-bcd1-bd3f4112d0de) v0 DEBUG toil.job:job.py:2624 Saving graph of 1 jobs, 1 non-service, 1 new DEBUG toil.job:job.py:2644 Processing job '_testWriteExportFileCompatibility' kind-_testWriteExportFileCompatibility/instance-knfauubn v0 DEBUG toil.job:job.py:1299 New job version: '_testWriteExportFileCompatibility' kind-_testWriteExportFileCompatibility/instance-knfauubn v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'e73f4718-c4a5-46fb-aefc-c118ee09214e', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-pi4f1az2', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-orqyb167', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281472854432672... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281472854432672 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-fcd95d5efbbe51f3b7b032ffeaa7e49e/deferred/func7ajjcopl DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-fcd95d5efbbe51f3b7b032ffeaa7e49e/deferred/func7ajjcopl DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-orqyb167/toilwf-fcd95d5efbbe51f3b7b032ffeaa7e49e DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-fcd95d5efbbe51f3b7b032ffeaa7e49e DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.013262510299682617 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-pi4f1az2) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testWriteExportFileCompatibility ______ CachingFileStoreTestWithFileJobStore.testWriteLocalFileToJobStore _______ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 719, in testWriteLocalFileToJobStore Job.Runner.startToil(A, self.options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testWriteLocalFileToJobStore (Apr 03 2026 23:05:49:854558 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testWriteLocalFileToJobStore ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteLocalFileToJobStore-usjt5jhl/logFile'. DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteLocalFileToJobStore-usjt5jhl/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-13zw_lv1', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteLocalFileToJobStore-usjt5jhl', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-13zw_lv1'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '88157db9-4194-4c30-9f30-1544a8c109b8' DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteLocalFileToJobStore-usjt5jhl/toilwf-d5223c20315657188d18d83e8a3c1bb1 DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281472854441184. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281472854441184 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-a654783c4c9440c1999c66ba53158f79/stream for result of '_writeFileToJobStoreWithAsserts' TemporaryID(dc1b1e64-1e9a-4f86-ba66-70affb80f694) v0 DEBUG toil.job:job.py:2624 Saving graph of 1 jobs, 1 non-service, 1 new DEBUG toil.job:job.py:2644 Processing job '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-ajxsff_h v0 DEBUG toil.job:job.py:1299 New job version: '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-ajxsff_h v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '88157db9-4194-4c30-9f30-1544a8c109b8', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-13zw_lv1', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteLocalFileToJobStore-usjt5jhl', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281472854441184... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281472854441184 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-d5223c20315657188d18d83e8a3c1bb1/deferred/funcr7lp2rcp DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-d5223c20315657188d18d83e8a3c1bb1/deferred/funcr7lp2rcp DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteLocalFileToJobStore-usjt5jhl/toilwf-d5223c20315657188d18d83e8a3c1bb1 DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-d5223c20315657188d18d83e8a3c1bb1 DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.008495569229125977 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-13zw_lv1) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testWriteLocalFileToJobStore _____ CachingFileStoreTestWithFileJobStore.testWriteNonLocalFileToJobStore _____ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 711, in testWriteNonLocalFileToJobStore Job.Runner.startToil(A, self.options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testWriteNonLocalFileToJobStore (Apr 03 2026 23:05:50:462659 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testWriteNonLocalFileToJobStore ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteNonLocalFileToJobStore-vx_5msav/logFile'. DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteNonLocalFileToJobStore-vx_5msav/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-uhw1gn_j', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteNonLocalFileToJobStore-vx_5msav', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-uhw1gn_j'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '11f90b1e-b560-4793-85d7-9f4679270b72' DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteNonLocalFileToJobStore-vx_5msav/toilwf-5d8b53c7e6db5e899065e7a2450427ee DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281472854432672. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281472854432672 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-bb7ecdfe74414c609b80d0e7c81ee1d5/stream for result of '_writeFileToJobStoreWithAsserts' TemporaryID(118e7ecb-40f0-49e5-93a5-24ef753f57ef) v0 DEBUG toil.job:job.py:2624 Saving graph of 1 jobs, 1 non-service, 1 new DEBUG toil.job:job.py:2644 Processing job '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-5y6j47tr v0 DEBUG toil.job:job.py:1299 New job version: '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-5y6j47tr v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '11f90b1e-b560-4793-85d7-9f4679270b72', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-uhw1gn_j', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteNonLocalFileToJobStore-vx_5msav', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281472854432672... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281472854432672 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-5d8b53c7e6db5e899065e7a2450427ee/deferred/funcis1sq3re DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-5d8b53c7e6db5e899065e7a2450427ee/deferred/funcis1sq3re DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteNonLocalFileToJobStore-vx_5msav/toilwf-5d8b53c7e6db5e899065e7a2450427ee DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-5d8b53c7e6db5e899065e7a2450427ee DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.007765293121337891 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-uhw1gn_j) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testWriteNonLocalFileToJobStore ___ CachingFileStoreTestWithFileJobStore.testWriteReadGlobalFilePermissions ____ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 Traceback (most recent call last): File "/usr/lib/python3.13/unittest/case.py", line 58, in testPartExecutor yield File "/usr/lib/python3.13/unittest/case.py", line 651, in run self._callTestMethod(testMethod) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^ File "/usr/lib/python3.13/unittest/case.py", line 606, in _callTestMethod if method() is not None: ~~~~~~^^ File "/build/reproducible-path/toil-6.1.0/src/toil/test/src/fileStoreTest.py", line 269, in testWriteReadGlobalFilePermissions Job.Runner.startToil(read_write_job, self.options) ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/job.py", line 2228, in startToil return toil.start(job) ~~~~~~~~~~^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 915, in start return self._runMainLoop(rootJobDescription) ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/toil-6.1.0/src/toil/common.py", line 1390, in _runMainLoop from toil.leader import Leader File "/build/reproducible-path/toil-6.1.0/src/toil/leader.py", line 51, in from toil.provisioners.abstractProvisioner import AbstractProvisioner File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in from toil.provisioners.node import Node File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in import pipes ModuleNotFoundError: No module named 'pipes' ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testWriteReadGlobalFilePermissions (Apr 03 2026 23:05:51:065217 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:115 Setting up toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testWriteReadGlobalFilePermissions ... DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.resource:resource.py:433 Module dir is /build/reproducible-path/toil-6.1.0/src, our prefix is /usr, virtualenv: False DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.statsAndLogging:statsAndLogging.py:281 Logging to file '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-07229sxs/logFile'. DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'asyncio', 'botocore', 'bcdocs', 'dill', 'boto', 'boto3', 'urllib3', 'debugWorkflow', 'charset_normalizer', 'docker', 'requests', 'concurrent'} DEBUG toil.statsAndLogging:statsAndLogging.py:295 Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'. DEBUG toil.common:common.py:665 Initialized default configuration: {"config_version": 1.0} DEBUG toil.batchSystems.options:options.py:188 Add options for single_machine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for grid_engine batch system DEBUG toil.batchSystems.options:options.py:188 Add options for lsf batch system DEBUG toil.batchSystems.options:options.py:188 Add options for slurm batch system DEBUG toil.batchSystems.options:options.py:188 Add options for torque batch system DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'INFO', 'logFile': None, 'logRotating': False, 'jobStore': None, 'workDir': None, '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': None, '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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, '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, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.common:common.py:414 Loaded configuration: {'config_version': '1.0', 'config': None, 'logLevel': 'DEBUG', 'logFile': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-07229sxs/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-h62tpsfm', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-07229sxs', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', '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, 'batch_logs_dir': None, 'scale': 1, 'allocate_mem': True, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'defaultPreemptible': False, 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': None, 'realTimeLogging': True, 'disableChaining': False, 'disableJobStoreChecksumVerification': False, 'sseKey': None, 'environment': {}, 'servicePollingInterval': 60.0, 'forceDockerAppliance': False, 'statusWait': 3600, 'disableProgress': False, '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, 'preserve_environment': ('PATH',), 'preserve_entire_environment': False, 'destBucket': None, '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, 'bypass_file_store': False, 'reference_inputs': False, 'disable_streaming': False, 'provenance': None, 'user_provenance': False, 'host_provenance': False, 'orcid': '', 'cwl_full_name': '', 'output_dialect': 'cromwell', 'output_directory': None, 'output_file': None, 'container': 'auto'} DEBUG toil.jobStores.fileJobStore:fileJobStore.py:88 Path to job store directory is '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-h62tpsfm'. DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'ccb1c641-03f7-46a2-9818-3de242870165' DEBUG toil.common:common.py:1041 Using the single machine batch system DEBUG toil.common:common.py:1339 Created the workflow directory for this machine at /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-07229sxs/toilwf-45b426efc15355dfb1502e8a0c720a0a DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 281472854425680. DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 281472854425680 in normal mode. DEBUG toil.common:common.py:1059 User script ModuleDescriptor(dirPath='/build/reproducible-path/toil-6.1.0/src', name='toil.test.src.fileStoreTest', fromVirtualEnv=False) belongs to Toil. No need to auto-deploy it. DEBUG toil.common:common.py:1087 No user script to auto-deploy. DEBUG toil.common:common.py:1222 Written the environment for the jobs to the environment file DEBUG toil.common:common.py:1226 Caching all jobs in job store DEBUG toil.common:common.py:1228 0 jobs downloaded. DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-6e8f1f7279254885b82b82487276fb86/stream for result of '_testWriteReadGlobalFilePermissions' TemporaryID(60180bcf-714e-494d-b536-7dbcef3a9190) v0 DEBUG toil.job:job.py:2624 Saving graph of 1 jobs, 1 non-service, 1 new DEBUG toil.job:job.py:2644 Processing job '_testWriteReadGlobalFilePermissions' kind-_testWriteReadGlobalFilePermissions/instance-0ov3lw7a v0 DEBUG toil.job:job.py:1299 New job version: '_testWriteReadGlobalFilePermissions' kind-_testWriteReadGlobalFilePermissions/instance-0ov3lw7a v1 INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host codethink03-arm64. DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'ccb1c641-03f7-46a2-9818-3de242870165', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-h62tpsfm', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-07229sxs', 'coordination_dir': None, 'noStdOutErr': False, 'stats': False, 'cleanWorkDir': 'always', 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'single_machine', 'scale': 1, 'allocate_mem': True, 'disableAutoDeployment': False, 'max_jobs': 9223372036854775807, 'max_local_jobs': None, 'manualMemArgs': False, 'run_local_jobs_on_workers': False, 'statePollingWait': None, 'batch_logs_dir': None, 'symlinkImports': True, 'moveOutputs': False, 'caching': 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': 1, 'defaultDisk': 2147483648, 'defaultAccelerators': [], 'maxCores': 9223372036854775807, 'maxMemory': 9223372036854775807, 'maxDisk': 9223372036854775807, 'defaultPreemptible': False, 'retryCount': 1, 'enableUnlimitedPreemptibleRetries': False, 'doubleMem': False, 'maxJobDuration': 9223372036854775807, 'rescueJobsFrequency': 60, 'maxLogFileSize': 104857600, 'writeLogs': None, 'writeLogsGzip': None, 'writeLogsFromAllJobs': False, 'write_messages': 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', 'workflowAttemptNumber': 0} INFO toil.realtimeLogger:realtimeLogger.py:139 Starting real-time logging. INFO toil.realtimeLogger:realtimeLogger.py:176 Stopping real-time logging server. INFO toil.realtimeLogger:realtimeLogger.py:180 Joining real-time logging server thread. DEBUG toil.common:common.py:1401 Shutting down batch system ... DEBUG toil.batchSystems.singleMachine:singleMachine.py:270 Daddy thread cleaning up 0 remaining children for batch system 281472854425680... DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 281472854425680 finishing because no children should now exist DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:474 Attempting worker cleanup DEBUG toil.deferred:deferred.py:203 Cleaning up deferred functions system DEBUG toil.deferred:deferred.py:145 Opened with own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-45b426efc15355dfb1502e8a0c720a0a/deferred/funcjmq2mu2e DEBUG toil.deferred:deferred.py:274 Running orphaned deferred functions DEBUG toil.deferred:deferred.py:351 Ran orphaned deferred functions from 0 abandoned state files DEBUG toil.deferred:deferred.py:153 Removing own state file /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-45b426efc15355dfb1502e8a0c720a0a/deferred/funcjmq2mu2e DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-07229sxs/toilwf-45b426efc15355dfb1502e8a0c720a0a DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-c4KDudsd/toil/toilwf-45b426efc15355dfb1502e8a0c720a0a DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.00525975227355957 seconds. INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-h62tpsfm) INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testWriteReadGlobalFilePermissions =========================== short test summary info ============================ FAILED src/toil/test/src/jobTest.py::JobTest::testDAGConsistency - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/busTest.py::MessageBusTest::test_restart_without_bus_path - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_import_export_restart_false - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/utils/toilDebugTest.py::testFetchJobStoreFiles - FileNotFoundError: [Errno 2] No such file or directory: 'python3.11' FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/utils/toilDebugTest.py::DebugJobTest::test_print_job_info - FileNotFoundError: [Errno 2] No such file or directory: 'python3.11' FAILED src/toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testEncapsulation - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/utils/toilDebugTest.py::DebugJobTest::test_run_job - FileNotFoundError: [Errno 2] No such file or directory: 'python3.11' FAILED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/resumabilityTest.py::ResumabilityTest::test_chaining - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/helloWorldTest.py::HelloWorldTest::testHelloWorld - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/promisesTest.py::PathIndexingPromiseTest::test - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/promisesTest.py::CachedUnpicklingJobStoreTest::test - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/promisesTest.py::ChainedIndexedPromisesTest::test - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/regularLogTest.py::RegularLogTest::testRegularLog - subprocess.CalledProcessError: Command '['/usr/bin/python3.13', '-m', 'toil.test.mesos.helloWorld', './toilTest', '--clean=always', '--batchSystem=single_machine', '--logLevel=debug']' returned non-zero exit status 1. FAILED src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/jobTest.py::JobTest::testStatic2 - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/regularLogTest.py::RegularLogTest::testWriteLogs - subprocess.CalledProcessError: Command '['/usr/bin/python3.13', '-m', 'toil.test.mesos.helloWorld', './toilTest', '--clean=always', '--logLevel=debug', '--writeLogs=/tmp/toil-test-src.regularLogTest.RegularLogTest-testWriteLogs-tempDir-711osmhj']' returned non-zero exit status 1. FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore - ModuleNotFoundError: No module named 'pipes' FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions - ModuleNotFoundError: No module named 'pipes' ERROR src/toil/test/cactus/test_cactus_integration.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::CactusIntegrationTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::CactusIntegrationTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/provisioners/clusterScalerTest.py ERROR src/toil/test/provisioners/clusterTest.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::CactusIntegrationTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/sort/sortTest.py ERROR src/toil/test/provisioners/clusterTest.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::CactusIntegrationTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::CactusIntegrationTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/src/jobServiceTest.py ERROR src/toil/test/cactus/test_cactus_integration.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::CactusIntegrationTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/utils/toilKillTest.py::ToilKillTestWithAWSJobStore - toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed ERROR src/toil/test/cactus/test_cactus_integration.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::CactusIntegrationTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/utils/utilsTest.py ERROR src/toil/test/provisioners/clusterTest.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/provisioners/clusterTest.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/provisioners/clusterTest.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::CactusIntegrationTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::CactusIntegrationTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::CactusIntegrationTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/provisioners/clusterTest.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/provisioners/clusterTest.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/utils/toilKillTest.py::ToilKillTestWithAWSJobStore - toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed ERROR src/toil/test/provisioners/clusterTest.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::CactusIntegrationTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/provisioners/clusterTest.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/utils/toilKillTest.py::ToilKillTestWithAWSJobStore - toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed ERROR src/toil/test/cactus/test_cactus_integration.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/cactus/test_cactus_integration.py::CactusIntegrationTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/utils/toilKillTest.py::ToilKillTestWithAWSJobStore - toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed ERROR src/toil/test/provisioners/clusterTest.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/utils/toilKillTest.py::ToilKillTestWithAWSJobStore - toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed ERROR src/toil/test/utils/toilKillTest.py::ToilKillTestWithAWSJobStore - toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed ERROR src/toil/test/utils/toilKillTest.py::ToilKillTestWithAWSJobStore - toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed ERROR src/toil/test/utils/toilKillTest.py::ToilKillTestWithAWSJobStore - toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed ERROR src/toil/test/provisioners/clusterTest.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/provisioners/clusterTest.py::AbstractClusterTest - AttributeError: 'NoneType' object has no attribute 'strip' ERROR src/toil/test/utils/toilKillTest.py::ToilKillTestWithAWSJobStore - toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed ERROR src/toil/test/utils/toilKillTest.py::ToilKillTestWithAWSJobStore - toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed ERROR src/toil/test/utils/toilKillTest.py::ToilKillTestWithAWSJobStore - toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed ERROR src/toil/test/utils/toilKillTest.py::ToilKillTestWithAWSJobStore - toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed ====== 37 failed, 104 passed, 328 skipped, 52 errors in 95.46s (0:01:35) ======= E: pybuild pybuild:389: test: plugin custom failed with: exit code=1: HOME=/build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil python3.13 setup.py develop --user && PYTHONPATH=/build/reproducible-path/toil-6.1.0/src:$PYTHONPATH PATH=/build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/.local/bin/:$PATH TOIL_TEST_QUICK=True TOIL_SKIP_DOCKER=True python3.13 -m pytest -n auto --dist loadscope -vv -W ignore --ignore src/toil/test/lib/aws/test_s3.py --ignore src/toil/test/provisioners/aws/awsProvisionerTest.py --ignore src/toil/test/wdl/wdltoil_test.py --ignore src/toil/test/cwl/cwlTest.py --ignore src/toil/test/src/promisedRequirementTest.py --ignore src/toil/test/lib/test_ec2.py --ignore src/toil/test/batchSystems/batchSystemTest.py --ignore src/toil/test/lib/aws/test_iam.py -k "not (test_bioconda or test_run_conformance or testImportFtpFile or ToilWdlIntegrationTest or SortTest or testCwlexample or testVirtualEnv or ToilDocumentationTest or test_cwl_toil_kill or testImportReadFileCompatibility or CleanWorkDirTest or DeferredFunctionTest or WdlToilTest or test_cactus_integration)" /build/reproducible-path/toil-6.1.0/src/toil/test dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13 make[1]: *** [debian/rules:25: override_dh_auto_test] Error 25 make[1]: Leaving directory '/build/reproducible-path/toil-6.1.0' make: *** [debian/rules:11: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2971413 and its subdirectories