I: pbuilder: network access will be disabled during build
I: Current time: Thu Jan 23 08:08:12 -12 2025
I: pbuilder-time-stamp: 1737662892
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: using eatmydata during job
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/13135/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='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='0f439ed3a727420fa5ad8b451d67c21e'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
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='13135'
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.bC3vmgjY/pbuilderrc_Q6Zo --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.bC3vmgjY/b1 --logfile b1/build.log toil_6.1.0-4.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://46.16.76.132:3128'
I: uname -a
Linux ionos2-i386 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/13135/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: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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 ... 19818 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} libaom3{a} libarchive-zip-perl{a} libavif16{a} libbrotli1{a} libcairo2{a} libcdt5{a} libcgraph6{a} libcom-err2{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} libgssapi-krb5-2{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} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} liblerc4{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmnl0{a} libnetfilter-conntrack3{a} libnfnetlink0{a} libnftnl11{a} libnsl2{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} libpython3.12-minimal{a} libpython3.12-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} libtirpc-common{a} libtirpc3t64{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-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} python3.12{a} python3.12-minimal{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 curl dbus-user-session docker-cli fonts-liberation git javascript-common krb5-locales 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, 243 newly installed, 0 to remove and 0 not upgraded.
Need to get 151 MB of archives. After unpacking 722 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main i386 runc i386 1.1.15+ds1-1+b1 [2687 kB]
Get: 2 http://deb.debian.org/debian unstable/main i386 containerd i386 1.7.24~ds1-4 [20.0 MB]
Get: 3 http://deb.debian.org/debian unstable/main i386 libip4tc2 i386 1.8.11-2 [20.8 kB]
Get: 4 http://deb.debian.org/debian unstable/main i386 libip6tc2 i386 1.8.11-2 [21.2 kB]
Get: 5 http://deb.debian.org/debian unstable/main i386 libxtables12 i386 1.8.11-2 [34.0 kB]
Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main i386 libmnl0 i386 1.0.5-3 [12.3 kB]
Get: 8 http://deb.debian.org/debian unstable/main i386 libnfnetlink0 i386 1.0.2-3 [15.0 kB]
Get: 9 http://deb.debian.org/debian unstable/main i386 libnetfilter-conntrack3 i386 1.1.0-1 [45.5 kB]
Get: 10 http://deb.debian.org/debian unstable/main i386 libnftnl11 i386 1.2.8-1 [69.1 kB]
Get: 11 http://deb.debian.org/debian unstable/main i386 iptables i386 1.8.11-2 [374 kB]
Get: 12 http://deb.debian.org/debian unstable/main i386 tini i386 0.19.0-1 [256 kB]
Get: 13 http://deb.debian.org/debian unstable/main i386 docker.io i386 26.1.5+dfsg1-4+b1 [17.1 MB]
Get: 14 http://deb.debian.org/debian unstable/main i386 libpython3.13-minimal i386 3.13.1-3 [858 kB]
Get: 15 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 16 http://deb.debian.org/debian unstable/main i386 python3.13-minimal i386 3.13.1-3 [2264 kB]
Get: 17 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.13.1-2 [27.0 kB]
Get: 18 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB]
Get: 19 http://deb.debian.org/debian unstable/main i386 tzdata all 2025a-1 [259 kB]
Get: 20 http://deb.debian.org/debian unstable/main i386 libffi8 i386 3.4.6-1 [21.2 kB]
Get: 21 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 22 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 23 http://deb.debian.org/debian unstable/main i386 libpython3.13-stdlib i386 3.13.1-3 [1980 kB]
Get: 24 http://deb.debian.org/debian unstable/main i386 python3.13 i386 3.13.1-3 [740 kB]
Get: 25 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.13.1-2 [9952 B]
Get: 26 http://deb.debian.org/debian unstable/main i386 python3 i386 3.13.1-2 [28.0 kB]
Get: 27 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.8-5 [816 kB]
Get: 28 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.8-5 [2241 kB]
Get: 29 http://deb.debian.org/debian unstable/main i386 libpopt0 i386 1.19+dfsg-2 [46.0 kB]
Get: 30 http://deb.debian.org/debian unstable/main i386 rsync i386 3.3.0+ds1-4 [435 kB]
Get: 31 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB]
Get: 32 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 33 http://deb.debian.org/debian unstable/main i386 openssl i386 3.4.0-2 [1427 kB]
Get: 34 http://deb.debian.org/debian unstable/main i386 ca-certificates all 20241223 [164 kB]
Get: 35 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 36 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 37 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 38 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 39 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 40 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 41 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.4-1 [96.1 kB]
Get: 42 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 43 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 44 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 45 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB]
Get: 46 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 47 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 48 http://deb.debian.org/debian unstable/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 49 http://deb.debian.org/debian unstable/main i386 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 50 http://deb.debian.org/debian unstable/main i386 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 51 http://deb.debian.org/debian unstable/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 52 http://deb.debian.org/debian unstable/main i386 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 53 http://deb.debian.org/debian unstable/main i386 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 54 http://deb.debian.org/debian unstable/main i386 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 55 http://deb.debian.org/debian unstable/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 56 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 75.6.0-1 [222 kB]
Get: 57 http://deb.debian.org/debian unstable/main i386 python3-ruamel.yaml.clib i386 0.2.12+ds-1 [175 kB]
Get: 58 http://deb.debian.org/debian unstable/main i386 python3-ruamel.yaml all 0.18.6+ds-3 [145 kB]
Get: 59 http://deb.debian.org/debian unstable/main i386 python3-certifi all 2024.12.14+ds-1 [9624 B]
Get: 60 http://deb.debian.org/debian unstable/main i386 python3-charset-normalizer i386 3.4.0-1+b1 [139 kB]
Get: 61 http://deb.debian.org/debian unstable/main i386 python3-idna all 3.8-2 [41.6 kB]
Get: 62 http://deb.debian.org/debian unstable/main i386 python3-urllib3 all 2.3.0-1 [114 kB]
Get: 63 http://deb.debian.org/debian unstable/main i386 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 64 http://deb.debian.org/debian unstable/main i386 python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get: 65 http://deb.debian.org/debian unstable/main i386 python3-msgpack i386 1.0.3-3+b3 [109 kB]
Get: 66 http://deb.debian.org/debian unstable/main i386 python3-cachecontrol all 0.14.2-1 [18.3 kB]
Get: 67 http://deb.debian.org/debian unstable/main i386 python3-mistune all 3.0.2-2 [33.2 kB]
Get: 68 http://deb.debian.org/debian unstable/main i386 python3-mypy-extensions all 1.0.0-1 [6064 B]
Get: 69 http://deb.debian.org/debian unstable/main i386 python3-pyparsing all 3.1.2-1 [146 kB]
Get: 70 http://deb.debian.org/debian unstable/main i386 python3-rdflib all 7.1.1-2 [472 kB]
Get: 71 http://deb.debian.org/debian unstable/main i386 python3-filelock all 3.16.1-1 [12.6 kB]
Get: 72 http://deb.debian.org/debian unstable/main i386 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB]
Get: 73 http://deb.debian.org/debian unstable/main i386 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB]
Get: 74 http://deb.debian.org/debian unstable/main i386 python3-schema-salad i386 8.8.20241206093842-2 [1312 kB]
Get: 75 http://deb.debian.org/debian unstable/main i386 cwl-upgrader all 1.2.12-1 [15.7 kB]
Get: 76 http://deb.debian.org/debian unstable/main i386 python3-argcomplete all 3.5.3-1 [40.4 kB]
Get: 77 http://deb.debian.org/debian unstable/main i386 python3-humanfriendly all 10.0-6 [85.6 kB]
Get: 78 http://deb.debian.org/debian unstable/main i386 python3-coloredlogs all 15.0.1-1 [47.4 kB]
Get: 79 http://deb.debian.org/debian unstable/main i386 python3-packaging all 24.2-1 [55.3 kB]
Get: 80 http://deb.debian.org/debian unstable/main i386 python3-cwl-utils all 0.36-1 [125 kB]
Get: 81 http://deb.debian.org/debian unstable/main i386 python3-dateutil all 2.9.0-3 [79.3 kB]
Get: 82 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 83 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 84 http://deb.debian.org/debian unstable/main i386 libgpg-error0 i386 1.51-3 [87.3 kB]
Get: 85 http://deb.debian.org/debian unstable/main i386 libgcrypt20 i386 1.11.0-7 [799 kB]
Get: 86 http://deb.debian.org/debian unstable/main i386 libxslt1.1 i386 1.1.35-1.1+b1 [243 kB]
Get: 87 http://deb.debian.org/debian unstable/main i386 python3-lxml i386 5.3.0-1+b1 [1586 kB]
Get: 88 http://deb.debian.org/debian unstable/main i386 python3-networkx all 3.2.1-5 [13.0 MB]
Get: 89 http://deb.debian.org/debian unstable/main i386 python3-prov all 2.0.1-1 [95.1 kB]
Get: 90 http://deb.debian.org/debian unstable/main i386 python3-psutil i386 5.9.8-2 [226 kB]
Get: 91 http://deb.debian.org/debian unstable/main i386 libcdt5 i386 2.42.4-2+b2 [40.9 kB]
Get: 92 http://deb.debian.org/debian unstable/main i386 libcgraph6 i386 2.42.4-2+b2 [68.2 kB]
Get: 93 http://deb.debian.org/debian unstable/main i386 libaom3 i386 3.11.0-1 [1915 kB]
Get: 94 http://deb.debian.org/debian unstable/main i386 libdav1d7 i386 1.5.0-1+b1 [327 kB]
Get: 95 http://deb.debian.org/debian unstable/main i386 libabsl20230802 i386 20230802.1-4 [521 kB]
Get: 96 http://deb.debian.org/debian unstable/main i386 libgav1-1 i386 0.19.0-3 [326 kB]
Get: 97 http://deb.debian.org/debian unstable/main i386 librav1e0.7 i386 0.7.1-9 [664 kB]
Get: 98 http://deb.debian.org/debian unstable/main i386 libsvtav1enc2 i386 2.3.0+dfsg-1 [1053 kB]
Get: 99 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB]
Get: 100 http://deb.debian.org/debian unstable/main i386 libyuv0 i386 0.0.1899.20250103-1 [111 kB]
Get: 101 http://deb.debian.org/debian unstable/main i386 libavif16 i386 1.1.1-1 [124 kB]
Get: 102 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB]
Get: 103 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.45-1 [288 kB]
Get: 104 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB]
Get: 105 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 106 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 107 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-2 [317 kB]
Get: 108 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-2 [402 kB]
Get: 109 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.5.0-0.1 [115 kB]
Get: 110 http://deb.debian.org/debian unstable/main i386 libheif-plugin-dav1d i386 1.19.5-1+b1 [11.8 kB]
Get: 111 http://deb.debian.org/debian unstable/main i386 libde265-0 i386 1.0.15-1+b2 [199 kB]
Get: 112 http://deb.debian.org/debian unstable/main i386 libheif-plugin-libde265 i386 1.19.5-1+b1 [16.3 kB]
Get: 113 http://deb.debian.org/debian unstable/main i386 libheif1 i386 1.19.5-1+b1 [540 kB]
Get: 114 http://deb.debian.org/debian unstable/main i386 libimagequant0 i386 2.18.0-1+b2 [36.0 kB]
Get: 115 http://deb.debian.org/debian unstable/main i386 libfribidi0 i386 1.0.16-1 [27.0 kB]
Get: 116 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.82.4-2 [1573 kB]
Get: 117 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB]
Get: 118 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 10.2.0-1 [504 kB]
Get: 119 http://deb.debian.org/debian unstable/main i386 libraqm0 i386 0.10.2-1 [14.6 kB]
Get: 120 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.23-1+b1 [48.4 kB]
Get: 121 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b2 [32.2 kB]
Get: 122 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-5 [191 kB]
Get: 123 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.5.0-0.1 [329 kB]
Get: 124 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB]
Get: 125 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB]
Get: 126 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.5-1 [28.2 kB]
Get: 127 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB]
Get: 128 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.10-2 [337 kB]
Get: 129 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.10-2 [834 kB]
Get: 130 http://deb.debian.org/debian unstable/main i386 libxpm4 i386 1:3.5.17-1+b3 [58.3 kB]
Get: 131 http://deb.debian.org/debian unstable/main i386 libgd3 i386 2.3.3-12+b1 [131 kB]
Get: 132 http://deb.debian.org/debian unstable/main i386 libgts-0.7-5t64 i386 0.7.6+darcs121130-5.2+b1 [160 kB]
Get: 133 http://deb.debian.org/debian unstable/main i386 libpixman-1-0 i386 0.44.0-3 [246 kB]
Get: 134 http://deb.debian.org/debian unstable/main i386 libxcb-render0 i386 1.17.0-2+b1 [116 kB]
Get: 135 http://deb.debian.org/debian unstable/main i386 libxcb-shm0 i386 1.17.0-2+b1 [105 kB]
Get: 136 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b3 [52.5 kB]
Get: 137 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1+b3 [28.8 kB]
Get: 138 http://deb.debian.org/debian unstable/main i386 libcairo2 i386 1.18.2-2 [591 kB]
Get: 139 http://deb.debian.org/debian unstable/main i386 libltdl7 i386 2.5.4-2 [417 kB]
Get: 140 http://deb.debian.org/debian unstable/main i386 fontconfig i386 2.15.0-2 [463 kB]
Get: 141 http://deb.debian.org/debian unstable/main i386 libthai-data all 0.1.29-2 [168 kB]
Get: 142 http://deb.debian.org/debian unstable/main i386 libdatrie1 i386 0.2.13-3+b1 [39.9 kB]
Get: 143 http://deb.debian.org/debian unstable/main i386 libthai0 i386 0.1.29-2+b1 [50.3 kB]
Get: 144 http://deb.debian.org/debian unstable/main i386 libpango-1.0-0 i386 1.56.1-1 [234 kB]
Get: 145 http://deb.debian.org/debian unstable/main i386 libpangoft2-1.0-0 i386 1.56.1-1 [59.1 kB]
Get: 146 http://deb.debian.org/debian unstable/main i386 libpangocairo-1.0-0 i386 1.56.1-1 [36.8 kB]
Get: 147 http://deb.debian.org/debian unstable/main i386 libpathplan4 i386 2.42.4-2+b2 [42.8 kB]
Get: 148 http://deb.debian.org/debian unstable/main i386 libgvc6 i386 2.42.4-2+b2 [717 kB]
Get: 149 http://deb.debian.org/debian unstable/main i386 libgvpr2 i386 2.42.4-2+b2 [203 kB]
Get: 150 http://deb.debian.org/debian unstable/main i386 liblab-gamut1 i386 2.42.4-2+b2 [198 kB]
Get: 151 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23.2 [216 kB]
Get: 152 http://deb.debian.org/debian unstable/main i386 libice6 i386 2:1.1.1-1 [67.8 kB]
Get: 153 http://deb.debian.org/debian unstable/main i386 libsm6 i386 2:1.2.4-1 [35.9 kB]
Get: 154 http://deb.debian.org/debian unstable/main i386 libxt6t64 i386 1:1.2.1-1.2+b2 [194 kB]
Get: 155 http://deb.debian.org/debian unstable/main i386 libxmu6 i386 2:1.1.3-3+b4 [60.8 kB]
Get: 156 http://deb.debian.org/debian unstable/main i386 libxaw7 i386 2:1.0.16-1 [220 kB]
Get: 157 http://deb.debian.org/debian unstable/main i386 graphviz i386 2.42.4-2+b2 [579 kB]
Get: 158 http://deb.debian.org/debian unstable/main i386 python3-pydot all 2.0.0-3 [32.6 kB]
Get: 159 http://deb.debian.org/debian unstable/main i386 python3-mdurl all 0.1.2-1 [9444 B]
Get: 160 http://deb.debian.org/debian unstable/main i386 python3-markdown-it all 3.0.0-2 [62.5 kB]
Get: 161 http://deb.debian.org/debian unstable/main i386 python3-pygments all 2.18.0+dfsg-2 [836 kB]
Get: 162 http://deb.debian.org/debian unstable/main i386 python3-rich all 13.9.4-1 [203 kB]
Get: 163 http://deb.debian.org/debian unstable/main i386 python3-rich-argparse all 1.6.0-2 [16.9 kB]
Get: 164 http://deb.debian.org/debian unstable/main i386 python3-spython all 0.3.13-2 [55.2 kB]
Get: 165 http://deb.debian.org/debian unstable/main i386 python3-arcp all 0.2.1-7 [13.6 kB]
Get: 166 http://deb.debian.org/debian unstable/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 167 http://deb.debian.org/debian unstable/main i386 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 168 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 75.6.0-1 [720 kB]
Get: 169 http://deb.debian.org/debian unstable/main i386 cwltool all 3.1.20250110105449-1 [514 kB]
Get: 170 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 171 http://deb.debian.org/debian unstable/main i386 libtool all 2.5.4-2 [539 kB]
Get: 172 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 173 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 174 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB]
Get: 175 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.1-1 [8584 B]
Get: 176 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 177 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 178 http://deb.debian.org/debian unstable/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 179 http://deb.debian.org/debian unstable/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 180 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 181 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 182 http://deb.debian.org/debian unstable/main i386 debhelper all 13.24.1 [920 kB]
Get: 183 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20250108 [113 kB]
Get: 184 http://deb.debian.org/debian unstable/main i386 xml-core all 0.19 [20.1 kB]
Get: 185 http://deb.debian.org/debian unstable/main i386 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get: 186 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2-1 [24.3 kB]
Get: 187 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-4 [35.0 kB]
Get: 188 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-4 [83.7 kB]
Get: 189 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 190 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-4 [354 kB]
Get: 191 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-4 [149 kB]
Get: 192 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 193 http://deb.debian.org/debian unstable/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 194 http://deb.debian.org/debian unstable/main i386 libjs-sphinxdoc all 8.1.3-4 [30.4 kB]
Get: 195 http://deb.debian.org/debian unstable/main i386 libjson-perl all 4.10000-1 [87.5 kB]
Get: 196 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 197 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB]
Get: 198 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB]
Get: 199 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.8-5 [1969 kB]
Get: 200 http://deb.debian.org/debian unstable/main i386 libyaml-0-2 i386 0.2.5-2 [55.8 kB]
Get: 201 http://deb.debian.org/debian unstable/main i386 python-babel-localedata all 2.16.0-1 [5696 kB]
Get: 202 http://deb.debian.org/debian unstable/main i386 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get: 203 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.8-5 [677 kB]
Get: 204 http://deb.debian.org/debian unstable/main i386 python3-all i386 3.13.1-2 [1052 B]
Get: 205 http://deb.debian.org/debian unstable/main i386 python3-antlr4 all 4.9.2-1 [98.1 kB]
Get: 206 http://deb.debian.org/debian unstable/main i386 python3-astroid all 3.3.8-2 [213 kB]
Get: 207 http://deb.debian.org/debian unstable/main i386 python3-babel all 2.16.0-1 [114 kB]
Get: 208 http://deb.debian.org/debian unstable/main i386 python3-six all 1.17.0-1 [16.5 kB]
Get: 209 http://deb.debian.org/debian unstable/main i386 python3-wcwidth all 0.2.13+dfsg1-1 [24.9 kB]
Get: 210 http://deb.debian.org/debian unstable/main i386 python3-blessed all 1.20.0-2 [54.3 kB]
Get: 211 http://deb.debian.org/debian unstable/main i386 python3-jmespath all 1.0.1-1 [21.1 kB]
Get: 212 http://deb.debian.org/debian unstable/main i386 python3-botocore all 1.35.92+repack-2 [7236 kB]
Get: 213 http://deb.debian.org/debian unstable/main i386 python3-s3transfer all 0.10.4-1 [56.4 kB]
Get: 214 http://deb.debian.org/debian unstable/main i386 python3-boto3 all 1.36.0+dfsg-1 [330 kB]
Get: 215 http://deb.debian.org/debian unstable/main i386 python3-configargparse all 1.7-2 [31.4 kB]
Get: 216 http://deb.debian.org/debian unstable/main i386 python3-defusedxml all 0.7.1-3 [43.4 kB]
Get: 217 http://deb.debian.org/debian unstable/main i386 python3-dill all 0.3.9-1 [83.5 kB]
Get: 218 http://deb.debian.org/debian unstable/main i386 python3.13-doc all 3.13.1-3 [15.2 MB]
Get: 219 http://deb.debian.org/debian unstable/main i386 python3-doc all 3.13.1-2 [10.1 kB]
Get: 220 http://deb.debian.org/debian unstable/main i386 python3-docker all 7.1.0-2 [89.8 kB]
Get: 221 http://deb.debian.org/debian unstable/main i386 python3-roman all 4.2-1 [10.4 kB]
Get: 222 http://deb.debian.org/debian unstable/main i386 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get: 223 http://deb.debian.org/debian unstable/main i386 python3-prefixed all 0.7.0-1 [7984 B]
Get: 224 http://deb.debian.org/debian unstable/main i386 python3-enlighten i386 1.11.2-1 [41.4 kB]
Get: 225 http://deb.debian.org/debian unstable/main i386 python3-execnet all 2.1.1-1 [40.2 kB]
Get: 226 http://deb.debian.org/debian unstable/main i386 python3-imagesize all 1.4.1-1 [6688 B]
Get: 227 http://deb.debian.org/debian unstable/main i386 python3-iniconfig all 1.1.1-2 [6396 B]
Get: 228 http://deb.debian.org/debian unstable/main i386 python3-markupsafe i386 2.1.5-1+b2 [13.9 kB]
Get: 229 http://deb.debian.org/debian unstable/main i386 python3-jinja2 all 3.1.5-1 [107 kB]
Get: 230 http://deb.debian.org/debian unstable/main i386 python3-pluggy all 1.5.0-1 [26.9 kB]
Get: 231 http://deb.debian.org/debian unstable/main i386 python3-pubsub all 4.0.3-7 [46.7 kB]
Get: 232 http://deb.debian.org/debian unstable/main i386 python3-pytest all 8.3.4-1 [250 kB]
Get: 233 http://deb.debian.org/debian unstable/main i386 python3-pytest-xdist all 3.6.1-1 [44.4 kB]
Get: 234 http://deb.debian.org/debian unstable/main i386 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get: 235 http://deb.debian.org/debian unstable/main i386 sphinx-common all 8.1.3-4 [616 kB]
Get: 236 http://deb.debian.org/debian unstable/main i386 python3-sphinx all 8.1.3-4 [468 kB]
Get: 237 http://deb.debian.org/debian unstable/main i386 python3-yaml i386 6.0.2-1+b1 [173 kB]
Get: 238 http://deb.debian.org/debian unstable/main i386 python3-sphinx-autoapi all 3.3.3-1 [108 kB]
Get: 239 http://deb.debian.org/debian unstable/main i386 python3-sphinx-autodoc-typehints all 2.3.0-2 [25.3 kB]
Get: 240 http://deb.debian.org/debian unstable/main i386 python3-sphinxcontrib.autoprogram all 0.1.9-1 [10.6 kB]
Get: 241 http://deb.debian.org/debian unstable/main i386 python3-stubserver all 1.1-4 [7764 B]
Get: 242 http://deb.debian.org/debian unstable/main i386 python3-tz all 2024.2-1 [31.0 kB]
Get: 243 http://deb.debian.org/debian unstable/main i386 python3-wdlparse all 0.1.0-3 [66.1 kB]
Fetched 151 MB in 3s (51.1 MB/s)
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Unpacking libnetfilter-conntrack3:i386 (1.1.0-1) ...
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Unpacking python3.13-minimal (3.13.1-3) ...
Setting up libpython3.13-minimal:i386 (3.13.1-3) ...
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Setting up libxdmcp6:i386 (1:1.1.5-1) ...
Setting up libkeyutils1:i386 (1.6.3-4) ...
Setting up libxcb1:i386 (1.17.0-2+b1) ...
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Setting up liblerc4:i386 (4.0.0+ds-5) ...
Setting up bsdextrautils (2.40.4-1) ...
Setting up libgpg-error0:i386 (1.51-3) ...
Setting up libdatrie1:i386 (0.2.13-3+b1) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libxcb-render0:i386 (1.17.0-2+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libyaml-0-2:i386 (0.2.5-2) ...
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Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
Setting up libtirpc-common (1.3.4+ds-1.3) ...
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Setting up libbrotli1:i386 (1.1.0-2+b6) ...
Setting up liblab-gamut1:i386 (2.42.4-2+b2) ...
Setting up libmagic1t64:i386 (1:5.45-3+b1) ...
Setting up libpython3.12-minimal:i386 (3.12.8-5) ...
Setting up x11-common (1:7.7+23.2) ...
invoke-rc.d: could not determine current runlevel
Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix.
Setting up libdeflate0:i386 (1.23-1+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-5) ...
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Setting up libcom-err2:i386 (1.47.2-1) ...
Setting up file (1:5.45-3+b1) ...
Setting up libjbig0:i386 (2.1-6.1+b2) ...
Setting up runc (1.1.15+ds1-1+b1) ...
Setting up libelf1t64:i386 (0.192-4) ...
Setting up python-babel-localedata (2.16.0-1) ...
Setting up libkrb5support0:i386 (1.21.3-4) ...
Setting up tzdata (2025a-1) ...
Current default time zone: 'Etc/UTC'
Local time is now: Thu Jan 23 20:08:53 UTC 2025.
Universal Time is now: Thu Jan 23 20:08:53 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up autotools-dev (20220109.1) ...
Setting up libjpeg62-turbo:i386 (1:2.1.5-3+b1) ...
Setting up libx11-data (2:1.8.10-2) ...
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Setting up libimagequant0:i386 (2.18.0-1+b2) ...
Setting up libunistring5:i386 (1.3-1) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libpng16-16t64:i386 (1.6.45-1) ...
Setting up libmnl0:i386 (1.0.5-3) ...
Setting up tini (0.19.0-1) ...
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Setting up libxtables12:i386 (1.8.11-2) ...
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Setting up autoconf (2.72-3) ...
Setting up libwebp7:i386 (1.5.0-0.1) ...
Setting up libffi8:i386 (3.4.6-1) ...
Setting up dwz (0.15-1+b1) ...
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Setting up libjson-perl (4.10000-1) ...
Setting up libx11-6:i386 (2:1.8.10-2) ...
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Setting up sgml-base (1.31) ...
Setting up libcdt5:i386 (2.42.4-2+b2) ...
Setting up libkrb5-3:i386 (1.21.3-4) ...
Setting up libcgraph6:i386 (2.42.4-2+b2) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libde265-0:i386 (1.0.15-1+b2) ...
Setting up containerd (1.7.24~ds1-4) ...
Setting up openssl (3.4.0-2) ...
Setting up libyuv0:i386 (0.0.1899.20250103-1) ...
Setting up readline-common (8.2-6) ...
Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up libjs-bootstrap (3.4.1+dfsg-3) ...
Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
Setting up libpopt0:i386 (1.19+dfsg-2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-1) ...
Setting up python3.12-minimal (3.12.8-5) ...
Setting up libice6:i386 (2:1.1.1-1) ...
Setting up gettext (0.23.1-1) ...
Setting up libxpm4:i386 (1:3.5.17-1+b3) ...
Setting up libxrender1:i386 (1:0.9.10-1.1+b3) ...
Setting up libtool (2.5.4-2) ...
Setting up fontconfig-config (2.15.0-2) ...
Setting up libxext6:i386 (2:1.3.4-1+b3) ...
Setting up libnftnl11:i386 (1.2.8-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up python3.13-doc (3.13.1-3) ...
Setting up libthai0:i386 (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:i386 (2.82.4-2) ...
No schema files found: doing nothing.
Setting up libfreetype6:i386 (2.13.3+dfsg-1) ...
Setting up libgssapi-krb5-2:i386 (1.21.3-4) ...
Setting up libgav1-1:i386 (0.19.0-3) ...
Setting up libjs-sphinxdoc (8.1.3-4) ...
Setting up libreadline8t64:i386 (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.1-1) ...
Setting up libgvpr2:i386 (2.42.4-2+b2) ...
Setting up libnetfilter-conntrack3:i386 (1.1.0-1) ...
Setting up groff-base (1.23.0-7) ...
Setting up xml-core (0.19) ...
Setting up libxslt1.1:i386 (1.1.35-1.1+b1) ...
Setting up libharfbuzz0b:i386 (10.2.0-1) ...
Setting up libgts-0.7-5t64:i386 (0.7.6+darcs121130-5.2+b1) ...
Setting up libfontconfig1:i386 (2.15.0-2) ...
Setting up libsm6:i386 (2:1.2.4-1) ...
Setting up libpython3.13-stdlib:i386 (3.13.1-3) ...
Setting up python3-doc (3.13.1-2) ...
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:i386 (3.13.1-2) ...
Setting up fontconfig (2.15.0-2) ...
Regenerating fonts cache... done.
Setting up libavif16:i386 (1.1.1-1) ...
Setting up libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ...
Setting up python3.13 (3.13.1-3) ...
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:i386 (1.56.1-1) ...
Setting up python3 (3.13.1-2) ...
Setting up docker.io (26.1.5+dfsg1-4+b1) ...
info: Selecting GID from range 100 to 999 ...
info: Adding group `docker' (GID 101) ...
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+b2) ...
Setting up libcairo2:i386 (1.18.2-2) ...
Setting up python3-psutil (5.9.8-2) ...
Setting up python3-tz (2024.2-1) ...
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 (4.2-1) ...
Setting up python3-jinja2 (3.1.5-1) ...
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 (2024.12.14+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:i386 (0.10.2-1) ...
Setting up python3-mdurl (0.1.2-1) ...
Setting up sphinx-common (8.1.3-4) ...
Setting up libxt6t64:i386 (1:1.2.1-1.2+b2) ...
Setting up python3-idna (3.8-2) ...
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:i386 (5.3.0-1+b1) ...
Setting up python3-rdflib (7.1.1-2) ...
Setting up libnsl2:i386 (1.3.0-3+b3) ...
Setting up python3-dateutil (2.9.0-3) ...
Setting up python3-msgpack (1.0.3-3+b3) ...
Setting up libpangoft2-1.0-0:i386 (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:i386 (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 (3.16.1-1) ...
Setting up libxmu6:i386 (2:1.1.3-3+b4) ...
Setting up python3-jaraco.functools (4.1.0-1) ...
Setting up libpython3.12-stdlib:i386 (3.12.8-5) ...
Setting up python3-jaraco.context (6.0.0-1) ...
Setting up python3-rich (13.9.4-1) ...
Setting up python3-defusedxml (0.7.1-3) ...
Setting up python3-charset-normalizer (3.4.0-1+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 python3.12 (3.12.8-5) ...
Setting up python3-blessed (1.20.0-2) ...
Setting up python3-typeguard (4.4.1-1) ...
Setting up python3-ruamel.yaml.clib (0.2.12+ds-1) ...
Setting up python3-all (3.13.1-2) ...
Setting up python3-yaml (6.0.2-1+b1) ...
Setting up debhelper (13.24.1) ...
Setting up libxaw7:i386 (2:1.0.16-1) ...
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-1) ...
Setting up python3-ruamel.yaml (0.18.6+ds-3) ...
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 (75.6.0-1) ...
Setting up python3-setuptools (75.6.0-1) ...
Setting up python3-pytest-xdist (3.6.1-1) ...
Setting up python3-babel (2.16.0-1) ...
update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
Setting up python3-docker (7.1.0-2) ...
Setting up python3-schema-salad (8.8.20241206093842-2) ...
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 (1.35.92+repack-2) ...
Setting up dh-python (6.20250108) ...
Setting up python3-s3transfer (0.10.4-1) ...
Setting up python3-cwl-utils (0.36-1) ...
Setting up python3-boto3 (1.36.0+dfsg-1) ...
Setting up libheif-plugin-libde265:i386 (1.19.5-1+b1) ...
Setting up libheif1:i386 (1.19.5-1+b1) ...
Setting up libgd3:i386 (2.3.3-12+b1) ...
Setting up libgvc6 (2.42.4-2+b2) ...
Setting up libheif-plugin-dav1d:i386 (1.19.5-1+b1) ...
Setting up graphviz (2.42.4-2+b2) ...
Setting up python3-pydot (2.0.0-3) ...
Setting up cwltool (3.1.20250110105449-1) ...
Processing triggers for libc-bin (2.40-6) ...
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 (8.1.3-4) ...
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 <crusoe@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
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: python3.12 setup.py config
running config
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/python3.12 setup.py build
running build
running build_py
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
copying src/toil/exceptions.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
copying src/toil/resource.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
copying src/toil/common.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
copying src/toil/bus.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
copying src/toil/worker.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
copying src/toil/serviceManager.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
copying src/toil/job.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
copying src/toil/statsAndLogging.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
copying src/toil/realtimeLogger.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
copying src/toil/toilState.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
copying src/toil/version.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
copying src/toil/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
copying src/toil/leader.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
copying src/toil/deferred.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test
copying src/toil/test/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/fileStores
copying src/toil/fileStores/nonCachingFileStore.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/fileStores
copying src/toil/fileStores/cachingFileStore.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/fileStores
copying src/toil/fileStores/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/fileStores
copying src/toil/fileStores/abstractFileStore.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/fileStores
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/provisioners
copying src/toil/provisioners/node.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/provisioners
copying src/toil/provisioners/clusterScaler.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/provisioners
copying src/toil/provisioners/abstractProvisioner.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/provisioners
copying src/toil/provisioners/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/provisioners
copying src/toil/provisioners/gceProvisioner.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/provisioners
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/toilClean.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/toilUpdateEC2Instances.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/toilStatus.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/toilStats.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/toilMain.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/toilConfig.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/toilLaunchCluster.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/toilSshCluster.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/toilDebugFile.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/toilDebugJob.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/toilKill.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/toilDestroyCluster.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/toilRsyncCluster.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
copying src/toil/utils/toilServer.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/utils
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copying src/toil/server/wsgi_app.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/server
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copying src/toil/test/src/resumabilityTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/src
copying src/toil/test/src/toilContextManagerTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/src
copying src/toil/test/src/threadingTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/src
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/options
copying src/toil/test/options/options.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/options
copying src/toil/test/options/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/options
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/docs
copying src/toil/test/docs/scriptsTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/docs
copying src/toil/test/docs/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/docs
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/wdl
copying src/toil/test/wdl/wdltoil_test.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/wdl
copying src/toil/test/wdl/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/wdl
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/jobStores
copying src/toil/test/jobStores/jobStoreTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/jobStores
copying src/toil/test/jobStores/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/jobStores
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cactus
copying src/toil/test/cactus/test_cactus_integration.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cactus
copying src/toil/test/cactus/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cactus
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/provisioners/aws
copying src/toil/test/provisioners/aws/awsProvisionerTest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/provisioners/aws
copying src/toil/test/provisioners/aws/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/provisioners/aws
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/lib/aws
copying src/toil/test/lib/aws/test_iam.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/lib/aws
copying src/toil/test/lib/aws/test_utils.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/lib/aws
copying src/toil/test/lib/aws/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/lib/aws
copying src/toil/test/lib/aws/test_s3.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/lib/aws
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/provisioners/aws
copying src/toil/provisioners/aws/awsProvisioner.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/provisioners/aws
copying src/toil/provisioners/aws/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/provisioners/aws
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/server/cli
copying src/toil/server/cli/wes_cwl_runner.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/server/cli
copying src/toil/server/cli/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/server/cli
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/server/api_spec
copying src/toil/server/api_spec/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/server/api_spec
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/server/wes
copying src/toil/server/wes/amazon_wes_utils.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/server/wes
copying src/toil/server/wes/toil_backend.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/server/wes
copying src/toil/server/wes/abstract_backend.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/server/wes
copying src/toil/server/wes/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/server/wes
copying src/toil/server/wes/tasks.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/server/wes
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/lib/aws
copying src/toil/lib/aws/iam.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/lib/aws
copying src/toil/lib/aws/ami.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/lib/aws
copying src/toil/lib/aws/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/lib/aws
copying src/toil/lib/aws/utils.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/lib/aws
copying src/toil/lib/aws/session.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/lib/aws
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/lib/encryption
copying src/toil/lib/encryption/conftest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/lib/encryption
copying src/toil/lib/encryption/_dummy.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/lib/encryption
copying src/toil/lib/encryption/_nacl.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/lib/encryption
copying src/toil/lib/encryption/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/lib/encryption
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/batchSystems/mesos
copying src/toil/batchSystems/mesos/conftest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/batchSystems/mesos
copying src/toil/batchSystems/mesos/executor.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/batchSystems/mesos
copying src/toil/batchSystems/mesos/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/batchSystems/mesos
copying src/toil/batchSystems/mesos/batchSystem.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/batchSystems/mesos
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/batchSystems/mesos/test
copying src/toil/batchSystems/mesos/test/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/batchSystems/mesos/test
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/jobStores/aws
copying src/toil/jobStores/aws/jobStore.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/jobStores/aws
copying src/toil/jobStores/aws/__init__.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/jobStores/aws
copying src/toil/jobStores/aws/utils.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/jobStores/aws
copying src/toil/test/cwl/conditional_wf.yaml -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/colon_test_output_job.yaml -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/test_filename_conflict_resolution.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/preemptible_expression.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/echo.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/stream.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/colon_test_output.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/revtool2.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/alwaysfails.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/revtool.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/test_filename_conflict_detection.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/echo-stderr.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/mpi_simple.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/conditional_wf.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/download_directory.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/glob_dir.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/seqtk_seq.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/revsort2.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_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_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/s3_secondary_file.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/preemptible.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/file_from_directory.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/download_subdirectory.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/nvidia_smi.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/echo_string.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/download.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/echo-stdout-log-dir.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/sorttool.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/revsort.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_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_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/load_contents.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/build/toil/test/cwl
copying src/toil/test/cwl/directory_from_directory.cwl -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_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_3.12_toil/build/toil/server/api_spec
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
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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
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copying src/toil/realtimeLogger.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/version.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil
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copying src/toil/leader.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil
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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/__init__.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
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copying src/toil/provisioners/gceProvisioner.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/provisioners
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copying src/toil/utils/toilStats.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils
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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/toilDebugJob.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/toilRsyncCluster.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/utils
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copying src/toil/cwl/conftest.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/cwl
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copying src/toil/test/wdl/wdltoil_test.py -> /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/wdl
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creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/test/jobStores
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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/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/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
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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/__init__.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
creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/provisioners/aws
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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/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
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creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/server/wes
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creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/lib/aws
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creating /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.13_toil/build/toil/batchSystems/mesos
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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
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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/nvidia_smi.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/download.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/sorttool.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/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/load_contents.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/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'}`.
[autosummary] generating autosummary for: appendices/architecture.rst, appendices/aws_min_permissions.rst, appendices/deploy.rst, appendices/environment_vars.rst, contributing/checklists.rst, contributing/contributing.rst, cwl/introduction.rst, cwl/running.rst, gettingStarted/install.rst, gettingStarted/quickStart.rst, ..., running/cloud/kubernetes.rst, running/debugging.rst, running/hpcEnvironments.rst, running/introduction.rst, running/server/wes.rst, running/utils.rst, wdl/conformance.rst, wdl/developing.rst, wdl/introduction.rst, wdl/running.rst
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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 <class 'requests.exceptions.ConnectionError'>: HTTPSConnectionPool(host='cwltool.readthedocs.io', port=443): Max retries exceeded with url: /en/latest/objects.inv (Caused by NameResolutionError("<urllib3.connection.HTTPSConnection object at 0xebe5e5f0>: Failed to resolve 'cwltool.readthedocs.io' ([Errno -3] Temporary failure in name resolution)"))
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WARNING: You are using cwltool version 3.1.20250110105449, which is not the version Toil is tested against. To install the correct cwltool for Toil, do:
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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
autoapi/toil/batchSystems/registry/index
autoapi/toil/batchSystems/singleMachine/index
autoapi/toil/batchSystems/slurm/index
autoapi/toil/batchSystems/torque/index
autoapi/toil/bus/index
autoapi/toil/common/index
autoapi/toil/cwl/index
autoapi/toil/cwl/conftest/index
autoapi/toil/cwl/cwltoil/index
autoapi/toil/cwl/utils/index
autoapi/toil/deferred/index
autoapi/toil/exceptions/index
autoapi/toil/fileStores/index
autoapi/toil/fileStores/abstractFileStore/index
autoapi/toil/fileStores/cachingFileStore/index
autoapi/toil/fileStores/nonCachingFileStore/index
autoapi/toil/job/index
autoapi/toil/jobStores/index
autoapi/toil/jobStores/abstractJobStore/index
autoapi/toil/jobStores/aws/index
autoapi/toil/jobStores/aws/jobStore/index
autoapi/toil/jobStores/aws/utils/index
autoapi/toil/jobStores/conftest/index
autoapi/toil/jobStores/fileJobStore/index
autoapi/toil/jobStores/googleJobStore/index
autoapi/toil/jobStores/utils/index
autoapi/toil/leader/index
autoapi/toil/lib/index
autoapi/toil/lib/accelerators/index
autoapi/toil/lib/aws/index
autoapi/toil/lib/aws/ami/index
autoapi/toil/lib/aws/iam/index
autoapi/toil/lib/aws/session/index
autoapi/toil/lib/aws/utils/index
autoapi/toil/lib/bioio/index
autoapi/toil/lib/compatibility/index
autoapi/toil/lib/conversions/index
autoapi/toil/lib/docker/index
autoapi/toil/lib/ec2/index
autoapi/toil/lib/ec2nodes/index
autoapi/toil/lib/encryption/index
autoapi/toil/lib/encryption/conftest/index
autoapi/toil/lib/exceptions/index
autoapi/toil/lib/expando/index
autoapi/toil/lib/generatedEC2Lists/index
autoapi/toil/lib/humanize/index
autoapi/toil/lib/io/index
autoapi/toil/lib/iterables/index
autoapi/toil/lib/memoize/index
autoapi/toil/lib/misc/index
autoapi/toil/lib/objects/index
autoapi/toil/lib/resources/index
autoapi/toil/lib/retry/index
autoapi/toil/lib/threading/index
autoapi/toil/lib/throttle/index
autoapi/toil/options/index
autoapi/toil/options/common/index
autoapi/toil/options/cwl/index
autoapi/toil/options/wdl/index
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
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autoapi/toil/test/cwl/conftest/index
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autoapi/toil/test/docs/index
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autoapi/toil/test/jobStores/jobStoreTest/index
autoapi/toil/test/lib/index
autoapi/toil/test/lib/aws/index
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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
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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
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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
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autoapi/toil/utils/toilRsyncCluster/index
autoapi/toil/utils/toilServer/index
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autoapi/toil/wdl/index
autoapi/toil/wdl/utils/index
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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_3.12_toil python3.12 setup.py develop --user && PYTHONPATH=/build/reproducible-path/toil-6.1.0/src:$PYTHONPATH PATH=/build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/.local/bin/:$PATH TOIL_TEST_QUICK=True TOIL_SKIP_DOCKER=True python3.12 -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:66: 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_3.12_toil/.local/lib/python3.12/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_3.12_toil/.local/bin
Installing _toil_mesos_executor script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/.local/bin
Installing _toil_worker script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/.local/bin
Installing cwltoil script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/.local/bin
Installing toil script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/.local/bin
Installing toil-cwl-runner script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/.local/bin
Installing toil-wdl-runner script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/.local/bin
Installing toil-wes-cwl-runner script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_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==0.18.6
Best match: ruamel.yaml 0.18.6
Adding ruamel.yaml 0.18.6 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==2024.2
Best match: pytz 2024.2
Adding pytz 2024.2 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 ruamel.yaml.clib==0.2.12
Best match: ruamel.yaml.clib 0.2.12
Adding ruamel.yaml.clib 0.2.12 to easy-install.pth file
Using /usr/lib/python3/dist-packages
Searching for idna==3.8
Best match: idna 3.8
Adding idna 3.8 to easy-install.pth file
Using /usr/lib/python3/dist-packages
Searching for charset-normalizer==3.4.0
Best match: charset-normalizer 3.4.0
Adding charset-normalizer 3.4.0 to easy-install.pth file
Installing normalizer script to /build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/.local/bin
Using /usr/lib/python3/dist-packages
Searching for certifi==2024.12.14
Best match: certifi 2024.12.14
Adding certifi 2024.12.14 to easy-install.pth file
Using /usr/lib/python3/dist-packages
Finished processing dependencies for toil==6.1.0
============================= test session starts ==============================
platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3.12
cachedir: .pytest_cache
rootdir: /build/reproducible-path/toil-6.1.0
configfile: setup.cfg
plugins: typeguard-4.4.1, xdist-3.6.1
created: 13/13 workers
13 workers [515 items]
scheduling tests via LoadScopeScheduling
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate
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/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testCleanCache
[gw0] [ 0%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testCleanCache
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testConfigEquality
[gw0] [ 0%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testConfigEquality
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testDestructionIdempotence
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean
[gw4] [ 0%] 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
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src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CRx_RM
[gw4] [ 1%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CRx_RM
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CRx_STOP
[gw4] [ 1%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CRx_STOP
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_FORGO
[gw4] [ 1%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_FORGO
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testAsyncWriteWithCaching
[gw7] [ 2%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testAsyncWriteWithCaching
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionFailCase
[gw7] [ 2%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionFailCase
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionPartialEvict
[gw7] [ 2%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionPartialEvict
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionTotalEvict
[gw7] [ 2%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionTotalEvict
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testControlledFailedWorkerRetry
[gw7] [ 2%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testControlledFailedWorkerRetry
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testDeleteLocalFile
[gw7] [ 3%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testDeleteLocalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testExtremeCacheSetup
[gw7] [ 3%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testExtremeCacheSetup
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreExportFile
[gw7] [ 3%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreExportFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreLogging
[gw7] [ 3%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreLogging
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreOperations
src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_many_all_exist
[gw0] [ 3%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testDestructionIdempotence
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testDestructionOfCorruptedJobStore
[gw0] [ 4%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testDestructionOfCorruptedJobStore
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testEmptyFileStoreIDIsReadable
[gw0] [ 4%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testEmptyFileStoreIDIsReadable
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testEncrypted
[gw0] [ 4%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testEncrypted
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testFileDeletion
[gw0] [ 4%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testFileDeletion
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testGrowingAndShrinkingJob
[gw0] [ 4%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testGrowingAndShrinkingJob
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testImportHttpFile
[gw0] [ 5%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testImportHttpFile
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testInitialState
[gw0] [ 5%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testInitialState
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testInlinedFiles
[gw0] [ 5%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testInlinedFiles
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobCreation
[gw0] [ 5%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobCreation
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobDeletions
[gw0] [ 5%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobDeletions
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobLoadEquality
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_None
[gw4] [ 6%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_None
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_RM
[gw4] [ 6%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_RM
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_STOP
[gw4] [ 6%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_STOP
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_FORGO
[gw4] [ 6%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_FORGO
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_None
[gw4] [ 6%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_None
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_RM
[gw4] [ 6%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_RM
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_STOP
src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testAsyncWriteWithCaching
[gw6] [ 7%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testAsyncWriteWithCaching
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionFailCase
[gw6] [ 7%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionFailCase
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionPartialEvict
[gw6] [ 7%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionPartialEvict
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionTotalEvict
[gw6] [ 7%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionTotalEvict
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testControlledFailedWorkerRetry
[gw6] [ 7%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testControlledFailedWorkerRetry
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testDeleteLocalFile
[gw6] [ 8%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testDeleteLocalFile
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testApplianceParser
[gw10] [ 8%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testApplianceParser
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo
[gw10] [ 8%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo
[gw10] [ 8%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag
[gw10] [ 8%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag
[gw10] [ 9%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo
[gw10] [ 9%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo
src/toil/test/utils/utilsTest.py::UtilsTest::testAWSProvisionerUtils
[gw9] [ 9%] SKIPPED src/toil/test/utils/utilsTest.py::UtilsTest::testAWSProvisionerUtils
src/toil/test/utils/utilsTest.py::UtilsTest::testGetPIDStatus
[gw7] [ 9%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreOperations
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testMultipleJobsReadSameCacheHitGlobalFile
[gw7] [ 9%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testMultipleJobsReadSameCacheHitGlobalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testMultipleJobsReadSameCacheMissGlobalFile
[gw7] [ 10%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testMultipleJobsReadSameCacheMissGlobalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCachHitFileFromJobStore
[gw7] [ 10%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCachHitFileFromJobStore
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile
[gw7] [ 10%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile
[gw7] [ 10%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode
[gw7] [ 10%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testRemoveLocalImmutablyReadFile
[gw7] [ 11%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testRemoveLocalImmutablyReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testRemoveLocalMutablyReadFile
[gw7] [ 11%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testRemoveLocalMutablyReadFile
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testBatchCreate
[gw3] [ 11%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testBatchCreate
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testChildLoadingEquality
[gw3] [ 11%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testChildLoadingEquality
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testCleanCache
[gw3] [ 11%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testCleanCache
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality
[gw3] [ 12%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence
[gw3] [ 12%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionOfCorruptedJobStore
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReturnFileSizes
[gw7] [ 12%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReturnFileSizes
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReturnFileSizesWithBadWorker
[gw7] [ 12%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReturnFileSizesWithBadWorker
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testSimultaneousReadsUncachedStream
[gw7] [ 12%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testSimultaneousReadsUncachedStream
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken
[gw7] [ 13%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility
[gw7] [ 13%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteLocalFileToJobStore
[gw7] [ 13%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteLocalFileToJobStore
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteNonLocalFileToJobStore
[gw7] [ 13%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteNonLocalFileToJobStore
[gw9] [ 13%] FAILED src/toil/test/utils/utilsTest.py::UtilsTest::testGetPIDStatus
src/toil/test/utils/utilsTest.py::UtilsTest::testGetStatusFailedCWLWF
[gw9] [ 13%] SKIPPED src/toil/test/utils/utilsTest.py::UtilsTest::testGetStatusFailedCWLWF
[gw0] [ 14%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobLoadEquality
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testLargeFile
[gw0] [ 14%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testLargeFile
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testMultiThreadImportFile
[gw0] [ 14%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testMultiThreadImportFile
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testMultipartUploads
[gw0] [ 14%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testMultipartUploads
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testOverlargeJob
[gw0] [ 14%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testOverlargeJob
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPartialReadFromStream
[gw0] [ 15%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPartialReadFromStream
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPerJobFiles
[gw0] [ 15%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPerJobFiles
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPersistantFilesToDelete
[gw0] [ 15%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPersistantFilesToDelete
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag
[gw10] [ 15%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo
[gw10] [ 15%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo
[gw3] [ 16%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionOfCorruptedJobStore
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable
[gw3] [ 16%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testFileDeletion
[gw3] [ 16%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testFileDeletion
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testGrowingAndShrinkingJob
[gw3] [ 16%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testGrowingAndShrinkingJob
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportHttpFile
[gw3] [ 16%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testImportHttpFile
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testInitialState
[gw3] [ 17%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testInitialState
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobCreation
[gw3] [ 17%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobCreation
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions
[gw3] [ 17%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobDeletions
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality
[gw3] [ 17%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testJobLoadEquality
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testLargeFile
[gw3] [ 17%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testLargeFile
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testMultipartUploads
[gw3] [ 18%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testMultipartUploads
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream
[gw3] [ 18%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testPartialReadFromStream
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testPerJobFiles
[gw3] [ 18%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testPerJobFiles
[gw4] [ 18%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_STOP
[gw10] [ 18%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testAsyncWriteWithCaching
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testExtremeCacheSetup
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testReadWriteFileStreamTextMode
[gw5] [ 19%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testAsyncWriteWithCaching
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testCacheEvictionFailCase
src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows
[gw0] [ 19%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testReadWriteFileStreamTextMode
src/toil/test/utils/utilsTest.py::UtilsTest::testGetStatusFailedToilWF
[gw5] [ 19%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testCacheEvictionFailCase
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete
[gw12] [ 19%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_and_cancel_workflows
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testCacheEvictionPartialEvict
src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url
[gw5] [ 19%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testCacheEvictionPartialEvict
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testCacheEvictionTotalEvict
[gw3] [ 20%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete
[gw10] [ 20%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo
[gw5] [ 20%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testCacheEvictionTotalEvict
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testControlledFailedWorkerRetry
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testReadWriteSharedFilesTextMode
[gw5] [ 20%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testControlledFailedWorkerRetry
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile
[gw12] [ 20%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_https_url
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testBatchCreate
[gw2] [ 20%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testBatchCreate
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode
[gw3] [ 21%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode
[gw0] [ 21%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testReadWriteSharedFilesTextMode
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode
[gw3] [ 21%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testSDBDomainsDeletedOnFailedJobstoreBucketCreation
[gw0] [ 21%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testSDBDomainsDeletedOnFailedJobstoreBucketCreation
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles
[gw3] [ 21%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_FORGO
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testSharedFiles
src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip
[gw0] [ 22%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testSharedFiles
[gw6] [ 22%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testExtremeCacheSetup
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testChildLoadingEquality
[gw4] [ 22%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_FORGO
[gw12] [ 22%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_inputs_zip
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testStatsAndLogging
[gw2] [ 22%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testChildLoadingEquality
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testCleanCache
[gw2] [ 23%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testCleanCache
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testConfigEquality
[gw0] [ 23%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testStatsAndLogging
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging
[gw2] [ 23%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testConfigEquality
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testDestructionIdempotence
[gw2] [ 23%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testDestructionIdempotence
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testDestructionOfCorruptedJobStore
[gw2] [ 23%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testDestructionOfCorruptedJobStore
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testEmptyFileStoreIDIsReadable
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testUpdateBehavior
[gw2] [ 24%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testEmptyFileStoreIDIsReadable
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreExportFile
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testFileDeletion
[gw3] [ 24%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging
[gw0] [ 24%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testUpdateBehavior
src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip
[gw6] [ 24%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreExportFile
[gw12] [ 24%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_and_inputs_zip
src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip
[gw2] [ 25%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testFileDeletion
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testGrowingAndShrinkingJob
[gw3] [ 25%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior
[gw12] [ 25%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_manifest_zip
[gw2] [ 25%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testGrowingAndShrinkingJob
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreLogging
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_None
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile
[gw6] [ 25%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreLogging
[gw4] [ 26%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_None
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreOperations
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles
[gw2] [ 26%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testImportHttpFile
src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip
[gw12] [ 26%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_multi_file_zip
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_RM
src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip
[gw12] [ 26%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_no_params_zip
[gw4] [ 26%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_RM
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState
src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url
[gw12] [ 26%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_STOP
src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails
[gw4] [ 27%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_STOP
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testWriteLogFiles
[gw2] [ 27%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testInitialState
[gw12] [ 27%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails
[gw6] [ 27%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreOperations
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_FORGO
[gw3] [ 27%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles
[gw0] [ 28%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testWriteLogFiles
[gw4] [ 28%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_FORGO
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testInlinedFiles
[gw2] [ 28%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testInlinedFiles
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testMultipleJobsReadSameCacheHitGlobalFile
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles
[gw3] [ 28%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles
[gw6] [ 28%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testMultipleJobsReadSameCacheHitGlobalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testMultipleJobsReadSameCacheMissGlobalFile
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::EncryptedAWSJobStoreTest::testZeroLengthFiles
[gw3] [ 29%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py
[gw6] [ 29%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testMultipleJobsReadSameCacheMissGlobalFile
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation
[gw0] [ 29%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testZeroLengthFiles
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCachHitFileFromJobStore
[gw2] [ 29%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation
[gw3] [ 29%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py
[gw6] [ 30%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCachHitFileFromJobStore
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py
[gw3] [ 30%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py
[gw6] [ 30%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py
[gw6] [ 30%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile
[gw2] [ 30%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions
[gw3] [ 31%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py
[gw0] [ 31%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_None
[gw6] [ 31%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality
[gw3] [ 31%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py
[gw4] [ 31%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_None
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testRemoveLocalImmutablyReadFile
[gw2] [ 32%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality
[gw6] [ 32%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testRemoveLocalImmutablyReadFile
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_RM
[gw0] [ 32%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py
[gw4] [ 32%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_RM
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testRemoveLocalMutablyReadFile
[gw6] [ 32%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testRemoveLocalMutablyReadFile
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_STOP
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testLargeFile
[gw2] [ 33%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testLargeFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReturnFileSizes
[gw4] [ 33%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_STOP
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::GoogleJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py
[gw0] [ 33%] 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::AWSJobStoreTest::testMultiThreadImportFile
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_FORGO
[gw4] [ 33%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_FORGO
[gw2] [ 33%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_None
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py
[gw4] [ 33%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_None
[gw6] [ 34%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReturnFileSizes
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testMultipartUploads
[gw0] [ 34%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_RM
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReturnFileSizesWithBadWorker
[gw4] [ 34%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_RM
[gw2] [ 34%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testMultipartUploads
[gw6] [ 34%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReturnFileSizesWithBadWorker
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_STOP
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testSimultaneousReadsUncachedStream
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py
[gw4] [ 35%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_STOP
[gw6] [ 35%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testSimultaneousReadsUncachedStream
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob
src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testToilIsNotBroken
[gw4] [ 35%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs
[gw6] [ 35%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testToilIsNotBroken
[gw2] [ 35%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob
[gw0] [ 36%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py
src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Demux
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility
[gw4] [ 36%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Demux
[gw6] [ 36%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream
src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Demux_Stream
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteLocalFileToJobStore
[gw4] [ 36%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Demux_Stream
[gw6] [ 36%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteLocalFileToJobStore
[gw2] [ 37%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream
src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Stream
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteNonLocalFileToJobStore
[gw4] [ 37%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Stream
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py
[gw6] [ 37%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteNonLocalFileToJobStore
[gw3] [ 37%] 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::AWSJobStoreTest::testPerJobFiles
[gw0] [ 37%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py
src/toil/test/lib/dockerTest.py::DockerTest::testDockerPipeChain
[gw2] [ 38%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles
[gw4] [ 38%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerPipeChain
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py
[gw3] [ 38%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py
[gw3] [ 38%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py
[gw2] [ 38%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py
[gw3] [ 39%] 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::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- 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
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode
[gw3] [ 39%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py
[gw0] [ 39%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py
[gw2] [ 39%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsizeplusone <- src/toil/test/__init__.py
[gw3] [ 39%] 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::AWSJobStoreTest::testReadWriteSharedFilesTextMode
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- 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] [ 40%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py
[gw2] [ 40%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode
[gw0] [ 40%] 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::AWSJobStoreTest::testSDBDomainsDeletedOnFailedJobstoreBucketCreation
src/toil/test/lib/dockerTest.py::DockerTest::testDockerPipeChainErrorDetection
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py
[gw2] [ 40%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testSDBDomainsDeletedOnFailedJobstoreBucketCreation
[gw4] [ 40%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerPipeChainErrorDetection
src/toil/test/lib/dockerTest.py::DockerTest::testNonCachingDockerChain
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles
[gw4] [ 40%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testNonCachingDockerChain
[gw2] [ 41%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles
[gw9] [ 41%] FAILED src/toil/test/utils/utilsTest.py::UtilsTest::testGetStatusFailedToilWF
src/toil/test/utils/utilsTest.py::UtilsTest::testGetStatusSuccessfulCWLWF
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging
[gw9] [ 41%] SKIPPED src/toil/test/utils/utilsTest.py::UtilsTest::testGetStatusSuccessfulCWLWF
[gw2] [ 41%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior
[gw2] [ 41%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior
[gw0] [ 42%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py
src/toil/test/utils/utilsTest.py::UtilsTest::testMultipleJobsPerWorkerStats
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles
[gw2] [ 42%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles
[gw2] [ 42%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py
[gw2] [ 42%] 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
[gw2] [ 42%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py
[gw9] [ 43%] SKIPPED src/toil/test/utils/utilsTest.py::UtilsTest::testMultipleJobsPerWorkerStats
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py
[gw2] [ 43%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsize <- src/toil/test/__init__.py
src/toil/test/utils/utilsTest.py::UtilsTest::testPrintJobLog
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
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_partsizeminusone <- src/toil/test/__init__.py
[gw2] [ 44%] 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
[gw2] [ 44%] 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
[gw2] [ 44%] 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
[gw2] [ 44%] 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
[gw2] [ 44%] 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
[gw2] [ 45%] 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
[gw2] [ 45%] 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
[gw2] [ 45%] 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
[gw2] [ 45%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions
[gw7] [ 45%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions
src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_and_cancel_workflows
[gw7] [ 46%] 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
[gw7] [ 46%] 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
[gw7] [ 46%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_inputs_zip
src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip
[gw7] [ 46%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_and_inputs_zip
src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip
[gw7] [ 46%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_manifest_zip
src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip
[gw7] [ 46%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_multi_file_zip
src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip
[gw7] [ 47%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_no_params_zip
src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url
[gw7] [ 47%] 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
[gw7] [ 47%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_relative_url_no_attachments_fails
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] [ 48%] 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
[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
[gw10] [ 48%] 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] [ 49%] 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] [ 49%] 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] [ 49%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_relative_url_no_attachments_fails
src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip
[gw12] [ 49%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip
src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode
[gw11] [ 49%] PASSED src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testBetaInertia
src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes
[gw8] [ 50%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_many_all_exist
[gw12] [ 50%] PASSED src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testAddingInitialNode
src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_exists
src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions
[gw6] [ 50%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions
src/toil/test/src/jobTest.py::JobTest::testDAGConsistency
src/toil/test/lib/dockerTest.py::DockerTest::testNonCachingDockerChainErrorDetection
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py
[gw3] [ 50%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py
src/toil/test/src/miscTests.py::MiscTests::testGetSizeOfDirectoryWorks
[gw4] [ 50%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testNonCachingDockerChainErrorDetection
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testFileStoreLogging
[gw8] [ 51%] 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
[gw3] [ 51%] SKIPPED src/toil/test/src/miscTests.py::MiscTests::testGetSizeOfDirectoryWorks
src/toil/test/src/miscTests.py::MiscTests::testIDStability
[gw4] [ 51%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testFileStoreLogging
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testFileStoreOperations
[gw3] [ 51%] PASSED src/toil/test/src/miscTests.py::MiscTests::testIDStability
src/toil/test/src/miscTests.py::MiscTests::test_atomic_context_error
[gw4] [ 51%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testFileStoreOperations
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode
[gw3] [ 52%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_atomic_context_error
src/toil/test/src/miscTests.py::MiscTests::test_atomic_context_ok
[gw3] [ 52%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_atomic_context_ok
src/toil/test/src/miscTests.py::MiscTests::test_atomic_install
[gw1] [ 52%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality
[gw3] [ 52%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_atomic_install
src/toil/test/src/miscTests.py::MiscTests::test_atomic_install_dev
[gw3] [ 52%] 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/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py
[gw0] [ 53%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testFileStoreLogging
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py
[gw0] [ 53%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testFileStoreLogging
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testFileStoreOperations
[gw0] [ 53%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testFileStoreOperations
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode
[gw8] [ 53%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_not_exists
[gw0] [ 53%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken
src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_exists
[gw0] [ 53%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility
[gw2] [ 54%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testFileStoreLogging
[gw2] [ 54%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testFileStoreLogging
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testFileStoreOperations
[gw2] [ 54%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testFileStoreOperations
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode
[gw0] [ 54%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility
[gw3] [ 54%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_call_command_err
[gw1] [ 55%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality
[gw11] [ 55%] PASSED src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testMaxNodes
src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testCleanCache
[gw1] [ 55%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testCleanCache
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality
[gw8] [ 55%] 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
src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip
[gw7] [ 55%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip
src/toil/test/src/jobServiceTest.py::JobServiceTest::testService
[gw2] [ 56%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken
[gw2] [ 56%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility
[gw2] [ 56%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility
[gw11] [ 56%] PASSED src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testMinNodes
src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet
[gw1] [ 56%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence
src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip
[gw10] [ 57%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip
src/toil/test/src/jobServiceTest.py::PerfectServiceTest::testService
[gw7] [ 57%] SKIPPED src/toil/test/src/jobServiceTest.py::JobServiceTest::testService
src/toil/test/src/jobServiceTest.py::JobServiceTest::testServiceDeadlock
[gw7] [ 57%] SKIPPED src/toil/test/src/jobServiceTest.py::JobServiceTest::testServiceDeadlock
src/toil/test/src/jobServiceTest.py::JobServiceTest::testServiceParallelRecursive
[gw7] [ 57%] SKIPPED src/toil/test/src/jobServiceTest.py::JobServiceTest::testServiceParallelRecursive
src/toil/test/src/jobServiceTest.py::JobServiceTest::testServiceRecursive
[gw7] [ 57%] SKIPPED src/toil/test/src/jobServiceTest.py::JobServiceTest::testServiceRecursive
src/toil/test/src/jobServiceTest.py::JobServiceTest::testServiceSerialization
[gw7] [ 58%] SKIPPED src/toil/test/src/jobServiceTest.py::JobServiceTest::testServiceSerialization
[gw8] [ 58%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_not_exists
[gw10] [ 58%] SKIPPED src/toil/test/src/jobServiceTest.py::PerfectServiceTest::testService
src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_some_exists
src/toil/test/src/jobServiceTest.py::PerfectServiceTest::testServiceDeadlock
[gw10] [ 58%] SKIPPED src/toil/test/src/jobServiceTest.py::PerfectServiceTest::testServiceDeadlock
src/toil/test/src/jobServiceTest.py::PerfectServiceTest::testServiceParallelRecursive
[gw10] [ 58%] SKIPPED src/toil/test/src/jobServiceTest.py::PerfectServiceTest::testServiceParallelRecursive
src/toil/test/src/jobServiceTest.py::PerfectServiceTest::testServiceRecursive
[gw10] [ 59%] SKIPPED src/toil/test/src/jobServiceTest.py::PerfectServiceTest::testServiceRecursive
src/toil/test/src/jobServiceTest.py::PerfectServiceTest::testServiceSerialization
[gw10] [ 59%] SKIPPED src/toil/test/src/jobServiceTest.py::PerfectServiceTest::testServiceSerialization
[gw1] [ 59%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionOfCorruptedJobStore
[gw11] [ 59%] PASSED src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testNoLaunchingIfDeltaAlreadyMet
src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet
[gw1] [ 59%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionOfCorruptedJobStore
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable
src/toil/test/src/miscTests.py::MiscTests::test_call_command_ok
[gw3] [ 60%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_call_command_ok
src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_build_tag
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions
[gw0] [ 60%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions
src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testDeferralWithConcurrentEncapsulation
[gw0] [ 60%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testDeferralWithConcurrentEncapsulation
[gw8] [ 60%] 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
[gw3] [ 60%] PASSED src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_build_tag
src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testDeferralWithFailureAndEncapsulation
[gw0] [ 60%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testDeferralWithFailureAndEncapsulation
src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testRestart
[gw0] [ 61%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testRestart
src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testSplitRootPackages
[gw0] [ 61%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testSplitRootPackages
[gw11] [ 61%] PASSED src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitIsSet
src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse
[gw1] [ 61%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testFileDeletion
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions
[gw2] [ 61%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions
src/toil/test/src/regularLogTest.py::RegularLogTest::testLogToMaster
[gw2] [ 62%] SKIPPED src/toil/test/src/regularLogTest.py::RegularLogTest::testLogToMaster
src/toil/test/src/regularLogTest.py::RegularLogTest::testMultipleLogToMaster
[gw2] [ 62%] SKIPPED src/toil/test/src/regularLogTest.py::RegularLogTest::testMultipleLogToMaster
src/toil/test/src/regularLogTest.py::RegularLogTest::testRegularLog
[gw1] [ 62%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testFileDeletion
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob
src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags
[gw3] [ 62%] 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] [ 62%] PASSED src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags
src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji
[gw3] [ 63%] PASSED src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji
[gw8] [ 63%] 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/jobServiceTest.py::JobServiceTest::testServiceWithCheckpoints
[gw7] [ 63%] SKIPPED src/toil/test/src/jobServiceTest.py::JobServiceTest::testServiceWithCheckpoints
src/toil/test/src/resourceTest.py::ResourceTest::testBuiltIn
src/toil/test/src/jobServiceTest.py::PerfectServiceTest::testServiceWithCheckpoints
[gw10] [ 63%] SKIPPED src/toil/test/src/jobServiceTest.py::PerfectServiceTest::testServiceWithCheckpoints
src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testUserTypesInJobFunctionArgs
src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore
[gw0] [ 63%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testUserTypesInJobFunctionArgs
src/toil/test/src/miscTests.py::TestPanic::test_nested_panic
[gw1] [ 64%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob
src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile
[gw3] [ 64%] PASSED src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object
[gw8] [ 64%] 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
[gw0] [ 64%] PASSED src/toil/test/src/miscTests.py::TestPanic::test_nested_panic
src/toil/test/src/miscTests.py::TestPanic::test_panic
[gw0] [ 64%] PASSED src/toil/test/src/miscTests.py::TestPanic::test_panic
src/toil/test/src/miscTests.py::TestPanic::test_panic_by_hand
src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClass
[gw11] [ 65%] PASSED src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testPreemptibleDeficitResponse
[gw0] [ 65%] PASSED src/toil/test/src/miscTests.py::TestPanic::test_panic_by_hand
src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding
src/toil/test/src/miscTests.py::TestPanic::test_panic_with_secondary
[gw0] [ 65%] PASSED src/toil/test/src/miscTests.py::TestPanic::test_panic_with_secondary
src/toil/test/lib/test_conversions.py::ConversionTest::test_convert
[gw3] [ 65%] SKIPPED src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClass
src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain
[gw8] [ 65%] 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
[gw11] [ 66%] PASSED src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::testRounding
src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large
[gw0] [ 66%] PASSED src/toil/test/lib/test_conversions.py::ConversionTest::test_convert
src/toil/test/lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds
[gw0] [ 66%] PASSED src/toil/test/lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds
src/toil/test/lib/test_conversions.py::ConversionTest::test_human2bytes
[gw0] [ 66%] PASSED src/toil/test/lib/test_conversions.py::ConversionTest::test_human2bytes
src/toil/test/provisioners/clusterScalerTest.py::ScalerThreadTest::testClusterScaling
[gw8] [ 66%] 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
[gw11] [ 66%] PASSED src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_large
src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed
[gw0] [ 67%] SKIPPED src/toil/test/provisioners/clusterScalerTest.py::ScalerThreadTest::testClusterScaling
src/toil/test/provisioners/clusterScalerTest.py::ScalerThreadTest::testClusterScalingMultipleNodeTypes
[gw0] [ 67%] SKIPPED src/toil/test/provisioners/clusterScalerTest.py::ScalerThreadTest::testClusterScalingMultipleNodeTypes
src/toil/test/provisioners/clusterScalerTest.py::ScalerThreadTest::testClusterScalingWithPreemptibleJobs
[gw0] [ 67%] SKIPPED src/toil/test/provisioners/clusterScalerTest.py::ScalerThreadTest::testClusterScalingWithPreemptibleJobs
src/toil/test/src/busTest.py::MessageBusTest::test_cross_thread_messaging
[gw11] [ 67%] PASSED src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_observed
src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small
[gw8] [ 67%] 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
[gw11] [ 68%] PASSED src/toil/test/provisioners/clusterScalerTest.py::ClusterScalerTest::test_overhead_accounting_small
[gw8] [ 68%] 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
src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_get_service_info
[gw11] [ 68%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_get_service_info
src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_health
[gw11] [ 68%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_health
src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_home
[gw11] [ 68%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_home
src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried
[gw0] [ 69%] PASSED src/toil/test/src/busTest.py::MessageBusTest::test_cross_thread_messaging
src/toil/test/src/busTest.py::MessageBusTest::test_enum_ints_in_file
[gw0] [ 69%] PASSED src/toil/test/src/busTest.py::MessageBusTest::test_enum_ints_in_file
[gw8] [ 69%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_none_exist
src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist
src/toil/test/src/busTest.py::MessageBusTest::test_restart_without_bus_path
[gw12] [ 69%] PASSED src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testHighTargetTime
src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes
[gw12] [ 69%] PASSED src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testJobTooLargeForAllNodes
src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs
[gw8] [ 70%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist
src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_exists
[gw8] [ 70%] 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
[gw8] [ 70%] 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
[gw8] [ 70%] 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
[gw8] [ 70%] 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
[gw8] [ 71%] 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
[gw8] [ 71%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_not_exists
src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testContextManger
[gw8] [ 71%] SKIPPED src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testContextManger
src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testExportAfterFailedExport
[gw8] [ 71%] SKIPPED src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testExportAfterFailedExport
src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testNoContextManger
[gw8] [ 71%] SKIPPED src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testNoContextManger
src/toil/test/__init__.py::toil.test.make_tests
[gw8] [ 72%] PASSED src/toil/test/__init__.py::toil.test.make_tests
src/toil/test/__init__.py::toil.test.timeLimit
[gw7] [ 72%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testBuiltIn
src/toil/test/src/resourceTest.py::ResourceTest::testNonPyStandAlone
[gw1] [ 72%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState
[gw12] [ 72%] PASSED src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testLongRunningJobs
src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime
[gw3] [ 72%] PASSED src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain
src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction
[gw12] [ 73%] PASSED src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testLowTargetTime
src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape
[gw12] [ 73%] PASSED src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testPackingOneShape
src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase
[gw12] [ 73%] PASSED src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testPathologicalCase
src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testSorting
[gw12] [ 73%] PASSED src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testSorting
src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs
[gw12] [ 73%] PASSED src/toil/test/provisioners/clusterScalerTest.py::BinPackingTest::testZeroResourceJobs
src/toil/test/provisioners/gceProvisionerTest.py::GCEStaticAutoscaleTest::testAutoScale
[gw12] [ 73%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEStaticAutoscaleTest::testAutoScale
src/toil/test/provisioners/gceProvisionerTest.py::GCEStaticAutoscaleTest::testSpotAutoScale
[gw12] [ 74%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEStaticAutoscaleTest::testSpotAutoScale
src/toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store
[gw12] [ 74%] SKIPPED src/toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store
src/toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store_paths
[gw12] [ 74%] SKIPPED src/toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store_paths
src/toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription
[gw12] [ 74%] PASSED src/toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription
src/toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing
[gw12] [ 74%] PASSED src/toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing
src/toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testAddChildEncapsulate
[gw12] [ 75%] PASSED src/toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testAddChildEncapsulate
src/toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testEncapsulation
[gw7] [ 75%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testNonPyStandAlone
src/toil/test/src/resourceTest.py::ResourceTest::testPackage
[gw7] [ 75%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testPackage
src/toil/test/src/resourceTest.py::ResourceTest::testStandAlone
[gw7] [ 75%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testStandAlone
src/toil/test/src/resourceTest.py::ResourceTest::testStandAloneInPackage
[gw7] [ 75%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testStandAloneInPackage
src/toil/test/src/resumabilityTest.py::ResumabilityTest::test
[gw7] [ 76%] SKIPPED src/toil/test/src/resumabilityTest.py::ResumabilityTest::test
src/toil/test/src/resumabilityTest.py::ResumabilityTest::test_chaining
[gw9] [ 76%] FAILED src/toil/test/utils/utilsTest.py::UtilsTest::testPrintJobLog
src/toil/test/utils/utilsTest.py::UtilsTest::testRestartAttribute
[gw9] [ 76%] FAILED src/toil/test/utils/utilsTest.py::UtilsTest::testRestartAttribute
src/toil/test/utils/utilsTest.py::UtilsTest::testUnicodeSupport
[gw8] [ 76%] PASSED src/toil/test/__init__.py::toil.test.timeLimit
src/toil/test/options/options.py::OptionsTest::test_caching_option_priority
[gw8] [ 76%] PASSED src/toil/test/options/options.py::OptionsTest::test_caching_option_priority
src/toil/test/options/options.py::OptionsTest::test_default_caching_slurm
[gw8] [ 77%] PASSED src/toil/test/options/options.py::OptionsTest::test_default_caching_slurm
src/toil/test/utils/toilDebugTest.py::testJobStoreContents
[gw8] [ 77%] SKIPPED src/toil/test/utils/toilDebugTest.py::testJobStoreContents
src/toil/test/utils/toilDebugTest.py::testFetchJobStoreFiles
[gw8] [ 77%] FAILED src/toil/test/utils/toilDebugTest.py::testFetchJobStoreFiles
src/toil/test/utils/toilDebugTest.py::DebugJobTest::test_print_job_info
[gw8] [ 77%] FAILED src/toil/test/utils/toilDebugTest.py::DebugJobTest::test_print_job_info
src/toil/test/utils/toilDebugTest.py::DebugJobTest::test_run_job
[gw8] [ 77%] FAILED src/toil/test/utils/toilDebugTest.py::DebugJobTest::test_run_job
src/toil/test/batchSystems/test_lsf_helper.py::LSFHelperTest::test_parse_mem_and_cmd_from_output
[gw8] [ 78%] PASSED src/toil/test/batchSystems/test_lsf_helper.py::LSFHelperTest::test_parse_mem_and_cmd_from_output
src/toil/test/jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName
[gw8] [ 78%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName
src/toil/test/lib/test_misc.py::UserNameAvailableTest::test_get_user_name
[gw8] [ 78%] PASSED src/toil/test/lib/test_misc.py::UserNameAvailableTest::test_get_user_name
src/toil/test/lib/test_misc.py::UserNameUnvailableTest::test_get_user_name
[gw8] [ 78%] PASSED src/toil/test/lib/test_misc.py::UserNameUnvailableTest::test_get_user_name
src/toil/test/lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name
[gw8] [ 78%] PASSED src/toil/test/lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name
src/toil/test/mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue
[gw8] [ 79%] PASSED src/toil/test/mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue
src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTestMultipleNodeTypes::testAutoScale
[gw8] [ 79%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTestMultipleNodeTypes::testAutoScale
src/toil/test/provisioners/gceProvisionerTest.py::GCERestartTest::testAutoScaledCluster
[gw8] [ 79%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCERestartTest::testAutoScaledCluster
src/toil/test/provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing
[gw8] [ 79%] PASSED src/toil/test/provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing
src/toil/test/server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery
[gw8] [ 79%] SKIPPED src/toil/test/server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery
src/toil/test/server/serverTest.py::FileStateStoreTest::test_state_store
[gw8] [ 80%] SKIPPED src/toil/test/server/serverTest.py::FileStateStoreTest::test_state_store
src/toil/test/server/serverTest.py::FileStateStoreURLTest::test_state_store
[gw8] [ 80%] SKIPPED src/toil/test/server/serverTest.py::FileStateStoreURLTest::test_state_store
src/toil/test/src/helloWorldTest.py::HelloWorldTest::testHelloWorld
[gw10] [ 80%] PASSED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore
src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore
[gw5] [ 80%] PASSED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testExtremeCacheSetup
[gw5] [ 80%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testExtremeCacheSetup
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreExportFile
[gw5] [ 80%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreExportFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreLogging
[gw5] [ 81%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreLogging
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreOperations
[gw5] [ 81%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreOperations
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testMultipleJobsReadSameCacheHitGlobalFile
[gw5] [ 81%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testMultipleJobsReadSameCacheHitGlobalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testMultipleJobsReadSameCacheMissGlobalFile
[gw5] [ 81%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testMultipleJobsReadSameCacheMissGlobalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore
[gw4] [ 81%] PASSED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken
[gw2] [ 82%] PASSED src/toil/test/src/regularLogTest.py::RegularLogTest::testRegularLog
src/toil/test/src/regularLogTest.py::RegularLogTest::testWriteGzipLogs
[gw2] [ 82%] SKIPPED src/toil/test/src/regularLogTest.py::RegularLogTest::testWriteGzipLogs
src/toil/test/src/regularLogTest.py::RegularLogTest::testWriteLogs
[gw9] [ 82%] PASSED src/toil/test/utils/utilsTest.py::UtilsTest::testUnicodeSupport
src/toil/test/utils/utilsTest.py::UtilsTest::testUtilsSort
[gw9] [ 82%] SKIPPED src/toil/test/utils/utilsTest.py::UtilsTest::testUtilsSort
src/toil/test/utils/utilsTest.py::UtilsTest::testUtilsStatsSort
[gw9] [ 82%] SKIPPED src/toil/test/utils/utilsTest.py::UtilsTest::testUtilsStatsSort
src/toil/test/utils/utilsTest.py::UtilsTest::test_config_functionality
[gw9] [ 83%] PASSED src/toil/test/utils/utilsTest.py::UtilsTest::test_config_functionality
src/toil/test/src/systemTest.py::SystemTest::testAtomicityOfNonEmptyDirectoryRenames
[gw5] [ 83%] PASSED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile
[gw3] [ 83%] PASSED src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction
src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain
[gw3] [ 83%] PASSED src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain
src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTest::testAutoScale
[gw3] [ 83%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTest::testAutoScale
src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTest::testSpotAutoScale
[gw3] [ 84%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTest::testSpotAutoScale
[gw2] [ 84%] PASSED src/toil/test/src/regularLogTest.py::RegularLogTest::testWriteLogs
src/toil/test/src/promisesTest.py::PathIndexingPromiseTest::test
[gw11] [ 84%] PASSED src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried
src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointRetriedOnce
[gw11] [ 84%] SKIPPED src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointRetriedOnce
src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointedRestartSucceeds
[gw11] [ 84%] SKIPPED src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointedRestartSucceeds
[gw12] [ 85%] PASSED src/toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testEncapsulation
src/toil/test/src/restartDAGTest.py::RestartDAGTest::testRestartedWorkflowSchedulesCorrectJobsOnFailedParent
[gw12] [ 85%] SKIPPED src/toil/test/src/restartDAGTest.py::RestartDAGTest::testRestartedWorkflowSchedulesCorrectJobsOnFailedParent
src/toil/test/src/restartDAGTest.py::RestartDAGTest::testRestartedWorkflowSchedulesCorrectJobsOnKilledParent
[gw12] [ 85%] SKIPPED src/toil/test/src/restartDAGTest.py::RestartDAGTest::testRestartedWorkflowSchedulesCorrectJobsOnKilledParent
[gw6] [ 85%] PASSED src/toil/test/src/jobTest.py::JobTest::testDAGConsistency
src/toil/test/src/jobTest.py::JobTest::testDeadlockDetection
[gw7] [ 85%] PASSED src/toil/test/src/resumabilityTest.py::ResumabilityTest::test_chaining
src/toil/test/src/threadingTest.py::ThreadingTest::testGlobalMutexOrdering
[gw8] [ 86%] PASSED src/toil/test/src/helloWorldTest.py::HelloWorldTest::testHelloWorld
src/toil/test/src/promisesTest.py::CachedUnpicklingJobStoreTest::test
[gw5] [ 86%] PASSED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile
[gw0] [ 86%] PASSED src/toil/test/src/busTest.py::MessageBusTest::test_restart_without_bus_path
src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_basic_import_export
[gw0] [ 86%] PASSED src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_basic_import_export
src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_import_export_restart_false
[gw6] [ 86%] PASSED src/toil/test/src/jobTest.py::JobTest::testDeadlockDetection
src/toil/test/src/jobTest.py::JobTest::testEvaluatingRandomDAG
[gw6] [ 86%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testEvaluatingRandomDAG
src/toil/test/src/jobTest.py::JobTest::testNewCheckpointIsLeafVertexNonRootCase
[gw6] [ 87%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testNewCheckpointIsLeafVertexNonRootCase
src/toil/test/src/jobTest.py::JobTest::testNewCheckpointIsLeafVertexRootCase
[gw6] [ 87%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testNewCheckpointIsLeafVertexRootCase
src/toil/test/src/jobTest.py::JobTest::testSiblingDAGConsistency
[gw6] [ 87%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testSiblingDAGConsistency
src/toil/test/src/jobTest.py::JobTest::testStatic
[gw6] [ 87%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testStatic
src/toil/test/src/jobTest.py::JobTest::testStatic2
[gw2] [ 87%] PASSED src/toil/test/src/promisesTest.py::PathIndexingPromiseTest::test
src/toil/test/src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger
[gw0] [ 88%] PASSED src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_import_export_restart_false
src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_import_export_restart_true
[gw0] [ 88%] SKIPPED src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_import_export_restart_true
[gw4] [ 88%] PASSED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility
[gw9] [ 88%] PASSED src/toil/test/src/systemTest.py::SystemTest::testAtomicityOfNonEmptyDirectoryRenames
src/toil/test/src/workerTest.py::WorkerTests::testNextChainable
[gw6] [ 88%] PASSED src/toil/test/src/jobTest.py::JobTest::testStatic2
src/toil/test/src/jobTest.py::JobTest::testTrivialDAGConsistency
[gw6] [ 89%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testTrivialDAGConsistency
[gw9] [ 89%] PASSED src/toil/test/src/workerTest.py::WorkerTests::testNextChainable
[gw5] [ 89%] PASSED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode
[gw2] [ 89%] PASSED src/toil/test/src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger
[gw8] [ 89%] PASSED src/toil/test/src/promisesTest.py::CachedUnpicklingJobStoreTest::test
src/toil/test/src/promisesTest.py::ChainedIndexedPromisesTest::test
[gw10] [ 90%] PASSED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore
src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStoreWithBadWorker
[gw10] [ 90%] SKIPPED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStoreWithBadWorker
src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore
[gw5] [ 90%] PASSED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode
[gw7] [ 90%] PASSED src/toil/test/src/threadingTest.py::ThreadingTest::testGlobalMutexOrdering
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testRemoveLocalImmutablyReadFile
[gw5] [ 90%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testRemoveLocalImmutablyReadFile
src/toil/test/src/threadingTest.py::ThreadingTest::testLastProcessStanding
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testRemoveLocalMutablyReadFile
[gw5] [ 91%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testRemoveLocalMutablyReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReturnFileSizes
[gw5] [ 91%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReturnFileSizes
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReturnFileSizesWithBadWorker
[gw5] [ 91%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReturnFileSizesWithBadWorker
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream
[gw8] [ 91%] PASSED src/toil/test/src/promisesTest.py::ChainedIndexedPromisesTest::test
[gw10] [ 91%] PASSED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore
[gw4] [ 92%] PASSED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions
[gw7] [ 92%] PASSED src/toil/test/src/threadingTest.py::ThreadingTest::testLastProcessStanding
[gw1] [ 92%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation
[gw1] [ 92%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions
[gw4] [ 92%] PASSED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions
[gw1] [ 93%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality
[gw1] [ 93%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testLargeFile
[gw1] [ 93%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testLargeFile
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testMultipartUploads
[gw1] [ 93%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testMultipartUploads
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream
[gw1] [ 93%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles
[gw1] [ 93%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete
[gw1] [ 94%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName
[gw1] [ 94%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode
[gw1] [ 94%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode
[gw1] [ 94%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles
[gw1] [ 94%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging
[gw1] [ 95%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior
[gw1] [ 95%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles
[gw1] [ 95%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles
[gw1] [ 95%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports
[gw1] [ 95%] 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
[gw1] [ 96%] 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
[gw1] [ 96%] 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
[gw1] [ 96%] 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
[gw1] [ 96%] 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
[gw1] [ 96%] 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
[gw1] [ 97%] 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
[gw1] [ 97%] 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
[gw1] [ 97%] 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
[gw1] [ 97%] 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
[gw1] [ 97%] 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
[gw1] [ 98%] 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
[gw1] [ 98%] 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
[gw1] [ 98%] 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
[gw1] [ 98%] 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
[gw1] [ 98%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py
[gw5] [ 99%] PASSED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken
[gw5] [ 99%] PASSED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility
[gw5] [ 99%] PASSED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore
[gw5] [ 99%] PASSED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteLocalFileToJobStore
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore
[gw5] [ 99%] PASSED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteNonLocalFileToJobStore
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions
[gw5] [100%] PASSED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions
==================================== 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/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/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/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/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/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/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/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/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/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 <module>
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 <module>
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 <module>
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 <module>
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 <module>
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 <module>
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 <module>
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 <module>
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 <module>
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 <module>
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 <module>
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 <module>
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 <module>
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 ===================================
__________________________ UtilsTest.testGetPIDStatus __________________________
[gw9] linux -- Python 3.12.8 /usr/bin/python3.12
Traceback (most recent call last):
File "/usr/lib/python3.12/unittest/case.py", line 58, in testPartExecutor
yield
File "/usr/lib/python3.12/unittest/case.py", line 634, in run
self._callTestMethod(testMethod)
File "/usr/lib/python3.12/unittest/case.py", line 589, in _callTestMethod
if method() is not None:
^^^^^^^^
File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/utilsTest.py", line 316, in testGetPIDStatus
wf = subprocess.Popen(self.sort_workflow_cmd)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.12/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/usr/lib/python3.12/subprocess.py", line 1955, 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.utilsTest.UtilsTest:testGetPIDStatus (Jan 23 2025 08:11:24:328046 PST)
_____________________ UtilsTest.testGetStatusFailedToilWF ______________________
[gw9] linux -- Python 3.12.8 /usr/bin/python3.12
Traceback (most recent call last):
File "/usr/lib/python3.12/unittest/case.py", line 58, in testPartExecutor
yield
File "/usr/lib/python3.12/unittest/case.py", line 634, in run
self._callTestMethod(testMethod)
File "/usr/lib/python3.12/unittest/case.py", line 589, in _callTestMethod
if method() is not None:
^^^^^^^^
File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/utilsTest.py", line 333, in testGetStatusFailedToilWF
wf = subprocess.Popen(self.sort_workflow_cmd + ['--badWorker=1'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.12/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/usr/lib/python3.12/subprocess.py", line 1955, 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.utilsTest.UtilsTest:testGetStatusFailedToilWF (Jan 23 2025 08:11:24:394540 PST)
__________________________ UtilsTest.testPrintJobLog ___________________________
[gw9] linux -- Python 3.12.8 /usr/bin/python3.12
Traceback (most recent call last):
File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/fileJobStore.py", line 713, in read_shared_file_stream
with open(self._get_shared_file_path(shared_file_name), 'rb' if encoding == None else 'rt', encoding=encoding, errors=errors) as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/toil-test-utils.utilsTest.UtilsTest-testPrintJobLog-cso35_6z/jobstore/files/shared/rootJobStoreID'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/abstractJobStore.py", line 275, in load_root_job
with self.read_shared_file_stream(self.rootJobStoreIDFileName) as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.12/contextlib.py", line 137, in __enter__
return next(self.gen)
^^^^^^^^^^^^^^
File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/fileJobStore.py", line 718, in read_shared_file_stream
raise NoSuchFileException(shared_file_name)
toil.jobStores.abstractJobStore.NoSuchFileException: File 'rootJobStoreID' does not exist.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.12/unittest/case.py", line 58, in testPartExecutor
yield
File "/usr/lib/python3.12/unittest/case.py", line 634, in run
self._callTestMethod(testMethod)
File "/usr/lib/python3.12/unittest/case.py", line 589, in _callTestMethod
if method() is not None:
^^^^^^^^
File "/usr/lib/python3.12/unittest/mock.py", line 1396, in patched
return func(*newargs, **newkeywargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/utilsTest.py", line 371, in testPrintJobLog
status = ToilStatus(self.toilDir)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/build/reproducible-path/toil-6.1.0/src/toil/utils/toilStatus.py", line 38, in __init__
rootJob = self.fetchRootJob()
^^^^^^^^^^^^^^^^^^^
File "/build/reproducible-path/toil-6.1.0/src/toil/utils/toilStatus.py", line 253, in fetchRootJob
return self.jobStore.load_root_job()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/build/reproducible-path/toil-6.1.0/src/toil/jobStores/abstractJobStore.py", line 278, in load_root_job
raise JobException('No job has been set as the root in this job store')
toil.job.JobException: No job has been set as the root in this job store
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.utils.utilsTest.UtilsTest:testPrintJobLog (Jan 23 2025 08:11:24:566215 PST)
----------------------------- Captured stderr call -----------------------------
WARNING: You are using cwltool version 3.1.20250110105449, which is not the version Toil is tested against. To install the correct cwltool for Toil, do:
pip install cwltool==3.1.20240112164112
[2025-01-23T08:11:25-1200] [MainThread] [I] [cwltool] Resolved 'src/toil/test/cwl/alwaysfails.cwl' to 'file:///build/reproducible-path/toil-6.1.0/src/toil/test/cwl/alwaysfails.cwl'
Usage: src/toil/test/cwl/alwaysfails.cwl [-h] --message MESSAGE [job_order]
src/toil/test/cwl/alwaysfails.cwl: error: argument --message: expected one argument
If both a CWL file and an input object (YAML/JSON) file were provided, this may be the argument order.
* All positional arguments [cwl, yml_or_json] must always be specified last for toil-cwl-runner.
Note: If you're trying to specify a jobstore, please use --jobStore.
Usage: toil-cwl-runner [options] example.cwl example-job.yaml
Example: toil-cwl-runner \
--jobStore aws:us-west-2:jobstore \
--realTimeLogging \
--logInfo \
example.cwl \
example-job.yaml
________________________ UtilsTest.testRestartAttribute ________________________
[gw9] linux -- Python 3.12.8 /usr/bin/python3.12
Traceback (most recent call last):
File "/usr/lib/python3.12/unittest/case.py", line 58, in testPartExecutor
yield
File "/usr/lib/python3.12/unittest/case.py", line 634, in run
self._callTestMethod(testMethod)
File "/usr/lib/python3.12/unittest/case.py", line 589, in _callTestMethod
if method() is not None:
^^^^^^^^
File "/build/reproducible-path/toil-6.1.0/src/toil/test/utils/utilsTest.py", line 386, in testRestartAttribute
subprocess.run(cmd)
File "/usr/lib/python3.12/subprocess.py", line 548, in run
with Popen(*popenargs, **kwargs) as process:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.12/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/usr/lib/python3.12/subprocess.py", line 1955, 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.utilsTest.UtilsTest:testRestartAttribute (Jan 23 2025 08:11:27:089656 PST)
____________________________ testFetchJobStoreFiles ____________________________
[gw8] linux -- Python 3.12.8 /usr/bin/python3.12
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>
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(
File "/usr/lib/python3.12/subprocess.py", line 408, in check_call
retcode = call(*popenargs, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.12/subprocess.py", line 389, in call
with Popen(*popenargs, **kwargs) as p:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.12/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/usr/lib/python3.12/subprocess.py", line 1955, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.11'
_______________________ DebugJobTest.test_print_job_info _______________________
[gw8] linux -- Python 3.12.8 /usr/bin/python3.12
Traceback (most recent call last):
File "/usr/lib/python3.12/unittest/case.py", line 58, in testPartExecutor
yield
File "/usr/lib/python3.12/unittest/case.py", line 634, in run
self._callTestMethod(testMethod)
File "/usr/lib/python3.12/unittest/case.py", line 589, 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([
File "/usr/lib/python3.12/subprocess.py", line 408, in check_call
retcode = call(*popenargs, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.12/subprocess.py", line 389, in call
with Popen(*popenargs, **kwargs) as p:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.12/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/usr/lib/python3.12/subprocess.py", line 1955, 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 (Jan 23 2025 08:11:27:471185 PST)
------------------------------ 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
__________________________ DebugJobTest.test_run_job ___________________________
[gw8] linux -- Python 3.12.8 /usr/bin/python3.12
Traceback (most recent call last):
File "/usr/lib/python3.12/unittest/case.py", line 58, in testPartExecutor
yield
File "/usr/lib/python3.12/unittest/case.py", line 634, in run
self._callTestMethod(testMethod)
File "/usr/lib/python3.12/unittest/case.py", line 589, 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([
File "/usr/lib/python3.12/subprocess.py", line 408, in check_call
retcode = call(*popenargs, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.12/subprocess.py", line 389, in call
with Popen(*popenargs, **kwargs) as p:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.12/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/usr/lib/python3.12/subprocess.py", line 1955, 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 (Jan 23 2025 08:11:27:482085 PST)
------------------------------ 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
=========================== short test summary info ============================
FAILED src/toil/test/utils/utilsTest.py::UtilsTest::testGetPIDStatus - FileNotFoundError: [Errno 2] No such file or directory: 'python3.11'
FAILED src/toil/test/utils/utilsTest.py::UtilsTest::testGetStatusFailedToilWF - FileNotFoundError: [Errno 2] No such file or directory: 'python3.11'
FAILED src/toil/test/utils/utilsTest.py::UtilsTest::testPrintJobLog - toil.job.JobException: No job has been set as the root in this job store
FAILED src/toil/test/utils/utilsTest.py::UtilsTest::testRestartAttribute - FileNotFoundError: [Errno 2] No such file or directory: 'python3.11'
FAILED src/toil/test/utils/toilDebugTest.py::testFetchJobStoreFiles - FileNotFoundError: [Errno 2] No such file or directory: 'python3.11'
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/utils/toilDebugTest.py::DebugJobTest::test_run_job - FileNotFoundError: [Errno 2] No such file or directory: 'python3.11'
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::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::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/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/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/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/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/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/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/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/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/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/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/utils/toilKillTest.py::ToilKillTestWithAWSJobStore - toil.jobStores.utils.JobStoreUnavailableException: libraries for aws job store are not installed
====== 7 failed, 159 passed, 349 skipped, 52 errors in 308.30s (0:05:08) =======
E: pybuild pybuild:389: test: plugin custom failed with: exit code=1: HOME=/build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil python3.12 setup.py develop --user && PYTHONPATH=/build/reproducible-path/toil-6.1.0/src:$PYTHONPATH PATH=/build/reproducible-path/toil-6.1.0/.pybuild/cpython3_3.12_toil/.local/bin/:$PATH TOIL_TEST_QUICK=True TOIL_SKIP_DOCKER=True python3.12 -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
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:66: 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
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
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==0.18.6
Best match: ruamel.yaml 0.18.6
Adding ruamel.yaml 0.18.6 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==2024.2
Best match: pytz 2024.2
Adding pytz 2024.2 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 idna==3.8
Best match: idna 3.8
Adding idna 3.8 to easy-install.pth file
Using /usr/lib/python3/dist-packages
Searching for charset-normalizer==3.4.0
Best match: charset-normalizer 3.4.0
Adding charset-normalizer 3.4.0 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
Searching for certifi==2024.12.14
Best match: certifi 2024.12.14
Adding certifi 2024.12.14 to easy-install.pth file
Using /usr/lib/python3/dist-packages
Finished processing dependencies for toil==6.1.0
============================= test session starts ==============================
platform linux -- Python 3.13.1, 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: typeguard-4.4.1, xdist-3.6.1
created: 13/13 workers
13 workers [469 items]
scheduling tests via LoadScopeScheduling
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/jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testBatchCreate
[gw3] [ 0%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testBatchCreate
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testChildLoadingEquality
[gw3] [ 0%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testChildLoadingEquality
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testCleanCache
[gw3] [ 1%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testCleanCache
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality
[gw3] [ 1%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testConfigEquality
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionIdempotence
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src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testDestructionOfCorruptedJobStore
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src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testConfigEquality
[gw3] [ 2%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testEmptyFileStoreIDIsReadable
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src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testGrowingAndShrinkingJob
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src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_and_cancel_workflows
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src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_many_all_exist
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src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete
[gw3] [ 13%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testPersistantFilesToDelete
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testAsyncWriteWithCaching
[gw5] [ 13%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testAsyncWriteWithCaching
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testCacheEvictionFailCase
[gw5] [ 14%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testCacheEvictionFailCase
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testCacheEvictionPartialEvict
[gw5] [ 14%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testCacheEvictionPartialEvict
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testCacheEvictionTotalEvict
[gw5] [ 14%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testCacheEvictionTotalEvict
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testControlledFailedWorkerRetry
[gw5] [ 14%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testControlledFailedWorkerRetry
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testInlinedFiles
[gw2] [ 14%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testInlinedFiles
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation
[gw2] [ 15%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobCreation
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions
[gw2] [ 15%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobDeletions
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality
[gw2] [ 15%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testJobLoadEquality
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testLargeFile
[gw2] [ 15%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testLargeFile
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile
[gw2] [ 15%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testMultiThreadImportFile
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testMultipartUploads
[gw2] [ 16%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testMultipartUploads
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob
[gw2] [ 16%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testOverlargeJob
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream
[gw2] [ 16%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPartialReadFromStream
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles
[gw2] [ 16%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPerJobFiles
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete
[gw2] [ 17%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testPersistantFilesToDelete
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode
[gw2] [ 17%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteFileStreamTextMode
src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url
[gw10] [ 17%] 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
[gw10] [ 17%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_relative_url_no_attachments_fails
[gw0] [ 17%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testConfigEquality
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testDestructionIdempotence
[gw0] [ 18%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testDestructionIdempotence
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testDestructionOfCorruptedJobStore
[gw0] [ 18%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testDestructionOfCorruptedJobStore
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testEmptyFileStoreIDIsReadable
[gw0] [ 18%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testEmptyFileStoreIDIsReadable
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testEncrypted
[gw0] [ 18%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testEncrypted
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testFileDeletion
[gw0] [ 18%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testFileDeletion
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testGrowingAndShrinkingJob
[gw0] [ 19%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testGrowingAndShrinkingJob
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testImportHttpFile
[gw4] [ 19%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_None
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_RM
[gw4] [ 19%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_RM
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_STOP
[gw4] [ 19%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_CxD_STOP
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_FORGO
[gw4] [ 20%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_FORGO
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_None
[gw4] [ 20%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_None
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_RM
[gw4] [ 20%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_RM
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_STOP
[gw4] [ 20%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_Cxx_STOP
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_FORGO
[gw4] [ 20%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_FORGO
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_None
[gw4] [ 21%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_None
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_RM
[gw4] [ 21%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_RM
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_STOP
[gw4] [ 21%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xRx_STOP
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_FORGO
[gw4] [ 21%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_FORGO
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_None
[gw4] [ 21%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_None
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_RM
[gw4] [ 22%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_RM
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_STOP
[gw4] [ 22%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxD_STOP
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_FORGO
[gw4] [ 22%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_FORGO
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_None
[gw4] [ 22%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_None
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_RM
[gw4] [ 23%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_RM
src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_STOP
[gw4] [ 23%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerClean_xxx_STOP
src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs
[gw4] [ 23%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs
src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Demux
[gw4] [ 23%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Demux
src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Demux_Stream
[gw4] [ 23%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Demux_Stream
src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Stream
[gw4] [ 24%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerLogs_Stream
src/toil/test/lib/dockerTest.py::DockerTest::testDockerPipeChain
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testAsyncWriteWithCaching
[gw7] [ 24%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testAsyncWriteWithCaching
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionFailCase
[gw7] [ 24%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionFailCase
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionPartialEvict
[gw7] [ 24%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionPartialEvict
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionTotalEvict
[gw7] [ 24%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testCacheEvictionTotalEvict
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testControlledFailedWorkerRetry
[gw7] [ 25%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testControlledFailedWorkerRetry
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testDeleteLocalFile
[gw7] [ 25%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testDeleteLocalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testExtremeCacheSetup
[gw7] [ 25%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testExtremeCacheSetup
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreExportFile
[gw7] [ 25%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreExportFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreLogging
[gw7] [ 26%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreLogging
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreOperations
[gw7] [ 26%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testFileStoreOperations
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testMultipleJobsReadSameCacheHitGlobalFile
[gw7] [ 26%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testMultipleJobsReadSameCacheHitGlobalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testMultipleJobsReadSameCacheMissGlobalFile
[gw7] [ 26%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testMultipleJobsReadSameCacheMissGlobalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCachHitFileFromJobStore
[gw7] [ 26%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCachHitFileFromJobStore
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile
[gw7] [ 27%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testApplianceParser
[gw9] [ 27%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testApplianceParser
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo
[gw9] [ 27%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadGoogleRepo
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo
[gw9] [ 27%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepo
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag
[gw9] [ 27%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayRepoNTag
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag
[gw9] [ 28%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBadQuayTag
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo
[gw9] [ 28%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepo
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag
[gw9] [ 28%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testBroadDockerRepoBadTag
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo
[gw9] [ 28%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testGoogleRepo
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo
[gw9] [ 28%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testNonexistentRepo
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo
[gw9] [ 29%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testOfficialUbuntuRepo
[gw4] [ 29%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerPipeChain
src/toil/test/lib/dockerTest.py::DockerTest::testDockerPipeChainErrorDetection
[gw4] [ 29%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testDockerPipeChainErrorDetection
src/toil/test/lib/dockerTest.py::DockerTest::testNonCachingDockerChain
[gw4] [ 29%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testNonCachingDockerChain
[gw0] [ 30%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testImportHttpFile
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testInitialState
[gw0] [ 30%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testInitialState
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testInlinedFiles
[gw0] [ 30%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testInlinedFiles
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobCreation
[gw0] [ 30%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobCreation
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobDeletions
[gw0] [ 30%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobDeletions
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobLoadEquality
[gw0] [ 31%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testJobLoadEquality
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testLargeFile
[gw0] [ 31%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testLargeFile
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testMultiThreadImportFile
[gw0] [ 31%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testMultiThreadImportFile
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testMultipartUploads
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode
[gw2] [ 31%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testReadWriteSharedFilesTextMode
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testSDBDomainsDeletedOnFailedJobstoreBucketCreation
[gw2] [ 31%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testSDBDomainsDeletedOnFailedJobstoreBucketCreation
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles
[gw2] [ 32%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testSharedFiles
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging
[gw2] [ 32%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testStatsAndLogging
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior
[gw2] [ 32%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testUpdateBehavior
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles
[gw2] [ 32%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testWriteLogFiles
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles
[gw2] [ 33%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::testZeroLengthFiles
src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_activated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py
[gw2] [ 33%] 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
[gw2] [ 33%] 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
[gw2] [ 33%] 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
[gw2] [ 33%] 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
[gw2] [ 34%] 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
[gw2] [ 34%] 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
[gw2] [ 34%] 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
[gw2] [ 34%] 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
[gw2] [ 34%] 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
[gw2] [ 35%] 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
[gw2] [ 35%] 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
[gw2] [ 35%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py
[gw7] [ 35%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode
[gw7] [ 36%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testRemoveLocalImmutablyReadFile
[gw7] [ 36%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testRemoveLocalImmutablyReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testRemoveLocalMutablyReadFile
[gw7] [ 36%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testRemoveLocalMutablyReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReturnFileSizes
[gw7] [ 36%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReturnFileSizes
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReturnFileSizesWithBadWorker
[gw7] [ 36%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testReturnFileSizesWithBadWorker
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testSimultaneousReadsUncachedStream
[gw7] [ 37%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testSimultaneousReadsUncachedStream
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken
[gw7] [ 37%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility
[gw7] [ 37%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteLocalFileToJobStore
[gw7] [ 37%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteLocalFileToJobStore
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteNonLocalFileToJobStore
[gw7] [ 37%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteNonLocalFileToJobStore
[gw8] [ 38%] 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
[gw0] [ 38%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testMultipartUploads
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testOverlargeJob
[gw0] [ 38%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testOverlargeJob
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPartialReadFromStream
[gw0] [ 38%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPartialReadFromStream
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPerJobFiles
[gw0] [ 39%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPerJobFiles
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPersistantFilesToDelete
[gw0] [ 39%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testPersistantFilesToDelete
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testReadWriteFileStreamTextMode
[gw0] [ 39%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testReadWriteFileStreamTextMode
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testReadWriteSharedFilesTextMode
[gw0] [ 39%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testReadWriteSharedFilesTextMode
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testSDBDomainsDeletedOnFailedJobstoreBucketCreation
[gw0] [ 39%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testSDBDomainsDeletedOnFailedJobstoreBucketCreation
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testSharedFiles
[gw0] [ 40%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testSharedFiles
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testStatsAndLogging
[gw0] [ 40%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testStatsAndLogging
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testUpdateBehavior
[gw0] [ 40%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testUpdateBehavior
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testWriteLogFiles
[gw0] [ 40%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testWriteLogFiles
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::testZeroLengthFiles
[gw0] [ 40%] 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
[gw0] [ 41%] 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] [ 41%] 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] [ 41%] 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] [ 41%] 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] [ 42%] 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
[gw0] [ 42%] 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] [ 42%] 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
[gw0] [ 42%] 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
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testAsyncWriteWithCaching
[gw6] [ 42%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testAsyncWriteWithCaching
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionFailCase
[gw6] [ 43%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionFailCase
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionPartialEvict
[gw6] [ 43%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionPartialEvict
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionTotalEvict
[gw6] [ 43%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testCacheEvictionTotalEvict
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testControlledFailedWorkerRetry
[gw6] [ 43%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testControlledFailedWorkerRetry
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testDeleteLocalFile
[gw6] [ 43%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testDeleteLocalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testExtremeCacheSetup
[gw6] [ 44%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testExtremeCacheSetup
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreExportFile
[gw6] [ 44%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreExportFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreLogging
[gw6] [ 44%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreLogging
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreOperations
[gw6] [ 44%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testFileStoreOperations
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testMultipleJobsReadSameCacheHitGlobalFile
[gw6] [ 44%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testMultipleJobsReadSameCacheHitGlobalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testMultipleJobsReadSameCacheMissGlobalFile
[gw6] [ 45%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testMultipleJobsReadSameCacheMissGlobalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCachHitFileFromJobStore
[gw6] [ 45%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCachHitFileFromJobStore
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile
[gw6] [ 45%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile
[gw6] [ 45%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode
[gw6] [ 46%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testRemoveLocalImmutablyReadFile
[gw6] [ 46%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testRemoveLocalImmutablyReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testRemoveLocalMutablyReadFile
[gw6] [ 46%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testRemoveLocalMutablyReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReturnFileSizes
[gw6] [ 46%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReturnFileSizes
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReturnFileSizesWithBadWorker
[gw6] [ 46%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testReturnFileSizesWithBadWorker
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testSimultaneousReadsUncachedStream
[gw6] [ 47%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testSimultaneousReadsUncachedStream
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testToilIsNotBroken
[gw6] [ 47%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testToilIsNotBroken
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility
[gw6] [ 47%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteLocalFileToJobStore
[gw6] [ 47%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteLocalFileToJobStore
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteNonLocalFileToJobStore
[gw6] [ 47%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteNonLocalFileToJobStore
[gw0] [ 48%] 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] [ 48%] 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] [ 48%] 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] [ 48%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py
[gw8] [ 49%] 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
[gw8] [ 49%] 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
[gw3] [ 49%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteFileStreamTextMode
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode
[gw3] [ 49%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testReadWriteSharedFilesTextMode
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles
[gw3] [ 49%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testSharedFiles
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging
[gw3] [ 50%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testStatsAndLogging
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior
[gw3] [ 50%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testUpdateBehavior
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles
[gw3] [ 50%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testWriteLogFiles
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::testZeroLengthFiles
[gw3] [ 50%] 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] [ 50%] 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] [ 51%] 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
[gw3] [ 51%] 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] [ 51%] 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] [ 51%] 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] [ 52%] 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] [ 52%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_one <- src/toil/test/__init__.py
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_onemib <- src/toil/test/__init__.py
[gw3] [ 52%] 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] [ 52%] 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] [ 52%] 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] [ 53%] 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
[gw3] [ 53%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportExportFile__moveExports_deactivated__otherCls_filejobstoretest__size_zero <- src/toil/test/__init__.py
[gw8] [ 53%] 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] [ 53%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testBatchCreate
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality
src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip
[gw12] [ 53%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryS3StateWorkflowTest::test_run_workflow_single_file_zip
src/toil/test/src/jobTest.py::JobTest::testDAGConsistency
[gw8] [ 54%] 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/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip
[gw11] [ 54%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerCeleryWorkflowTest::test_run_workflow_single_file_zip
src/toil/test/src/miscTests.py::MiscTests::testGetSizeOfDirectoryWorks
[gw11] [ 54%] SKIPPED src/toil/test/src/miscTests.py::MiscTests::testGetSizeOfDirectoryWorks
[gw8] [ 54%] 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/src/miscTests.py::MiscTests::testIDStability
[gw11] [ 55%] PASSED src/toil/test/src/miscTests.py::MiscTests::testIDStability
src/toil/test/src/miscTests.py::MiscTests::test_atomic_context_error
[gw11] [ 55%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_atomic_context_error
src/toil/test/src/miscTests.py::MiscTests::test_atomic_context_ok
[gw11] [ 55%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_atomic_context_ok
src/toil/test/src/miscTests.py::MiscTests::test_atomic_install
[gw11] [ 55%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_atomic_install
src/toil/test/src/miscTests.py::MiscTests::test_atomic_install_dev
[gw11] [ 55%] 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/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip
[gw10] [ 56%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerWorkflowTest::test_run_workflow_single_file_zip
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testFileStoreLogging
[gw10] [ 56%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testFileStoreLogging
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testFileStoreOperations
[gw10] [ 56%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testFileStoreOperations
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode
[gw1] [ 56%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testChildLoadingEquality
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testCleanCache
[gw1] [ 56%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testCleanCache
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality
[gw11] [ 57%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_call_command_err
[gw8] [ 57%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_all_exist
src/toil/test/lib/dockerTest.py::DockerTest::testNonCachingDockerChainErrorDetection
[gw4] [ 57%] SKIPPED src/toil/test/lib/dockerTest.py::DockerTest::testNonCachingDockerChainErrorDetection
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testFileStoreLogging
[gw4] [ 57%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testFileStoreLogging
src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo
[gw9] [ 57%] SKIPPED src/toil/test/src/dockerCheckTest.py::DockerCheckTest::testToilQuayRepo
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testFileStoreLogging
[gw9] [ 58%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testFileStoreLogging
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testFileStoreOperations
[gw9] [ 58%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testFileStoreOperations
src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_none_exist
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testFileStoreOperations
[gw4] [ 58%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testFileStoreOperations
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode
[gw4] [ 58%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testReadWriteFileStreamTextMode
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode
[gw9] [ 59%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testReadWriteFileStreamTextMode
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken
[gw4] [ 59%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testToilIsNotBroken
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility
[gw4] [ 59%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteExportFileCompatibility
[gw1] [ 59%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testConfigEquality
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence
[gw9] [ 59%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testToilIsNotBroken
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility
[gw9] [ 60%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteExportFileCompatibility
[gw8] [ 60%] 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/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py
[gw2] [ 60%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::AWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py
src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_build_tag
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions
[gw2] [ 60%] PASSED src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_build_tag
[gw7] [ 60%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions
src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testDeferralWithConcurrentEncapsulation
[gw7] [ 61%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testDeferralWithConcurrentEncapsulation
src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testDeferralWithFailureAndEncapsulation
src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_build_tag_with_tags
[gw2] [ 61%] 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
[gw2] [ 61%] PASSED src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_empty_aws_tags
src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji
[gw2] [ 61%] PASSED src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_emoji
[gw7] [ 62%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testDeferralWithFailureAndEncapsulation
src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testRestart
[gw7] [ 62%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testRestart
[gw1] [ 62%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionIdempotence
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionOfCorruptedJobStore
[gw1] [ 62%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testDestructionOfCorruptedJobStore
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions
[gw6] [ 62%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions
src/toil/test/src/regularLogTest.py::RegularLogTest::testLogToMaster
[gw6] [ 63%] SKIPPED src/toil/test/src/regularLogTest.py::RegularLogTest::testLogToMaster
src/toil/test/src/regularLogTest.py::RegularLogTest::testMultipleLogToMaster
[gw6] [ 63%] SKIPPED src/toil/test/src/regularLogTest.py::RegularLogTest::testMultipleLogToMaster
src/toil/test/src/regularLogTest.py::RegularLogTest::testRegularLog
src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py
[gw3] [ 63%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py
src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore
src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testSplitRootPackages
[gw7] [ 63%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testSplitRootPackages
[gw8] [ 63%] 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
[gw8] [ 64%] 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
src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py
[gw0] [ 64%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::EncryptedAWSJobStoreTest::test_testImportSharedFile__otherCls_filejobstoretest <- src/toil/test/__init__.py
src/toil/test/src/resourceTest.py::ResourceTest::testBuiltIn
src/toil/test/src/miscTests.py::MiscTests::test_call_command_ok
[gw11] [ 64%] PASSED src/toil/test/src/miscTests.py::MiscTests::test_call_command_ok
src/toil/test/src/miscTests.py::TestPanic::test_nested_panic
[gw11] [ 64%] PASSED src/toil/test/src/miscTests.py::TestPanic::test_nested_panic
src/toil/test/src/miscTests.py::TestPanic::test_panic
[gw11] [ 65%] PASSED src/toil/test/src/miscTests.py::TestPanic::test_panic
src/toil/test/src/miscTests.py::TestPanic::test_panic_by_hand
[gw11] [ 65%] PASSED src/toil/test/src/miscTests.py::TestPanic::test_panic_by_hand
[gw12] [ 65%] FAILED src/toil/test/src/jobTest.py::JobTest::testDAGConsistency
src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object
[gw2] [ 65%] PASSED src/toil/test/lib/aws/test_utils.py::TagGenerationTest::test_incorrect_json_object
src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_get_service_info
[gw2] [ 65%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_get_service_info
src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_health
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions
[gw9] [ 66%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithAwsJobStore::testWriteReadGlobalFilePermissions
src/toil/test/lib/test_conversions.py::ConversionTest::test_convert
[gw9] [ 66%] PASSED src/toil/test/lib/test_conversions.py::ConversionTest::test_convert
src/toil/test/lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds
[gw9] [ 66%] PASSED src/toil/test/lib/test_conversions.py::ConversionTest::test_hms_duration_to_seconds
[gw2] [ 66%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_health
src/toil/test/src/miscTests.py::TestPanic::test_panic_with_secondary
[gw11] [ 66%] PASSED src/toil/test/src/miscTests.py::TestPanic::test_panic_with_secondary
src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried
src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testUserTypesInJobFunctionArgs
[gw7] [ 67%] SKIPPED src/toil/test/src/autoDeploymentTest.py::AutoDeploymentTest::testUserTypesInJobFunctionArgs
src/toil/test/src/busTest.py::MessageBusTest::test_cross_thread_messaging
[gw7] [ 67%] PASSED src/toil/test/src/busTest.py::MessageBusTest::test_cross_thread_messaging
src/toil/test/src/busTest.py::MessageBusTest::test_enum_ints_in_file
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions
[gw4] [ 67%] SKIPPED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithGoogleJobStore::testWriteReadGlobalFilePermissions
src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClass
[gw4] [ 67%] SKIPPED src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClass
src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain
src/toil/test/src/jobTest.py::JobTest::testDeadlockDetection
[gw1] [ 68%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testEmptyFileStoreIDIsReadable
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testFileDeletion
[gw1] [ 68%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testFileDeletion
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob
[gw1] [ 68%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testGrowingAndShrinkingJob
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile
[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
[gw8] [ 68%] 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
src/toil/test/lib/test_conversions.py::ConversionTest::test_human2bytes
[gw9] [ 69%] PASSED src/toil/test/lib/test_conversions.py::ConversionTest::test_human2bytes
[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
src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testContextManger
src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_home
[gw2] [ 69%] SKIPPED src/toil/test/server/serverTest.py::ToilWESServerBenchTest::test_home
src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_basic_import_export
[gw9] [ 69%] SKIPPED src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testContextManger
src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testExportAfterFailedExport
[gw9] [ 69%] SKIPPED src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testExportAfterFailedExport
src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testNoContextManger
[gw9] [ 70%] SKIPPED src/toil/test/src/toilContextManagerTest.py::ToilContextManagerTest::testNoContextManger
[gw8] [ 70%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_none_exist
src/toil/test/options/options.py::OptionsTest::test_caching_option_priority
src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist
[gw8] [ 70%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_many_some_exist
src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromScontrol_one_exists
[gw3] [ 70%] FAILED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testCachingFileStore
src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore
[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
[gw1] [ 71%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testImportHttpFile
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState
[gw8] [ 71%] 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
[gw8] [ 71%] 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
[gw9] [ 71%] PASSED src/toil/test/options/options.py::OptionsTest::test_caching_option_priority
src/toil/test/options/options.py::OptionsTest::test_default_caching_slurm
[gw11] [ 72%] FAILED src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointNotRetried
src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointRetriedOnce
[gw11] [ 72%] SKIPPED src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointRetriedOnce
[gw2] [ 72%] PASSED src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_basic_import_export
src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_import_export_restart_false
src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointedRestartSucceeds
[gw11] [ 72%] SKIPPED src/toil/test/src/checkpointTest.py::CheckpointTest::testCheckpointedRestartSucceeds
src/toil/test/provisioners/gceProvisionerTest.py::GCEStaticAutoscaleTest::testAutoScale
[gw11] [ 72%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEStaticAutoscaleTest::testAutoScale
src/toil/test/provisioners/gceProvisionerTest.py::GCEStaticAutoscaleTest::testSpotAutoScale
[gw7] [ 73%] FAILED src/toil/test/src/busTest.py::MessageBusTest::test_restart_without_bus_path
[gw11] [ 73%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEStaticAutoscaleTest::testSpotAutoScale
src/toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription
[gw8] [ 73%] 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
src/toil/test/__init__.py::toil.test.make_tests
[gw7] [ 73%] PASSED src/toil/test/__init__.py::toil.test.make_tests
src/toil/test/__init__.py::toil.test.timeLimit
[gw8] [ 73%] 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
[gw9] [ 74%] PASSED src/toil/test/options/options.py::OptionsTest::test_default_caching_slurm
src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTest::testAutoScale
[gw9] [ 74%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTest::testAutoScale
[gw8] [ 74%] PASSED src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobExitCode_sacct_raises_job_not_exists
src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTest::testSpotAutoScale
src/toil/test/src/restartDAGTest.py::RestartDAGTest::testRestartedWorkflowSchedulesCorrectJobsOnFailedParent
[gw9] [ 74%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTest::testSpotAutoScale
src/toil/test/src/threadingTest.py::ThreadingTest::testGlobalMutexOrdering
[gw8] [ 75%] SKIPPED src/toil/test/src/restartDAGTest.py::RestartDAGTest::testRestartedWorkflowSchedulesCorrectJobsOnFailedParent
src/toil/test/src/restartDAGTest.py::RestartDAGTest::testRestartedWorkflowSchedulesCorrectJobsOnKilledParent
[gw8] [ 75%] SKIPPED src/toil/test/src/restartDAGTest.py::RestartDAGTest::testRestartedWorkflowSchedulesCorrectJobsOnKilledParent
src/toil/test/utils/toilDebugTest.py::testJobStoreContents
[gw8] [ 75%] SKIPPED src/toil/test/utils/toilDebugTest.py::testJobStoreContents
src/toil/test/utils/toilDebugTest.py::testFetchJobStoreFiles
[gw11] [ 75%] PASSED src/toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescription
src/toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing
[gw2] [ 75%] 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
[gw2] [ 76%] SKIPPED src/toil/test/src/importExportFileTest.py::ImportExportFileTest::test_import_export_restart_true
[gw8] [ 76%] FAILED src/toil/test/utils/toilDebugTest.py::testFetchJobStoreFiles
src/toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store
src/toil/test/batchSystems/test_lsf_helper.py::LSFHelperTest::test_parse_mem_and_cmd_from_output
[gw8] [ 76%] PASSED src/toil/test/batchSystems/test_lsf_helper.py::LSFHelperTest::test_parse_mem_and_cmd_from_output
[gw2] [ 76%] SKIPPED src/toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store
src/toil/test/jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName
[gw8] [ 76%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::InvalidAWSJobStoreTest::testInvalidJobStoreName
src/toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store_paths
src/toil/test/lib/test_misc.py::UserNameAvailableTest::test_get_user_name
[gw2] [ 77%] SKIPPED src/toil/test/server/serverTest.py::AWSStateStoreTest::test_state_store_paths
src/toil/test/lib/test_misc.py::UserNameUnvailableTest::test_get_user_name
[gw8] [ 77%] PASSED src/toil/test/lib/test_misc.py::UserNameAvailableTest::test_get_user_name
src/toil/test/mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue
[gw2] [ 77%] PASSED src/toil/test/lib/test_misc.py::UserNameUnvailableTest::test_get_user_name
src/toil/test/lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name
[gw11] [ 77%] PASSED src/toil/test/src/jobDescriptionTest.py::JobDescriptionTest::testJobDescriptionSequencing
[gw2] [ 78%] PASSED src/toil/test/lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name
src/toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testAddChildEncapsulate
[gw8] [ 78%] FAILED src/toil/test/mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue
src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTestMultipleNodeTypes::testAutoScale
[gw11] [ 78%] PASSED src/toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testAddChildEncapsulate
src/toil/test/provisioners/gceProvisionerTest.py::GCERestartTest::testAutoScaledCluster
[gw8] [ 78%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCEAutoscaleTestMultipleNodeTypes::testAutoScale
src/toil/test/provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing
src/toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testEncapsulation
[gw2] [ 78%] SKIPPED src/toil/test/provisioners/gceProvisionerTest.py::GCERestartTest::testAutoScaledCluster
src/toil/test/server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery
[gw8] [ 79%] PASSED src/toil/test/provisioners/provisionerTest.py::ProvisionerTest::test_node_type_parsing
src/toil/test/src/helloWorldTest.py::HelloWorldTest::testHelloWorld
[gw2] [ 79%] SKIPPED src/toil/test/server/serverTest.py::ToilServerUtilsTest::test_workflow_canceling_recovery
src/toil/test/server/serverTest.py::FileStateStoreURLTest::test_state_store
[gw2] [ 79%] SKIPPED src/toil/test/server/serverTest.py::FileStateStoreURLTest::test_state_store
src/toil/test/src/promisesTest.py::PathIndexingPromiseTest::test
[gw11] [ 79%] FAILED src/toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testEncapsulation
src/toil/test/server/serverTest.py::FileStateStoreTest::test_state_store
[gw8] [ 79%] FAILED src/toil/test/src/helloWorldTest.py::HelloWorldTest::testHelloWorld
[gw5] [ 80%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testExtremeCacheSetup
[gw11] [ 80%] SKIPPED src/toil/test/server/serverTest.py::FileStateStoreTest::test_state_store
src/toil/test/src/promisesTest.py::CachedUnpicklingJobStoreTest::test
src/toil/test/src/promisesTest.py::ChainedIndexedPromisesTest::test
[gw5] [ 80%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testExtremeCacheSetup
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreExportFile
[gw5] [ 80%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreExportFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreLogging
[gw5] [ 81%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreLogging
[gw2] [ 81%] FAILED src/toil/test/src/promisesTest.py::PathIndexingPromiseTest::test
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreOperations
[gw5] [ 81%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testFileStoreOperations
src/toil/test/src/systemTest.py::SystemTest::testAtomicityOfNonEmptyDirectoryRenames
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testMultipleJobsReadSameCacheHitGlobalFile
[gw5] [ 81%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testMultipleJobsReadSameCacheHitGlobalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testMultipleJobsReadSameCacheMissGlobalFile
[gw5] [ 81%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testMultipleJobsReadSameCacheMissGlobalFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore
[gw11] [ 82%] FAILED src/toil/test/src/promisesTest.py::CachedUnpicklingJobStoreTest::test
[gw8] [ 82%] FAILED src/toil/test/src/promisesTest.py::ChainedIndexedPromisesTest::test
src/toil/test/src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger
[gw10] [ 82%] FAILED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken
[gw0] [ 82%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testBuiltIn
src/toil/test/src/resourceTest.py::ResourceTest::testNonPyStandAlone
[gw6] [ 82%] FAILED src/toil/test/src/regularLogTest.py::RegularLogTest::testRegularLog
src/toil/test/src/regularLogTest.py::RegularLogTest::testWriteGzipLogs
[gw6] [ 83%] SKIPPED src/toil/test/src/regularLogTest.py::RegularLogTest::testWriteGzipLogs
src/toil/test/src/regularLogTest.py::RegularLogTest::testWriteLogs
[gw4] [ 83%] PASSED src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobClassFromMain
src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction
[gw4] [ 83%] FAILED src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunction
src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain
[gw5] [ 83%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCachHitFileFromJobStore
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile
[gw8] [ 84%] FAILED src/toil/test/src/realtimeLoggerTest.py::RealtimeLoggerTest::testRealtimeLogger
[gw10] [ 84%] FAILED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility
[gw5] [ 84%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile
[gw0] [ 84%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testNonPyStandAlone
src/toil/test/src/resourceTest.py::ResourceTest::testPackage
[gw0] [ 84%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testPackage
src/toil/test/src/resourceTest.py::ResourceTest::testStandAlone
[gw0] [ 85%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testStandAlone
src/toil/test/src/resourceTest.py::ResourceTest::testStandAloneInPackage
[gw0] [ 85%] PASSED src/toil/test/src/resourceTest.py::ResourceTest::testStandAloneInPackage
[gw4] [ 85%] PASSED src/toil/test/src/userDefinedJobArgTypeTest.py::UserDefinedJobArgTypeTest::testJobFunctionFromMain
[gw10] [ 85%] FAILED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility
src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions
[gw6] [ 85%] FAILED src/toil/test/src/regularLogTest.py::RegularLogTest::testWriteLogs
[gw5] [ 86%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadWriteFileStreamTextMode
[gw7] [ 86%] PASSED src/toil/test/__init__.py::toil.test.timeLimit
src/toil/test/src/resumabilityTest.py::ResumabilityTest::test
[gw7] [ 86%] SKIPPED src/toil/test/src/resumabilityTest.py::ResumabilityTest::test
src/toil/test/src/resumabilityTest.py::ResumabilityTest::test_chaining
[gw7] [ 86%] FAILED src/toil/test/src/resumabilityTest.py::ResumabilityTest::test_chaining
[gw10] [ 86%] FAILED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions
[gw12] [ 87%] PASSED src/toil/test/src/jobTest.py::JobTest::testDeadlockDetection
src/toil/test/src/jobTest.py::JobTest::testEvaluatingRandomDAG
[gw12] [ 87%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testEvaluatingRandomDAG
src/toil/test/src/jobTest.py::JobTest::testNewCheckpointIsLeafVertexNonRootCase
[gw12] [ 87%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testNewCheckpointIsLeafVertexNonRootCase
src/toil/test/src/jobTest.py::JobTest::testNewCheckpointIsLeafVertexRootCase
[gw12] [ 87%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testNewCheckpointIsLeafVertexRootCase
src/toil/test/src/jobTest.py::JobTest::testSiblingDAGConsistency
[gw12] [ 88%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testSiblingDAGConsistency
src/toil/test/src/jobTest.py::JobTest::testStatic
[gw12] [ 88%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testStatic
src/toil/test/src/jobTest.py::JobTest::testStatic2
[gw12] [ 88%] FAILED src/toil/test/src/jobTest.py::JobTest::testStatic2
src/toil/test/src/jobTest.py::JobTest::testTrivialDAGConsistency
[gw12] [ 88%] SKIPPED src/toil/test/src/jobTest.py::JobTest::testTrivialDAGConsistency
[gw5] [ 88%] 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] [ 89%] SKIPPED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReturnFileSizesWithBadWorker
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream
[gw3] [ 89%] FAILED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStore
src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStoreWithBadWorker
[gw3] [ 90%] SKIPPED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testJobFileStoreWithBadWorker
src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore
[gw3] [ 90%] FAILED src/toil/test/src/jobFileStoreTest.py::JobFileStoreTest::testNonCachingFileStore
[gw5] [ 90%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testSimultaneousReadsUncachedStream
src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testToilIsNotBroken
[gw5] [ 90%] 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] [ 91%] FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions
[gw9] [ 91%] PASSED src/toil/test/src/threadingTest.py::ThreadingTest::testGlobalMutexOrdering
src/toil/test/src/threadingTest.py::ThreadingTest::testLastProcessStanding
[gw2] [ 92%] PASSED src/toil/test/src/systemTest.py::SystemTest::testAtomicityOfNonEmptyDirectoryRenames
src/toil/test/src/workerTest.py::WorkerTests::testNextChainable
[gw2] [ 92%] PASSED src/toil/test/src/workerTest.py::WorkerTests::testNextChainable
[gw9] [ 92%] PASSED src/toil/test/src/threadingTest.py::ThreadingTest::testLastProcessStanding
src/toil/test/utils/toilDebugTest.py::DebugJobTest::test_print_job_info
[gw9] [ 92%] FAILED src/toil/test/utils/toilDebugTest.py::DebugJobTest::test_print_job_info
src/toil/test/utils/toilDebugTest.py::DebugJobTest::test_run_job
[gw9] [ 92%] FAILED src/toil/test/utils/toilDebugTest.py::DebugJobTest::test_run_job
[gw1] [ 93%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testInitialState
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation
[gw1] [ 93%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobCreation
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions
[gw1] [ 93%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobDeletions
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality
[gw1] [ 93%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testJobLoadEquality
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testLargeFile
[gw1] [ 94%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testLargeFile
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testMultipartUploads
[gw1] [ 94%] SKIPPED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testMultipartUploads
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream
[gw1] [ 94%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPartialReadFromStream
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles
[gw1] [ 94%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPerJobFiles
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete
[gw1] [ 94%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPersistantFilesToDelete
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName
[gw1] [ 95%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testPreserveFileName
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode
[gw1] [ 95%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteFileStreamTextMode
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode
[gw1] [ 95%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testReadWriteSharedFilesTextMode
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles
[gw1] [ 95%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testSharedFiles
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging
[gw1] [ 95%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testStatsAndLogging
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior
[gw1] [ 96%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testUpdateBehavior
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles
[gw1] [ 96%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testWriteLogFiles
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles
[gw1] [ 96%] PASSED src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::testZeroLengthFiles
src/toil/test/jobStores/jobStoreTest.py::FileJobStoreTest::test_file_link_imports
[gw1] [ 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
[gw1] [ 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
[gw1] [ 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
[gw1] [ 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
[gw1] [ 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
[gw1] [ 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
[gw1] [ 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
[gw1] [ 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
[gw1] [ 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
[gw1] [ 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
[gw1] [ 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
[gw1] [ 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
[gw1] [ 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
[gw1] [ 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
[gw1] [ 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
[gw1] [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/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/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/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)
<frozen importlib._bootstrap>:1387: in _gcd_import
???
<frozen importlib._bootstrap>:1360: in _find_and_load
???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:935: in _load_unlocked
???
<frozen importlib._bootstrap_external>:1026: in exec_module
???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
???
src/toil/test/provisioners/clusterScalerTest.py:34: in <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner, Shape
src/toil/provisioners/abstractProvisioner.py:29: in <module>
from toil.provisioners.node import Node
src/toil/provisioners/node.py:16: in <module>
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/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/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/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/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)
<frozen importlib._bootstrap>:1387: in _gcd_import
???
<frozen importlib._bootstrap>:1360: in _find_and_load
???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:935: in _load_unlocked
???
<frozen importlib._bootstrap_external>:1026: in exec_module
???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
???
src/toil/test/sort/sortTest.py:24: in <module>
from toil.batchSystems.mesos.test import MesosTestSupport
src/toil/batchSystems/mesos/__init__.py:20: in <module>
from toil.provisioners.abstractProvisioner import Shape
src/toil/provisioners/abstractProvisioner.py:29: in <module>
from toil.provisioners.node import Node
src/toil/provisioners/node.py:16: in <module>
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/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/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)
<frozen importlib._bootstrap>:1387: in _gcd_import
???
<frozen importlib._bootstrap>:1360: in _find_and_load
???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:935: in _load_unlocked
???
<frozen importlib._bootstrap_external>:1026: in exec_module
???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
???
src/toil/test/src/jobServiceTest.py:29: in <module>
from toil.leader import DeadlockException
src/toil/leader.py:51: in <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
src/toil/provisioners/abstractProvisioner.py:29: in <module>
from toil.provisioners.node import Node
src/toil/provisioners/node.py:16: in <module>
import pipes
E ModuleNotFoundError: No module named 'pipes'
_____________ 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 <module>
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 <module>
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 <module>
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 <module>
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 <module>
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/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)
<frozen importlib._bootstrap>:1387: in _gcd_import
???
<frozen importlib._bootstrap>:1360: in _find_and_load
???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:935: in _load_unlocked
???
<frozen importlib._bootstrap_external>:1026: in exec_module
???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
???
src/toil/test/utils/utilsTest.py:41: in <module>
from toil.test.sort.sortTest import makeFileToSort
src/toil/test/sort/sortTest.py:24: in <module>
from toil.batchSystems.mesos.test import MesosTestSupport
src/toil/batchSystems/mesos/__init__.py:20: in <module>
from toil.provisioners.abstractProvisioner import Shape
src/toil/provisioners/abstractProvisioner.py:29: in <module>
from toil.provisioners.node import Node
src/toil/provisioners/node.py:16: in <module>
import pipes
E ModuleNotFoundError: No module named 'pipes'
_____________ 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 <module>
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 <module>
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 <module>
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 <module>
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 <module>
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 <module>
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 <module>
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 <module>
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 __________________________
[gw12] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.jobTest.JobTest:testDAGConsistency (Jan 23 2025 08:16:36:461710 PST)
------------------------------ Captured log call -------------------------------
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'docker', 'concurrent', 'bcdocs', 'requests', 'boto', 'asyncio', 'botocore', 'dill', 'boto3', 'urllib3', 'charset_normalizer', '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.jobTest.JobTest-testDAGConsistency-19u6gw4b/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-19u6gw4b/jobStore'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'a35b3d76-c955-413e-8ff8-b8ad190f7a2c'
DEBUG toil.common:common.py:740 Obtained node ID 33aff37d-8850-4714-bc7b-6a946b12f649 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-dd9141a3d50e5c6daeefecf498faca20
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4104403704.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4104403704 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-3e9ba616b02b485583a8d51cd16ee155/stream for result of 'parent' TemporaryID(68367123-ab4d-4944-aa13-48165dfef110) 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-ufdut5cx v0
DEBUG toil.job:job.py:1299 New job version: 'parent' kind-parent/instance-ufdut5cx v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'a35b3d76-c955-413e-8ff8-b8ad190f7a2c', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.jobTest.JobTest-testDAGConsistency-19u6gw4b/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 4104403704...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4104403704 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-KRFFmajH/toil/toilwf-dd9141a3d50e5c6daeefecf498faca20/deferred/func19j73poo
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-KRFFmajH/toil/toilwf-dd9141a3d50e5c6daeefecf498faca20/deferred/func19j73poo
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toilwf-dd9141a3d50e5c6daeefecf498faca20
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-dd9141a3d50e5c6daeefecf498faca20
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.0106048583984375 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.jobTest.JobTest-testDAGConsistency-19u6gw4b/jobStore)
INFO toil.test:__init__.py:120 Tore down toil.test.src.jobTest.JobTest.testDAGConsistency
____________________ JobFileStoreTest.testCachingFileStore _____________________
[gw3] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.jobFileStoreTest.JobFileStoreTest:testCachingFileStore (Jan 23 2025 08:16:36:574186 PST)
------------------------------ Captured log call -------------------------------
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
INFO toil.test:__init__.py:120 Tore down toil.test.src.jobFileStoreTest.JobFileStoreTest.testCachingFileStore
___________________ CheckpointTest.testCheckpointNotRetried ____________________
[gw11] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.checkpointTest.CheckpointTest:testCheckpointNotRetried (Jan 23 2025 08:16:36:621465 PST)
------------------------------ Captured log call -------------------------------
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
INFO toil.test:__init__.py:120 Tore down toil.test.src.checkpointTest.CheckpointTest.testCheckpointNotRetried
_________________ MessageBusTest.test_restart_without_bus_path _________________
[gw7] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.busTest.MessageBusTest:test_restart_without_bus_path (Jan 23 2025 08:16:36:636861 PST)
------------------------------ Captured log call -------------------------------
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'docker', 'charset_normalizer', 'dill', 'botocore', 'requests', 'urllib3', 'concurrent', 'bcdocs', 'asyncio', 'boto3', 'debugWorkflow', '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.busTest.MessageBusTest-jobstore-xv0el_qi', '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-iv3derz9/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-xv0el_qi'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'c39d6ec4-55a0-4986-951f-fd7698e843f7'
DEBUG toil.common:common.py:740 Obtained node ID 33aff37d-8850-4714-bc7b-6a946b12f649 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-d6407f14cf04577e9c8eb1382f9d840c
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4103823960.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4103823960 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-406bcb231da1455f9804993560b8a126/stream for result of 'failing_job_fn' TemporaryID(65a161be-54ae-429f-9e8c-cf7407ee7f88) 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-f9s8__yj v0
DEBUG toil.job:job.py:1299 New job version: 'failing_job_fn' kind-failing_job_fn/instance-f9s8__yj v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'c39d6ec4-55a0-4986-951f-fd7698e843f7', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.busTest.MessageBusTest-jobstore-xv0el_qi', '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-iv3derz9/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 4103823960...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4103823960 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-KRFFmajH/toil/toilwf-d6407f14cf04577e9c8eb1382f9d840c/deferred/funcnfy3ns9m
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-KRFFmajH/toil/toilwf-d6407f14cf04577e9c8eb1382f9d840c/deferred/funcnfy3ns9m
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toilwf-d6407f14cf04577e9c8eb1382f9d840c
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-d6407f14cf04577e9c8eb1382f9d840c
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.0069844722747802734 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 _____________
[gw2] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.importExportFileTest.ImportExportFileTest:test_import_export_restart_false (Jan 23 2025 08:16:36:767829 PST)
------------------------------ 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 ionos2-i386.
INFO toil.test:__init__.py:120 Tore down toil.test.src.importExportFileTest.ImportExportFileTest.test_import_export_restart_false
____________________________ testFetchJobStoreFiles ____________________________
[gw8] linux -- Python 3.13.1 /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>
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 414, in check_call
retcode = call(*popenargs, **kwargs)
File "/usr/lib/python3.13/subprocess.py", line 395, in call
with Popen(*popenargs, **kwargs) as p:
~~~~~^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.13/subprocess.py", line 1036, 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 1966, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.11'
_______________________ DataStructuresTest.testJobQueue ________________________
[gw8] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import Shape
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.mesos.MesosDataStructuresTest.DataStructuresTest:testJobQueue (Jan 23 2025 08:16:36:859559 PST)
____________________ JobEncapsulationTest.testEncapsulation ____________________
[gw11] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.jobEncapsulationTest.JobEncapsulationTest:testEncapsulation (Jan 23 2025 08:16:36:869939 PST)
------------------------------ 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 ionos2-i386.
INFO toil.test:__init__.py:120 Tore down toil.test.src.jobEncapsulationTest.JobEncapsulationTest.testEncapsulation
________________________ HelloWorldTest.testHelloWorld _________________________
[gw8] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.helloWorldTest.HelloWorldTest:testHelloWorld (Jan 23 2025 08:16:36:873318 PST)
------------------------------ Captured log call -------------------------------
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
INFO toil.test:__init__.py:120 Tore down toil.test.src.helloWorldTest.HelloWorldTest.testHelloWorld
___________ CachingFileStoreTestWithFileJobStore.testDeleteLocalFile ___________
[gw5] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testDeleteLocalFile (Jan 23 2025 08:16:36:260328 PST)
------------------------------ Captured log call -------------------------------
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', 'requests'}
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-ia7ozc1z/logFile'.
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', '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': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testDeleteLocalFile-ia7ozc1z/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-7b6g1igr', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testDeleteLocalFile-ia7ozc1z', '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-7b6g1igr'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'ccba5d12-3a31-4954-bc7a-27255c8c1305'
DEBUG toil.common:common.py:740 Obtained node ID 33aff37d-8850-4714-bc7b-6a946b12f649 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-ia7ozc1z/toilwf-fdf21a6707a053cd8a0048d29c45ff86
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4106654848.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4106654848 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-fac7f67b4d3e409887006f3f4c3eddcb/stream for result of '_deleteLocalFileFn' TemporaryID(0b9bde65-7620-4f9f-ba14-6d24000eee11) 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-x821sukf v0
DEBUG toil.job:job.py:1299 New job version: '_deleteLocalFileFn' kind-_deleteLocalFileFn/instance-x821sukf v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'ccba5d12-3a31-4954-bc7a-27255c8c1305', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-7b6g1igr', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testDeleteLocalFile-ia7ozc1z', '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 4106654848...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4106654848 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-KRFFmajH/toil/toilwf-fdf21a6707a053cd8a0048d29c45ff86/deferred/funcko_1yzok
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-KRFFmajH/toil/toilwf-fdf21a6707a053cd8a0048d29c45ff86/deferred/funcko_1yzok
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testDeleteLocalFile-ia7ozc1z/toilwf-fdf21a6707a053cd8a0048d29c45ff86
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-fdf21a6707a053cd8a0048d29c45ff86
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.006663799285888672 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-7b6g1igr)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testDeleteLocalFile
_________________________ PathIndexingPromiseTest.test _________________________
[gw2] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.promisesTest.PathIndexingPromiseTest:test (Jan 23 2025 08:16:36:883310 PST)
------------------------------ Captured log call -------------------------------
INFO toil.test:__init__.py:115 Setting up toil.test.src.promisesTest.PathIndexingPromiseTest.test ...
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
INFO toil.test:__init__.py:120 Tore down toil.test.src.promisesTest.PathIndexingPromiseTest.test
______________________ CachedUnpicklingJobStoreTest.test _______________________
[gw11] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.promisesTest.CachedUnpicklingJobStoreTest:test (Jan 23 2025 08:16:36:941849 PST)
------------------------------ 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 ionos2-i386.
INFO toil.test:__init__.py:120 Tore down toil.test.src.promisesTest.CachedUnpicklingJobStoreTest.test
_______________________ ChainedIndexedPromisesTest.test ________________________
[gw8] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.promisesTest.ChainedIndexedPromisesTest:test (Jan 23 2025 08:16:36:943986 PST)
------------------------------ 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 ionos2-i386.
INFO toil.test:__init__.py:120 Tore down toil.test.src.promisesTest.ChainedIndexedPromisesTest.test
___ NonCachingFileStoreTestWithFileJobStore.testReadWriteFileStreamTextMode ____
[gw10] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore:testReadWriteFileStreamTextMode (Jan 23 2025 08:16:36:490062 PST)
------------------------------ Captured log call -------------------------------
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'charset_normalizer', 'debugWorkflow', 'asyncio', 'botocore', 'concurrent', 'dill', 'boto3', 'requests', 'bcdocs', 'boto', 'urllib3', 'docker'}
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-trkazp23/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-trkazp23/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-iirxpzoe', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-trkazp23', '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-iirxpzoe'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'c78238b2-d1b7-47b7-9560-82ca71123c89'
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 33aff37d-8850-4714-bc7b-6a946b12f649 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-trkazp23/toilwf-5f586db3881851ef9e39b503a5e16562
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4107193264.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4107193264 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-5c9b3633b65f4080b5514e6fbc26e696/stream for result of '_testReadWriteFileStreamTextMode' TemporaryID(e68fd37a-36b2-4c7b-a8f0-3becd7333b43) 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-2vapkt34 v0
DEBUG toil.job:job.py:1299 New job version: '_testReadWriteFileStreamTextMode' kind-_testReadWriteFileStreamTextMode/instance-2vapkt34 v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'c78238b2-d1b7-47b7-9560-82ca71123c89', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-iirxpzoe', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-trkazp23', '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 4107193264...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4107193264 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-KRFFmajH/toil/toilwf-5f586db3881851ef9e39b503a5e16562/deferred/funcvcmlmesy
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-KRFFmajH/toil/toilwf-5f586db3881851ef9e39b503a5e16562/deferred/funcvcmlmesy
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-trkazp23/toilwf-5f586db3881851ef9e39b503a5e16562
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-5f586db3881851ef9e39b503a5e16562
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.012258291244506836 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-iirxpzoe)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore.testReadWriteFileStreamTextMode
________________________ RegularLogTest.testRegularLog _________________________
[gw6] linux -- Python 3.13.1 /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 472, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**kwargs).stdout
^^^^^^^^^
File "/usr/lib/python3.13/subprocess.py", line 577, 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 (Jan 23 2025 08:16:36:569877 PST)
__________________ UserDefinedJobArgTypeTest.testJobFunction ___________________
[gw4] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.userDefinedJobArgTypeTest.UserDefinedJobArgTypeTest:testJobFunction (Jan 23 2025 08:16:37:459168 PST)
------------------------------ Captured log call -------------------------------
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
INFO toil.test:__init__.py:120 Tore down toil.test.src.userDefinedJobArgTypeTest.UserDefinedJobArgTypeTest.testJobFunction
_____ CachingFileStoreTestWithFileJobStore.testReadCachHitFileFromJobStore _____
[gw5] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testReadCachHitFileFromJobStore (Jan 23 2025 08:16:36:961806 PST)
------------------------------ 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: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', 'requests'}
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-wtidwmh5/logFile'.
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', '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': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCachHitFileFromJobStore-wtidwmh5/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-90khiqii', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCachHitFileFromJobStore-wtidwmh5', '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-90khiqii'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'b8e86704-6e61-491a-bbb5-44dc18319229'
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-wtidwmh5/toilwf-66b60599f50b591ca21bf020284a946b
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4106868848.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4106868848 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-afd8d4b5162545ca9e23450857f27658/stream for result of '_writeFileToJobStoreWithAsserts' TemporaryID(15a1c839-2df2-4292-97b9-2dc39b0ddc4a) 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-h8sk7bmb v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-299cf581bcbc49ea8df8c5b4cc60dc80/stream for result of '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-pgh_8agc v0
DEBUG toil.job:job.py:2644 Processing job '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-pgh_8agc v0
DEBUG toil.job:job.py:1299 New job version: '_readFromJobStore' kind-_readFromJobStore/instance-h8sk7bmb v1
DEBUG toil.job:job.py:1299 New job version: '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-pgh_8agc v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'b8e86704-6e61-491a-bbb5-44dc18319229', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-90khiqii', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCachHitFileFromJobStore-wtidwmh5', '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 4106868848...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4106868848 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-KRFFmajH/toil/toilwf-66b60599f50b591ca21bf020284a946b/deferred/funchyqwtsqw
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-KRFFmajH/toil/toilwf-66b60599f50b591ca21bf020284a946b/deferred/funchyqwtsqw
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCachHitFileFromJobStore-wtidwmh5/toilwf-66b60599f50b591ca21bf020284a946b
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-66b60599f50b591ca21bf020284a946b
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.008695840835571289 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-90khiqii)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testReadCachHitFileFromJobStore
____________________ RealtimeLoggerTest.testRealtimeLogger _____________________
[gw8] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.realtimeLoggerTest.RealtimeLoggerTest:testRealtimeLogger (Jan 23 2025 08:16:37:012123 PST)
------------------------------ 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 ionos2-i386.
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
_________ NonCachingFileStoreTestWithFileJobStore.testToilIsNotBroken __________
[gw10] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore:testToilIsNotBroken (Jan 23 2025 08:16:37:133967 PST)
------------------------------ 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: {'charset_normalizer', 'debugWorkflow', 'asyncio', 'botocore', 'concurrent', 'dill', 'boto3', 'requests', 'bcdocs', 'boto', 'urllib3', 'docker'}
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-xpx6uz13/logFile'.
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'charset_normalizer', 'debugWorkflow', 'asyncio', 'botocore', 'concurrent', 'dill', 'boto3', 'requests', 'bcdocs', 'boto', 'urllib3', 'docker'}
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-xpx6uz13/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-qtlms051', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testToilIsNotBroken-xpx6uz13', '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-qtlms051'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '9ee9c515-4845-499f-b51c-05c013b33ceb'
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-xpx6uz13/toilwf-7cde91ddf6a9520faaac712d0c9620c9
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4103633712.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4103633712 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-f45c21f82830430591a1ad36eeac1398/stream for result of '_uselessFunc' TemporaryID(45c44050-2858-42a4-a77b-75986c20b933) 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-usxy8z17 v0
DEBUG toil.job:job.py:2644 Processing job '_uselessFunc' kind-_uselessFunc/instance-1f6xa9tu v0
DEBUG toil.job:job.py:2644 Processing job '_uselessFunc' kind-_uselessFunc/instance-ukq0177h v0
DEBUG toil.job:job.py:2644 Processing job '_uselessFunc' kind-_uselessFunc/instance-ljaeb82p v0
DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-usxy8z17 v1
DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-1f6xa9tu v1
DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-ukq0177h v1
DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-ljaeb82p v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '9ee9c515-4845-499f-b51c-05c013b33ceb', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-qtlms051', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testToilIsNotBroken-xpx6uz13', '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 4103633712...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4103633712 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-KRFFmajH/toil/toilwf-7cde91ddf6a9520faaac712d0c9620c9/deferred/funcdwc5vzy2
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-KRFFmajH/toil/toilwf-7cde91ddf6a9520faaac712d0c9620c9/deferred/funcdwc5vzy2
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testToilIsNotBroken-xpx6uz13/toilwf-7cde91ddf6a9520faaac712d0c9620c9
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-7cde91ddf6a9520faaac712d0c9620c9
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.010139942169189453 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-qtlms051)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore.testToilIsNotBroken
_ CachingFileStoreTestWithFileJobStore.testReadCacheMissFileFromJobStoreWithCachingReadFile _
[gw5] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testReadCacheMissFileFromJobStoreWithCachingReadFile (Jan 23 2025 08:16:37:549131 PST)
------------------------------ 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: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', 'requests'}
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-pott60zm/logFile'.
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', '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': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithCachingReadFile-pott60zm/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-ythntxdv', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithCachingReadFile-pott60zm', '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-ythntxdv'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'c4eed080-3bf9-489f-af6c-c0ab0e47f85f'
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-pott60zm/toilwf-9bb6f16763b85a10be5a0bda411f345c
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4102921216.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4102921216 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-3028c07c9deb4dceb6e16dfd00748281/stream for result of '_writeFileToJobStoreWithAsserts' TemporaryID(0e792911-8b7c-443e-bf65-683e06f46c3d) 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-3q694t0n v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-a9abbb64226c470f81d559dfd2002375/stream for result of '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-ow2435gl v0
DEBUG toil.job:job.py:2644 Processing job '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-ow2435gl v0
DEBUG toil.job:job.py:1299 New job version: '_readFromJobStore' kind-_readFromJobStore/instance-3q694t0n v1
DEBUG toil.job:job.py:1299 New job version: '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-ow2435gl v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'c4eed080-3bf9-489f-af6c-c0ab0e47f85f', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-ythntxdv', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithCachingReadFile-pott60zm', '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 4102921216...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4102921216 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-KRFFmajH/toil/toilwf-9bb6f16763b85a10be5a0bda411f345c/deferred/func87e9uy6y
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-KRFFmajH/toil/toilwf-9bb6f16763b85a10be5a0bda411f345c/deferred/func87e9uy6y
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithCachingReadFile-pott60zm/toilwf-9bb6f16763b85a10be5a0bda411f345c
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-9bb6f16763b85a10be5a0bda411f345c
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.012849807739257812 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-ythntxdv)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testReadCacheMissFileFromJobStoreWithCachingReadFile
___ NonCachingFileStoreTestWithFileJobStore.testWriteExportFileCompatibility ___
[gw10] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore:testWriteExportFileCompatibility (Jan 23 2025 08:16:37:751186 PST)
------------------------------ 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: {'charset_normalizer', 'debugWorkflow', 'asyncio', 'botocore', 'concurrent', 'dill', 'boto3', 'requests', 'bcdocs', 'boto', 'urllib3', 'docker'}
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-4y7olo4_/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-4y7olo4_/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-nqxp0vr_', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-4y7olo4_', '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-nqxp0vr_'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '1e9a77a8-2e6c-45de-b1ef-f198b590bd15'
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-4y7olo4_/toilwf-d2de875bbf865c749ab4a6e43e6c2b89
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4103764152.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4103764152 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-442e58f06e4a4bffa645ecd230e22b19/stream for result of '_testWriteExportFileCompatibility' TemporaryID(53c4ead4-7c1f-4335-9575-eb01cc8b4d71) 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-n823rxag v0
DEBUG toil.job:job.py:1299 New job version: '_testWriteExportFileCompatibility' kind-_testWriteExportFileCompatibility/instance-n823rxag v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '1e9a77a8-2e6c-45de-b1ef-f198b590bd15', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-nqxp0vr_', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-4y7olo4_', '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 4103764152...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4103764152 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-KRFFmajH/toil/toilwf-d2de875bbf865c749ab4a6e43e6c2b89/deferred/func728mi1iu
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-KRFFmajH/toil/toilwf-d2de875bbf865c749ab4a6e43e6c2b89/deferred/func728mi1iu
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-4y7olo4_/toilwf-d2de875bbf865c749ab4a6e43e6c2b89
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-d2de875bbf865c749ab4a6e43e6c2b89
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.009604930877685547 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-nqxp0vr_)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore.testWriteExportFileCompatibility
_________________________ RegularLogTest.testWriteLogs _________________________
[gw6] linux -- Python 3.13.1 /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 419, 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-b5n_5fjb']' returned non-zero exit status 1.
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.regularLogTest.RegularLogTest:testWriteLogs (Jan 23 2025 08:16:37:449577 PST)
----------------------------- Captured stderr call -----------------------------
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'botocore', 'requests', 'charset_normalizer', 'dill', 'docker', 'urllib3', 'boto3', 'boto'}
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.statsAndLogging] Root logger is at level 'DEBUG', 'toil' logger at level 'DEBUG'.
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.common] Initialized default configuration: {"config_version": 1.0}
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.batchSystems.options] Add options for single_machine batch system
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.batchSystems.options] Add options for grid_engine batch system
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.batchSystems.options] Add options for lsf batch system
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.batchSystems.options] Add options for slurm batch system
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.batchSystems.options] Add options for torque batch system
[2025-01-23T08:16:38-1200] [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'}
[2025-01-23T08:16:38-1200] [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-b5n_5fjb', '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'}
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.jobStores.fileJobStore] Path to job store directory is '/build/reproducible-path/toil-6.1.0/toilTest'.
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.jobStores.abstractJobStore] The workflow ID is: '9474cf6f-b1fd-4efa-b535-db571c91a207'
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.common] Obtained node ID 33aff37d-8850-4714-bc7b-6a946b12f649 from file /proc/sys/kernel/random/boot_id
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.common] Using the single machine batch system
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.common] Created the workflow directory for this machine at /tmp/toilwf-b119dc66a2105bb49ef2d587717cf925
[2025-01-23T08:16:38-1200] [Thread-1 (daddy)] [D] [toil.batchSystems.singleMachine] Started daddy thread for batch system 4127247096.
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.batchSystems.singleMachine] Started batch system 4127247096 in normal mode.
[2025-01-23T08:16:38-1200] [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.
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.common] No user script to auto-deploy.
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.common] Written the environment for the jobs to the environment file
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.common] Caching all jobs in job store
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.common] 0 jobs downloaded.
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.job] Issuing promise files/no-job/file-1ace9dae8b6940af9ae712d25ae2b658/stream for result of 'hello_world' TemporaryID(7f30753c-8817-4186-b727-3708acb78937) v0
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.job] Saving graph of 1 jobs, 1 non-service, 1 new
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.job] Processing job 'hello_world' kind-hello_world/instance-l7uc0kfh v0
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.job] New job version: 'hello_world' kind-hello_world/instance-l7uc0kfh v1
[2025-01-23T08:16:38-1200] [MainThread] [I] [toil] Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil] Configuration: {'cwl': False, 'workflowID': '9474cf6f-b1fd-4efa-b535-db571c91a207', '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-b5n_5fjb', '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}
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.realtimeLogger] Real-time logging disabled
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.common] Shutting down batch system ...
[2025-01-23T08:16:38-1200] [Thread-1 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread cleaning up 0 remaining children for batch system 4127247096...
[2025-01-23T08:16:38-1200] [Thread-1 (daddy)] [D] [toil.batchSystems.singleMachine] Daddy thread for batch system 4127247096 finishing because no children should now exist
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Attempting worker cleanup
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.deferred] Cleaning up deferred functions system
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.deferred] Opened with own state file /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-b119dc66a2105bb49ef2d587717cf925/deferred/funcfmupxeun
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.deferred] Running orphaned deferred functions
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.deferred] Ran orphaned deferred functions from 0 abandoned state files
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.deferred] Removing own state file /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-b119dc66a2105bb49ef2d587717cf925/deferred/funcfmupxeun
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting workflow directory /tmp/toilwf-b119dc66a2105bb49ef2d587717cf925
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.batchSystems.abstractBatchSystem] Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-b119dc66a2105bb49ef2d587717cf925
[2025-01-23T08:16:38-1200] [MainThread] [D] [toil.common] ... finished shutting down the batch system in 0.007750988006591797 seconds.
[2025-01-23T08:16:38-1200] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/build/reproducible-path/toil-6.1.0/toilTest)
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/build/reproducible-path/toil-6.1.0/src/toil/test/mesos/helloWorld.py", line 71, in <module>
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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
_ CachingFileStoreTestWithFileJobStore.testReadCacheMissFileFromJobStoreWithoutCachingReadFile _
[gw5] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testReadCacheMissFileFromJobStoreWithoutCachingReadFile (Jan 23 2025 08:16:38:145482 PST)
------------------------------ 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: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', 'requests'}
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-l2w4c2hh/logFile'.
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', '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': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithoutCachingReadFile-l2w4c2hh/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-l7xnzoz6', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithoutCachingReadFile-l2w4c2hh', '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-l7xnzoz6'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'fd5d150d-633f-45a4-95d7-902aa05c8485'
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-l2w4c2hh/toilwf-558d737867f65a4a919c4c68075cfce3
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4102921552.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4102921552 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-6be63876c93548dfb2dc07c1f18673a7/stream for result of '_writeFileToJobStoreWithAsserts' TemporaryID(fd6803cc-0809-48a0-8430-56b5973d9362) 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-8chf4blo v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-d2155d5574214b978cc0f580536717d0/stream for result of '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-dtuunjr2 v0
DEBUG toil.job:job.py:2644 Processing job '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-dtuunjr2 v0
DEBUG toil.job:job.py:1299 New job version: '_readFromJobStore' kind-_readFromJobStore/instance-8chf4blo v1
DEBUG toil.job:job.py:1299 New job version: '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-dtuunjr2 v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'fd5d150d-633f-45a4-95d7-902aa05c8485', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-l7xnzoz6', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithoutCachingReadFile-l2w4c2hh', '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 4102921552...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4102921552 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-KRFFmajH/toil/toilwf-558d737867f65a4a919c4c68075cfce3/deferred/funcl0pleq6q
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-KRFFmajH/toil/toilwf-558d737867f65a4a919c4c68075cfce3/deferred/funcl0pleq6q
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadCacheMissFileFromJobStoreWithoutCachingReadFile-l2w4c2hh/toilwf-558d737867f65a4a919c4c68075cfce3
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-558d737867f65a4a919c4c68075cfce3
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.009139299392700195 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-l7xnzoz6)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testReadCacheMissFileFromJobStoreWithoutCachingReadFile
________________________ ResumabilityTest.test_chaining ________________________
[gw7] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.resumabilityTest.ResumabilityTest:test_chaining (Jan 23 2025 08:16:38:807045 PST)
------------------------------ Captured log call -------------------------------
INFO toil.test:__init__.py:115 Setting up toil.test.src.resumabilityTest.ResumabilityTest.test_chaining ...
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: {'docker', 'charset_normalizer', 'dill', 'botocore', 'requests', 'urllib3', 'concurrent', 'bcdocs', 'asyncio', 'boto3', 'debugWorkflow', 'boto'}
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-b9mcl_9f/log.txt'.
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'docker', 'charset_normalizer', 'dill', 'botocore', 'requests', 'urllib3', 'concurrent', 'bcdocs', 'asyncio', 'boto3', 'debugWorkflow', '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': '/tmp/toil-test-src.resumabilityTest.ResumabilityTest-test_chaining-b9mcl_9f/log.txt', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.resumabilityTest.ResumabilityTest-jobstore-2no1wygf', '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-2no1wygf'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'c7e11879-69ed-4624-b226-973d71c1e44d'
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-d6d06b28e2345fa88c62a6b4edf4990b
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4110611536.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4110611536 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-65d9d3cdc0fc4881acb9bc16ef989845/stream for result of 'chaining_parent' TemporaryID(2538e525-bc5a-4c76-bc22-dc3e1de08ffd) 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-rp8djppk v0
DEBUG toil.job:job.py:1299 New job version: 'chaining_parent' kind-chaining_parent/instance-rp8djppk v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'c7e11879-69ed-4624-b226-973d71c1e44d', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.resumabilityTest.ResumabilityTest-jobstore-2no1wygf', '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 4110611536...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4110611536 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-KRFFmajH/toil/toilwf-d6d06b28e2345fa88c62a6b4edf4990b/deferred/func5ldt6k5a
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-KRFFmajH/toil/toilwf-d6d06b28e2345fa88c62a6b4edf4990b/deferred/func5ldt6k5a
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toilwf-d6d06b28e2345fa88c62a6b4edf4990b
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-d6d06b28e2345fa88c62a6b4edf4990b
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.0066831111907958984 seconds.
INFO toil.test:__init__.py:120 Tore down toil.test.src.resumabilityTest.ResumabilityTest.test_chaining
__ NonCachingFileStoreTestWithFileJobStore.testWriteReadGlobalFilePermissions __
[gw10] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore:testWriteReadGlobalFilePermissions (Jan 23 2025 08:16:38:340834 PST)
------------------------------ 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: {'charset_normalizer', 'debugWorkflow', 'asyncio', 'botocore', 'concurrent', 'dill', 'boto3', 'requests', 'bcdocs', 'boto', 'urllib3', 'docker'}
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-_2xdsxtf/logFile'.
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'charset_normalizer', 'debugWorkflow', 'asyncio', 'botocore', 'concurrent', 'dill', 'boto3', 'requests', 'bcdocs', 'boto', 'urllib3', 'docker'}
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-_2xdsxtf/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-8hwz67cs', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-_2xdsxtf', '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-8hwz67cs'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '15e5c6ed-a7ec-4ab0-a123-b34135ba0ed1'
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-_2xdsxtf/toilwf-271723bee6035ebc839ec18ea664a51d
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4103764488.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4103764488 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-cd0b1360c8c54fd1b759e60af3a61de4/stream for result of '_testWriteReadGlobalFilePermissions' TemporaryID(2de080e0-d07e-47b3-b8de-f47f8961bf50) 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-u_iv0tf2 v0
DEBUG toil.job:job.py:1299 New job version: '_testWriteReadGlobalFilePermissions' kind-_testWriteReadGlobalFilePermissions/instance-u_iv0tf2 v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '15e5c6ed-a7ec-4ab0-a123-b34135ba0ed1', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-8hwz67cs', 'workDir': '/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-_2xdsxtf', '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 4103764488...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4103764488 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-KRFFmajH/toil/toilwf-271723bee6035ebc839ec18ea664a51d/deferred/func4f6xoxkq
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-KRFFmajH/toil/toilwf-271723bee6035ebc839ec18ea664a51d/deferred/func4f6xoxkq
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-_2xdsxtf/toilwf-271723bee6035ebc839ec18ea664a51d
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-271723bee6035ebc839ec18ea664a51d
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.014791250228881836 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore-jobstore-8hwz67cs)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.NonCachingFileStoreTestWithFileJobStore.testWriteReadGlobalFilePermissions
_____________________________ JobTest.testStatic2 ______________________________
[gw12] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.jobTest.JobTest:testStatic2 (Jan 23 2025 08:16:39:040366 PST)
------------------------------ 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 ionos2-i386.
INFO toil.test:__init__.py:120 Tore down toil.test.src.jobTest.JobTest.testStatic2
_____ CachingFileStoreTestWithFileJobStore.testReadWriteFileStreamTextMode _____
[gw5] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testReadWriteFileStreamTextMode (Jan 23 2025 08:16:38:731218 PST)
------------------------------ 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: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', 'requests'}
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-bp_1n9xp/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-bp_1n9xp/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-hh1bhduo', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-bp_1n9xp', '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-hh1bhduo'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'b008c43a-bb1e-4d38-a8a4-b90145b4f6a5'
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-bp_1n9xp/toilwf-921500d9fb695266b9c3aba4c8c67291
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4103753200.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4103753200 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-c0489c3c2e3745f8b1f9cbebee5a0ead/stream for result of '_testReadWriteFileStreamTextMode' TemporaryID(e61734e5-a866-4d6e-b985-9cfbd5a22257) 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-h8r9o8v1 v0
DEBUG toil.job:job.py:1299 New job version: '_testReadWriteFileStreamTextMode' kind-_testReadWriteFileStreamTextMode/instance-h8r9o8v1 v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'b008c43a-bb1e-4d38-a8a4-b90145b4f6a5', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-hh1bhduo', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-bp_1n9xp', '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 4103753200...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4103753200 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-KRFFmajH/toil/toilwf-921500d9fb695266b9c3aba4c8c67291/deferred/func7xfp_zxa
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-KRFFmajH/toil/toilwf-921500d9fb695266b9c3aba4c8c67291/deferred/func7xfp_zxa
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testReadWriteFileStreamTextMode-bp_1n9xp/toilwf-921500d9fb695266b9c3aba4c8c67291
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-921500d9fb695266b9c3aba4c8c67291
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.013419866561889648 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-hh1bhduo)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testReadWriteFileStreamTextMode
______________________ JobFileStoreTest.testJobFileStore _______________________
[gw3] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.jobFileStoreTest.JobFileStoreTest:testJobFileStore (Jan 23 2025 08:16:36:684834 PST)
------------------------------ 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: {'boto3', 'boto', 'debugWorkflow', 'concurrent', 'requests', 'asyncio', 'botocore', 'charset_normalizer', 'urllib3', 'bcdocs', 'dill', 'docker'}
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: {'boto3', 'boto', 'debugWorkflow', 'concurrent', 'requests', 'asyncio', 'botocore', 'charset_normalizer', 'urllib3', 'bcdocs', 'dill', 'docker'}
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-v7j1174t', '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-v7j1174t'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'd6e8d4fd-1ec3-4a93-9ad0-5f4d796b6052'
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-4ad029e6e2ce5fe5812d6d73597ba877
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4102183024.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4102183024 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-c4fd392d0ad04398a1db4a212b7874b2/stream for result of 'fileTestJob' TemporaryID(e8918465-7f8c-44fc-895e-5cc5dc31d058) 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-0667du_t v0
DEBUG toil.job:job.py:1299 New job version: 'fileTestJob' kind-fileTestJob/instance-0667du_t v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'd6e8d4fd-1ec3-4a93-9ad0-5f4d796b6052', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.jobFileStoreTest.JobFileStoreTest-jobstore-v7j1174t', '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 4102183024...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4102183024 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-KRFFmajH/toil/toilwf-4ad029e6e2ce5fe5812d6d73597ba877/deferred/funczdimlebf
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-KRFFmajH/toil/toilwf-4ad029e6e2ce5fe5812d6d73597ba877/deferred/funczdimlebf
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toilwf-4ad029e6e2ce5fe5812d6d73597ba877
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-4ad029e6e2ce5fe5812d6d73597ba877
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.0060939788818359375 seconds.
INFO toil.test:__init__.py:120 Tore down toil.test.src.jobFileStoreTest.JobFileStoreTest.testJobFileStore
___________________ JobFileStoreTest.testNonCachingFileStore ___________________
[gw3] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.jobFileStoreTest.JobFileStoreTest:testNonCachingFileStore (Jan 23 2025 08:16:39:456398 PST)
------------------------------ 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 ionos2-i386.
INFO toil.test:__init__.py:120 Tore down toil.test.src.jobFileStoreTest.JobFileStoreTest.testNonCachingFileStore
___ CachingFileStoreTestWithFileJobStore.testSimultaneousReadsUncachedStream ___
[gw5] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testSimultaneousReadsUncachedStream (Jan 23 2025 08:16:39:318202 PST)
------------------------------ 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: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', 'requests'}
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-0dlkpskf/logFile'.
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', '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': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testSimultaneousReadsUncachedStream-0dlkpskf/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-ll3lw6li', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testSimultaneousReadsUncachedStream-0dlkpskf', '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-ll3lw6li'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '29c68022-3bf9-440b-a463-3b883336b482'
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-0dlkpskf/toilwf-d64334e5ef24506799501097a006cc0c
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4107098672.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4107098672 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-1e4a994e7b7d45c0888c866d9e3f455a/stream for result of '_createUncachedFileStream' TemporaryID(36ab1fee-b628-4522-846b-53bb601bde59) 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-xzc94h0e v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-ee137e0f857a40878ecaaa90f475aba5/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-vldzbpvn v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-50da82792ee44340ac022bfda44c0902/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-2mppn2j7 v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-a982279891324609944972ebe7cfaa96/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-e86s45b8 v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-f6fb0717336547f08f6852d9b82b06ae/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-pjoyxjma v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-0243b9f651244327b4928637c4054feb/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-lrfvp_wy v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-1ee717052413479a809c8d6772cbb4f8/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-t9_tukjj v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-33dbfef1fcee4edfa8cb9e5514e62135/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-1i5i_zqq v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-7dc88f7564d04da494a22d7b0d5ae821/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-52lgm7q_ v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-aa1f762aa25f4552a81a1fa382f251e9/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-clhyfdpm v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-a3a318c472b54a3da14ff20eb56c32db/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-z1bce_so v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-a13fb69749c64227bed1ce8279282303/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-p5qu6dg4 v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-65168d9294954ab9a2efe8e9e78c923a/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-yw8sdcft v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-03566692bc1b458ea5d385857c54261c/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-v1lev2yv v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-10956ea7458241b49b327965841b8beb/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-p871lse1 v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-e78cb6663c8f4ec2baa192c42cc27512/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-4s7ju811 v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-e4fbc09befe54b34a8aad9d86c3617ae/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-fhrwxy0x v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-4316255a9fde470d9102103484e2d7b7/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-v4li35hs v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-31b11a5b133e477b88c8c2958f34e9c9/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-ngyd_vzm v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-b7947c61ceb344caabfb5d10553d3c96/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-l8vk_bgq v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-d4708b6da39b46eb9cd39a474472ace0/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-9zl7w0s_ v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-c6594456c56b446990c7ab7d3cf1e8fe/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-u0w1usil v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-3cb60ab40a7743639a38ffc9bfb72929/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-wyhrtwbn v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-bef98032491c486ea67a3bb076759453/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-6qfubl62 v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-dbd0cbc39af24216b600ab9897267a51/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-55go2973 v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-70b0cafaa6ad4448aa98663de0a652c6/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-oee_gqh0 v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-a4a4b5cd636248689325fe991a0b0593/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-hl0mx0xz v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-25b2403ad841435f9515594402892f9e/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-_4zutqnp v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-ae9fbee8c0d94a48a2ccefd3f1748973/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-yoqkh10l v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-c23a37c236df4ad89c0c771990a55abc/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_readFileWithDelay' kind-_readFileWithDelay/instance-c8bdg566 v0
DEBUG toil.job:job.py:1924 Issuing promise files/no-job/file-2f0b9b8e88104f64b4fb9e5e0e25b25a/stream for result of '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:2644 Processing job '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v0
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-xzc94h0e v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-vldzbpvn v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-2mppn2j7 v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-e86s45b8 v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-pjoyxjma v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-lrfvp_wy v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-t9_tukjj v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-1i5i_zqq v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-52lgm7q_ v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-clhyfdpm v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-z1bce_so v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-p5qu6dg4 v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-yw8sdcft v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-v1lev2yv v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-p871lse1 v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-4s7ju811 v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-fhrwxy0x v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-v4li35hs v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-ngyd_vzm v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-l8vk_bgq v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-9zl7w0s_ v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-u0w1usil v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-wyhrtwbn v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-6qfubl62 v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-55go2973 v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-oee_gqh0 v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-hl0mx0xz v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-_4zutqnp v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-yoqkh10l v1
DEBUG toil.job:job.py:1299 New job version: '_readFileWithDelay' kind-_readFileWithDelay/instance-c8bdg566 v1
DEBUG toil.job:job.py:1299 New job version: '_createUncachedFileStream' kind-_createUncachedFileStream/instance-f88cl49p v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '29c68022-3bf9-440b-a463-3b883336b482', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-ll3lw6li', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testSimultaneousReadsUncachedStream-0dlkpskf', '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 4107098672...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4107098672 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-KRFFmajH/toil/toilwf-d64334e5ef24506799501097a006cc0c/deferred/funck40aihha
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-KRFFmajH/toil/toilwf-d64334e5ef24506799501097a006cc0c/deferred/funck40aihha
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testSimultaneousReadsUncachedStream-0dlkpskf/toilwf-d64334e5ef24506799501097a006cc0c
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-d64334e5ef24506799501097a006cc0c
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.010618209838867188 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-ll3lw6li)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testSimultaneousReadsUncachedStream
___________ CachingFileStoreTestWithFileJobStore.testToilIsNotBroken ___________
[gw5] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testToilIsNotBroken (Jan 23 2025 08:16:39:996247 PST)
------------------------------ 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: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', 'requests'}
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-tdyz2jii/logFile'.
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', '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': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testToilIsNotBroken-tdyz2jii/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-x06xxtrd', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testToilIsNotBroken-tdyz2jii', '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-x06xxtrd'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '33be7915-8473-405d-a9e1-09ef4595670a'
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-tdyz2jii/toilwf-d51c6763dfdf57fcbbc0e81f0390a51c
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4107018768.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4107018768 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-d6e375ed0a994cbc8bee96308947fbe1/stream for result of '_uselessFunc' TemporaryID(b097bfe5-301a-4536-bc8c-8ccb81fb6b80) 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-khm0k5qn v0
DEBUG toil.job:job.py:2644 Processing job '_uselessFunc' kind-_uselessFunc/instance-g64ga0xu v0
DEBUG toil.job:job.py:2644 Processing job '_uselessFunc' kind-_uselessFunc/instance-4mn0v01o v0
DEBUG toil.job:job.py:2644 Processing job '_uselessFunc' kind-_uselessFunc/instance-odd1vz4p v0
DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-khm0k5qn v1
DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-g64ga0xu v1
DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-4mn0v01o v1
DEBUG toil.job:job.py:1299 New job version: '_uselessFunc' kind-_uselessFunc/instance-odd1vz4p v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '33be7915-8473-405d-a9e1-09ef4595670a', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-x06xxtrd', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testToilIsNotBroken-tdyz2jii', '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 4107018768...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4107018768 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-KRFFmajH/toil/toilwf-d51c6763dfdf57fcbbc0e81f0390a51c/deferred/funcrxw5gp76
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-KRFFmajH/toil/toilwf-d51c6763dfdf57fcbbc0e81f0390a51c/deferred/funcrxw5gp76
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testToilIsNotBroken-tdyz2jii/toilwf-d51c6763dfdf57fcbbc0e81f0390a51c
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-d51c6763dfdf57fcbbc0e81f0390a51c
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.011878490447998047 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-x06xxtrd)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testToilIsNotBroken
____ CachingFileStoreTestWithFileJobStore.testWriteExportFileCompatibility _____
[gw5] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testWriteExportFileCompatibility (Jan 23 2025 08:16:40:583150 PST)
------------------------------ 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: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', 'requests'}
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-eyc9_z3d/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-eyc9_z3d/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-f20213yh', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-eyc9_z3d', '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-f20213yh'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '59b7d5fb-2518-40e3-b11d-fe72da0457cc'
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-eyc9_z3d/toilwf-77b334c143025ac794e77e723ce71cfd
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4103751920.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4103751920 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-3d6fd4dd7c6d4706a6ee5f64b3328e03/stream for result of '_testWriteExportFileCompatibility' TemporaryID(c1222f28-bcc2-4378-8c29-aaa17935f841) 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-x044gwld v0
DEBUG toil.job:job.py:1299 New job version: '_testWriteExportFileCompatibility' kind-_testWriteExportFileCompatibility/instance-x044gwld v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '59b7d5fb-2518-40e3-b11d-fe72da0457cc', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-f20213yh', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-eyc9_z3d', '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 4103751920...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4103751920 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-KRFFmajH/toil/toilwf-77b334c143025ac794e77e723ce71cfd/deferred/funcysgx92g1
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-KRFFmajH/toil/toilwf-77b334c143025ac794e77e723ce71cfd/deferred/funcysgx92g1
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteExportFileCompatibility-eyc9_z3d/toilwf-77b334c143025ac794e77e723ce71cfd
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-77b334c143025ac794e77e723ce71cfd
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.009880542755126953 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-f20213yh)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testWriteExportFileCompatibility
______ CachingFileStoreTestWithFileJobStore.testWriteLocalFileToJobStore _______
[gw5] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testWriteLocalFileToJobStore (Jan 23 2025 08:16:41:174954 PST)
------------------------------ 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: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', 'requests'}
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-mv1k7g99/logFile'.
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', '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': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteLocalFileToJobStore-mv1k7g99/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-sanhybkj', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteLocalFileToJobStore-mv1k7g99', '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-sanhybkj'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'f05abcc5-faec-4706-b274-2d5247224c82'
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-mv1k7g99/toilwf-278126ec7df95b3da0492a8d12802096
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4106850832.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4106850832 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-a91ac41fa62b49fbbdd58ccad05fd3bc/stream for result of '_writeFileToJobStoreWithAsserts' TemporaryID(3b220b2e-e646-4468-b5ba-e8fedb2f7423) 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-r4g2g8oi v0
DEBUG toil.job:job.py:1299 New job version: '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-r4g2g8oi v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'f05abcc5-faec-4706-b274-2d5247224c82', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-sanhybkj', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteLocalFileToJobStore-mv1k7g99', '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 4106850832...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4106850832 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-KRFFmajH/toil/toilwf-278126ec7df95b3da0492a8d12802096/deferred/funcuorfbqjd
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-KRFFmajH/toil/toilwf-278126ec7df95b3da0492a8d12802096/deferred/funcuorfbqjd
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteLocalFileToJobStore-mv1k7g99/toilwf-278126ec7df95b3da0492a8d12802096
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-278126ec7df95b3da0492a8d12802096
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.009419441223144531 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-sanhybkj)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testWriteLocalFileToJobStore
_____ CachingFileStoreTestWithFileJobStore.testWriteNonLocalFileToJobStore _____
[gw5] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testWriteNonLocalFileToJobStore (Jan 23 2025 08:16:41:757429 PST)
------------------------------ 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: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', 'requests'}
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-aqzh7c1n/logFile'.
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', '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': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteNonLocalFileToJobStore-aqzh7c1n/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-3b3acd27', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteNonLocalFileToJobStore-aqzh7c1n', '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-3b3acd27'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: 'cc33473b-31fb-4e4b-8959-30e5415f5fbe'
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-aqzh7c1n/toilwf-a391071010585c02ba8ef6eebf389d12
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4107364592.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4107364592 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-9b45b98e20364e78b623b47f5c3ea6a1/stream for result of '_writeFileToJobStoreWithAsserts' TemporaryID(6cde201c-0726-4ffe-9b86-cd8f5ae2782e) 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-uokeug1u v0
DEBUG toil.job:job.py:1299 New job version: '_writeFileToJobStoreWithAsserts' kind-_writeFileToJobStoreWithAsserts/instance-uokeug1u v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': 'cc33473b-31fb-4e4b-8959-30e5415f5fbe', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-3b3acd27', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteNonLocalFileToJobStore-aqzh7c1n', '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 4107364592...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4107364592 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-KRFFmajH/toil/toilwf-a391071010585c02ba8ef6eebf389d12/deferred/funcb9wtvzeh
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-KRFFmajH/toil/toilwf-a391071010585c02ba8ef6eebf389d12/deferred/funcb9wtvzeh
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteNonLocalFileToJobStore-aqzh7c1n/toilwf-a391071010585c02ba8ef6eebf389d12
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-a391071010585c02ba8ef6eebf389d12
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.004341840744018555 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-3b3acd27)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testWriteNonLocalFileToJobStore
___ CachingFileStoreTestWithFileJobStore.testWriteReadGlobalFilePermissions ____
[gw5] linux -- Python 3.13.1 /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 <module>
from toil.provisioners.abstractProvisioner import AbstractProvisioner
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/abstractProvisioner.py", line 29, in <module>
from toil.provisioners.node import Node
File "/build/reproducible-path/toil-6.1.0/src/toil/provisioners/node.py", line 16, in <module>
import pipes
ModuleNotFoundError: No module named 'pipes'
---------------------------- Captured stdout setup -----------------------------
[TEST] toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore:testWriteReadGlobalFilePermissions (Jan 23 2025 08:16:42:333552 PST)
------------------------------ 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: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', 'requests'}
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-ii9_5l05/logFile'.
DEBUG toil.statsAndLogging:statsAndLogging.py:328 Suppressing the following loggers: {'docker', 'boto', 'boto3', 'charset_normalizer', 'botocore', 'urllib3', 'dill', 'bcdocs', 'debugWorkflow', 'asyncio', 'concurrent', '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': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-ii9_5l05/logFile', 'logRotating': False, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-yrt47s5b', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-ii9_5l05', '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-yrt47s5b'.
DEBUG toil.jobStores.abstractJobStore:abstractJobStore.py:204 The workflow ID is: '15591d26-2e77-4e31-b848-be070cf67ce4'
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-ii9_5l05/toilwf-f5a44138a9135044ad1308feae13be78
DEBUG toil.batchSystems.singleMachine:singleMachine.py:217 Started daddy thread for batch system 4107019408.
DEBUG toil.batchSystems.singleMachine:singleMachine.py:199 Started batch system 4107019408 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-dcb8511b6df645f99fd4ffaacc063c92/stream for result of '_testWriteReadGlobalFilePermissions' TemporaryID(c1d3d40a-debd-46dd-876d-e411a9928b6a) 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-paqmxiba v0
DEBUG toil.job:job.py:1299 New job version: '_testWriteReadGlobalFilePermissions' kind-_testWriteReadGlobalFilePermissions/instance-paqmxiba v1
INFO toil:__init__.py:438 Running Toil version 6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f on host ionos2-i386.
DEBUG toil:__init__.py:439 Configuration: {'cwl': False, 'workflowID': '15591d26-2e77-4e31-b848-be070cf67ce4', 'kill_polling_interval': 5, 'jobStore': 'file:/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-yrt47s5b', 'workDir': '/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-ii9_5l05', '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 4107019408...
DEBUG toil.batchSystems.singleMachine:singleMachine.py:274 Daddy thread for batch system 4107019408 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-KRFFmajH/toil/toilwf-f5a44138a9135044ad1308feae13be78/deferred/funczy4br5oj
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-KRFFmajH/toil/toilwf-f5a44138a9135044ad1308feae13be78/deferred/funczy4br5oj
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:484 Deleting workflow directory /tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-testWriteReadGlobalFilePermissions-ii9_5l05/toilwf-f5a44138a9135044ad1308feae13be78
DEBUG toil.batchSystems.abstractBatchSystem:abstractBatchSystem.py:488 Deleting coordination directory /tmp/dh-xdg-rundir-KRFFmajH/toil/toilwf-f5a44138a9135044ad1308feae13be78
DEBUG toil.common:common.py:1403 ... finished shutting down the batch system in 0.004178285598754883 seconds.
INFO toil.common:common.py:860 Successfully deleted the job store: FileJobStore(/tmp/toil-test-src.fileStoreTest.CachingFileStoreTestWithFileJobStore-jobstore-yrt47s5b)
INFO toil.test:__init__.py:120 Tore down toil.test.src.fileStoreTest.CachingFileStoreTestWithFileJobStore.testWriteReadGlobalFilePermissions
_______________________ DebugJobTest.test_print_job_info _______________________
[gw9] linux -- Python 3.13.1 /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 414, in check_call
retcode = call(*popenargs, **kwargs)
File "/usr/lib/python3.13/subprocess.py", line 395, in call
with Popen(*popenargs, **kwargs) as p:
~~~~~^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.13/subprocess.py", line 1036, 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 1966, 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 (Jan 23 2025 08:16:45:638752 PST)
------------------------------ 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
__________________________ DebugJobTest.test_run_job ___________________________
[gw9] linux -- Python 3.13.1 /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 414, in check_call
retcode = call(*popenargs, **kwargs)
File "/usr/lib/python3.13/subprocess.py", line 395, in call
with Popen(*popenargs, **kwargs) as p:
~~~~~^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.13/subprocess.py", line 1036, 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 1966, 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 (Jan 23 2025 08:16:45:647211 PST)
------------------------------ 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
=========================== 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/mesos/MesosDataStructuresTest.py::DataStructuresTest::testJobQueue - ModuleNotFoundError: No module named 'pipes'
FAILED src/toil/test/src/jobEncapsulationTest.py::JobEncapsulationTest::testEncapsulation - ModuleNotFoundError: No module named 'pipes'
FAILED src/toil/test/src/helloWorldTest.py::HelloWorldTest::testHelloWorld - ModuleNotFoundError: No module named 'pipes'
FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testDeleteLocalFile - 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::testReadWriteFileStreamTextMode - 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::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/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testToilIsNotBroken - ModuleNotFoundError: No module named 'pipes'
FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithCachingReadFile - ModuleNotFoundError: No module named 'pipes'
FAILED src/toil/test/src/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteExportFileCompatibility - 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-b5n_5fjb']' returned non-zero exit status 1.
FAILED src/toil/test/src/fileStoreTest.py::CachingFileStoreTestWithFileJobStore::testReadCacheMissFileFromJobStoreWithoutCachingReadFile - 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/fileStoreTest.py::NonCachingFileStoreTestWithFileJobStore::testWriteReadGlobalFilePermissions - 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::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'
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/utils/toilDebugTest.py::DebugJobTest::test_run_job - FileNotFoundError: [Errno 2] No such file or directory: 'python3.11'
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/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/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/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/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/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/provisioners/clusterTest.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/sort/sortTest.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/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/src/jobServiceTest.py
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/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/utilsTest.py
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/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, 56 errors in 93.61s (0:01:33) =======
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 "3.12 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/13135 and its subdirectories