Mercurial > repos > richard-burhans > ncbi_egapx
changeset 41:d129c3d0e920 draft default tip
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 8278322cb9db499c593669d2bb8b740024ecf5dc
| author | richard-burhans |
|---|---|
| date | Mon, 28 Jul 2025 14:35:28 +0000 |
| parents | b095c69eab5b |
| children | |
| files | funny.bash lame.py macros.xml ncbi_egapx.xml serve.bash serve.out test.bash test.out |
| diffstat | 8 files changed, 3489 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/funny.bash Mon Jul 28 14:35:28 2025 +0000 @@ -0,0 +1,41 @@ +#!/usr/bin/env bash + +taskset -p $$ | sed -e 's/^.*: //' | awk ' + BEGIN { + split("0 1 2 3 4 5 6 7 8 9 a b c d e f", hex_chars, " ") + split("0 1 1 2 1 2 2 3 1 2 2 3 2 3 3 4", vals, " ") + for (i in hex_chars) { + ones[hex_chars[i]] = int(vals[i]) + } + total = 0 + } + + { + split($0, chars, "") + for (i in chars) { + if (chars[i] in ones) { + total += ones[chars[i]] + } + } + print total + } +' + + +# 0 0000 0 +# 1 0001 1 +# 2 0010 1 +# 3 0011 2 +# 4 0100 1 +# 5 0101 2 +# 6 0110 2 +# 7 0111 3 +# 8 1000 1 +# 9 1001 2 +# a 1010 2 +# b 1011 3 +# c 1100 2 +# d 1101 3 +# e 1110 3 +# f 1111 4 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lame.py Mon Jul 28 14:35:28 2025 +0000 @@ -0,0 +1,28 @@ +#!/usr/bin/env python3 + +for i in range(0, 16): + hex_value = f"{i:0x}" + bin_value = f"{i:04b}" + ones = len(bin_value.replace("0", "")) + + print(f'{ones}') + + + +# 0 0000 0 +# 1 0001 1 +# 2 0010 1 +# 3 0011 2 +# 4 0100 1 +# 5 0101 2 +# 6 0110 2 +# 7 0111 3 +# 8 1000 1 +# 9 1001 2 +# a 1010 2 +# b 1011 3 +# c 1100 2 +# d 1101 3 +# e 1110 3 +# f 1111 4 +
--- a/macros.xml Fri Jul 18 00:58:39 2025 +0000 +++ b/macros.xml Mon Jul 28 14:35:28 2025 +0000 @@ -5,7 +5,7 @@ </requirements> </xml> <token name="@TOOL_VERSION@">0.4.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">23.0</token> <xml name="edam_ontology"> <edam_operations>
--- a/ncbi_egapx.xml Fri Jul 18 00:58:39 2025 +0000 +++ b/ncbi_egapx.xml Mon Jul 28 14:35:28 2025 +0000 @@ -77,7 +77,11 @@ source /galaxy/env.bash && python3 /galaxy/scripts/galaxy-resource-config.py && ## run EGAPx - python3 /galaxy/egapx/ui/egapx.py '$yamlconfig' -e galaxy -o 'egapx_out' && + python3 /galaxy/egapx/ui/egapx.py + #if $developer.query_limit.query_limit_selector == "false" + --force + #end if + '$yamlconfig' -e galaxy -o 'egapx_out' && ## hack to support 0.2-alpha if [ -e egapx_out/accept.gff ]; then ln -s accept.gff egapx_out/complete.genomic.gff; fi #if $developer.collect_star_bams @@ -86,6 +90,7 @@ ]]></command> <environment_variables> <environment_variable name="NXF_DEBUG">3</environment_variable> + <environment_variable name="EGAPX_RNASEQ_QUERY_LIMIT">$getVar('developer.query_limit.rnaseq_query_limit', '20')</environment_variable> </environment_variables> <configfiles> <configfile name="short_reads_config"><![CDATA[#slurp @@ -262,6 +267,16 @@ </conditional> <section name="developer" title="Developer options" expanded="false"> <param name="collect_star_bams" type="boolean" checked="false" label="Collect BAM output from STAR"/> + <conditional name="query_limit"> + <param name="query_limit_selector" type="select" label="Enforce SRA query limit"> + <option value="true" selected="True">Yes</option> + <option value="false">No</option> + </param> + <when value="true"> + <param name="rnaseq_query_limit" type="integer" min="0" value="20" label="SRA query limit"/> + </when> + <when value="false"/> + </conditional> </section> </inputs> <outputs> @@ -299,7 +314,7 @@ </collection> </outputs> <tests> - <test expect_num_outputs="27" expect_test_failure="true"> + <test expect_num_outputs="27" expect_test_failure="false"> <conditional name="cond_input_style"> <param name="input_style" value="fillform"/> <conditional name="cond_genome_style"> @@ -314,16 +329,24 @@ </conditional> <section name="developer"> <param name="collect_star_bams" value="true"/> + <conditional name="query_limit"> + <param name="query_limit_selector" value="true"/> + <param name="rnaseq_query_limit" value="20"/> + </conditional> </section> <expand macro="test_outputs"/> </test> - <test expect_num_outputs="27" expect_test_failure="true"> + <test expect_num_outputs="27" expect_test_failure="false"> <conditional name="cond_input_style"> <param name="input_style" value="history"/> <param name="yamlin" value="input.yaml"/> </conditional> <section name="developer"> <param name="collect_star_bams" value="true"/> + <conditional name="query_limit"> + <param name="query_limit_selector" value="true"/> + <param name="rnaseq_query_limit" value="20"/> + </conditional> </section> <expand macro="test_outputs"/> </test>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/serve.bash Mon Jul 28 14:35:28 2025 +0000 @@ -0,0 +1,72 @@ +#!/usr/bin/env bash + +set -o errexit +set -o nounset +set -o pipefail +#set -o xtrace + +export TMP=/scratch/rico/tmp + +#source "/scratch/rico/new/env.bash" + +export PLANEMO_GLOBAL_WORKSPACE=/scratch/rico/planemo +export PLANEMO_GLOBAL_CONFIG_PATH=${PLANEMO_GLOBAL_WORKSPACE}/.planemo.yml +CLEAN=0 +CLEAN=1 + +if [ -e "/scratch/rico/galaxy" ]; then + z_time=$(stat --format="%Z" "/scratch/rico/galaxy") + + w_time=$(stat --format="%W" "/scratch/rico/galaxy") + if [ $w_time -ne 0 ]; then + if [ $w_time -lt $z_time ]; then + z_time="$w_time" + fi + fi + + now=$(date +%s) + delta=$(( now - z_time )) + if [ $delta -ge 86400 ]; then + CLEAN=1 + fi +else + CLEAN=1 +fi + +if [ $CLEAN -ne 0 ]; then + rm -rf /scratch/rico/galaxy + rm -rf "$PLANEMO_GLOBAL_WORKSPACE" + rm -rf /scratch/rico/.npm + mkdir /scratch/rico/.npm +fi + +rm -rf /tmp/tmp* "$TMP/tmp*" + +export GALAXY_SLOTS=64 +export GALAXY_MEMORY_MB=262144 + +if [ $CLEAN -ne 0 ]; then + planemo serve \ + --galaxy_root /scratch/rico/galaxy \ + --docker \ + --no_docker_sudo \ + --no_cleanup \ + 2>&1 \ + | tee serve.out +else + planemo serve \ + --galaxy_root /scratch/rico/galaxy \ + --docker \ + --no_docker_sudo \ + --skip_client_build \ + --no_cleanup \ + 2>&1 \ + | tee serve.out +fi + +# Galaxy upload tool fails when using planemo server on galaxy release branch 24 +# +# rm -rf /scratch/rico/galaxy; planemo serve --galaxy_branch release_23.2 --galaxy_root /scratch/rico/galaxy +# rm -rf /scratch/rico/galaxy; planemo serve --galaxy_branch release_24.0 --galaxy_root /scratch/rico/galaxy + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/serve.out Mon Jul 28 14:35:28 2025 +0000 @@ -0,0 +1,1323 @@ +git clone --mirror https://github.com/galaxyproject/galaxy /scratch/rico/planemo/gx_repo +Cloning into bare repository '/scratch/rico/planemo/gx_repo'... +git clone --branch master --depth 1 file:///scratch/rico/planemo/gx_repo /scratch/rico/galaxy +Cloning into '/scratch/rico/galaxy'... +Updating files: 61% (4763/7701) Updating files: 62% (4775/7701) Updating files: 63% (4852/7701) Updating files: 64% (4929/7701) Updating files: 65% (5006/7701) Updating files: 66% (5083/7701) Updating files: 67% (5160/7701) Updating files: 68% (5237/7701) Updating files: 69% (5314/7701) Updating files: 70% (5391/7701) Updating files: 71% (5468/7701) Updating files: 72% (5545/7701) Updating files: 73% (5622/7701) Updating files: 74% (5699/7701) Updating files: 75% (5776/7701) Updating files: 76% (5853/7701) Updating files: 77% (5930/7701) Updating files: 78% (6007/7701) Updating files: 79% (6084/7701) Updating files: 80% (6161/7701) Updating files: 81% (6238/7701) Updating files: 82% (6315/7701) Updating files: 83% (6392/7701) Updating files: 84% (6469/7701) Updating files: 85% (6546/7701) Updating files: 86% (6623/7701) Updating files: 87% (6700/7701) Updating files: 88% (6777/7701) Updating files: 89% (6854/7701) Updating files: 90% (6931/7701) Updating files: 91% (7008/7701) Updating files: 92% (7085/7701) Updating files: 93% (7162/7701) Updating files: 94% (7239/7701) Updating files: 95% (7316/7701) Updating files: 96% (7393/7701) Updating files: 97% (7470/7701) Updating files: 98% (7547/7701) Updating files: 99% (7624/7701) Updating files: 100% (7701/7701) Updating files: 100% (7701/7701), done. +if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/scratch/rico/planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /scratch/rico/.venv/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /scratch/rico/.venv/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS} +galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input +created virtual environment CPython3.9.19.final.0-64 in 9051ms + creator CPython3Posix(dest=/scratch/rico/planemo/gx_venv_3, clear=False, no_vcs_ignore=False, global=False) + seeder FromAppData(download=False, pip=bundle, setuptools=bundle, via=copy, app_data_dir=/afs/bx.psu.edu/home/rico/.local/share/virtualenv) + added seed packages: pip==25.1.1, setuptools==80.9.0 + activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator +Created virtualenv +Activated a virtualenv for Galaxy +/scratch/rico/planemo/gx_venv_3 +Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample +Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample +Activating virtualenv at /scratch/rico/planemo/gx_venv_3 +Requirement already satisfied: pip>=20.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (25.1.1) +Collecting wheel + Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB) +Using cached wheel-0.45.1-py3-none-any.whl (72 kB) +Installing collected packages: wheel +Successfully installed wheel-0.45.1 +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple +Ignoring colorama: markers 'sys_platform == "win32"' don't match your environment +Ignoring legacy-cgi: markers 'python_full_version >= "3.13"' don't match your environment +Ignoring limits: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring networkx: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring numpy: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring packaging: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring pyreadline3: markers 'sys_platform == "win32"' don't match your environment +Ignoring tifffile: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring urllib3: markers 'python_full_version >= "3.10"' don't match your environment +Collecting a2wsgi==1.10.8 (from -r requirements.txt (line 3)) + Using cached a2wsgi-1.10.8-py3-none-any.whl.metadata (3.9 kB) +Collecting adal==1.2.7 (from -r requirements.txt (line 4)) + Using cached adal-1.2.7-py2.py3-none-any.whl.metadata (6.9 kB) +Collecting aiobotocore==2.21.1 (from -r requirements.txt (line 5)) + Using cached aiobotocore-2.21.1-py3-none-any.whl.metadata (24 kB) +Collecting aiofiles==24.1.0 (from -r requirements.txt (line 6)) + Using cached aiofiles-24.1.0-py3-none-any.whl.metadata (10 kB) +Collecting aiohappyeyeballs==2.6.1 (from -r requirements.txt (line 7)) + Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB) +Collecting aiohttp==3.11.18 (from -r requirements.txt (line 8)) + Using cached aiohttp-3.11.18-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.7 kB) +Collecting aioitertools==0.12.0 (from -r requirements.txt (line 9)) + Using cached aioitertools-0.12.0-py3-none-any.whl.metadata (3.8 kB) +Collecting aiosignal==1.3.2 (from -r requirements.txt (line 10)) + Using cached aiosignal-1.3.2-py2.py3-none-any.whl.metadata (3.8 kB) +Collecting alembic==1.15.2 (from -r requirements.txt (line 11)) + Using cached alembic-1.15.2-py3-none-any.whl.metadata (7.3 kB) +Collecting amqp==5.3.1 (from -r requirements.txt (line 12)) + Using cached amqp-5.3.1-py3-none-any.whl.metadata (8.9 kB) +Collecting annotated-types==0.7.0 (from -r requirements.txt (line 13)) + Using cached annotated_types-0.7.0-py3-none-any.whl.metadata (15 kB) +Collecting anyio==4.9.0 (from -r requirements.txt (line 14)) + Using cached anyio-4.9.0-py3-none-any.whl.metadata (4.7 kB) +Collecting apispec==6.8.1 (from -r requirements.txt (line 15)) + Using cached apispec-6.8.1-py3-none-any.whl.metadata (10 kB) +Collecting appdirs==1.4.4 (from -r requirements.txt (line 16)) + Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB) +Collecting arcp==0.2.1 (from -r requirements.txt (line 17)) + Using cached arcp-0.2.1-py2.py3-none-any.whl.metadata (7.6 kB) +Collecting argcomplete==3.6.2 (from -r requirements.txt (line 18)) + Using cached argcomplete-3.6.2-py3-none-any.whl.metadata (16 kB) +Collecting async-timeout==5.0.1 (from -r requirements.txt (line 19)) + Using cached async_timeout-5.0.1-py3-none-any.whl.metadata (5.1 kB) +Collecting attmap==0.13.2 (from -r requirements.txt (line 20)) + Using cached attmap-0.13.2-py3-none-any.whl.metadata (1.1 kB) +Collecting attrs==25.3.0 (from -r requirements.txt (line 21)) + Using cached attrs-25.3.0-py3-none-any.whl.metadata (10 kB) +Collecting babel==2.17.0 (from -r requirements.txt (line 22)) + Using cached babel-2.17.0-py3-none-any.whl.metadata (2.0 kB) +Collecting bagit==1.8.1 (from -r requirements.txt (line 23)) + Using cached bagit-1.8.1-py2.py3-none-any.whl.metadata (8.3 kB) +Collecting bagit-profile==1.3.1 (from -r requirements.txt (line 24)) + Using cached bagit_profile-1.3.1-py3-none-any.whl.metadata (3.2 kB) +Collecting bcrypt==4.3.0 (from -r requirements.txt (line 25)) + Using cached bcrypt-4.3.0-cp39-abi3-manylinux_2_28_x86_64.whl.metadata (10 kB) +Collecting bdbag==1.7.3 (from -r requirements.txt (line 26)) + Using cached bdbag-1.7.3-py2.py3-none-any.whl.metadata (7.8 kB) +Collecting beaker==1.13.0 (from -r requirements.txt (line 27)) + Using cached Beaker-1.13.0-py3-none-any.whl +Collecting billiard==4.2.1 (from -r requirements.txt (line 28)) + Using cached billiard-4.2.1-py3-none-any.whl.metadata (4.4 kB) +Collecting bioblend==1.5.0 (from -r requirements.txt (line 29)) + Using cached bioblend-1.5.0-py3-none-any.whl.metadata (2.3 kB) +Collecting bleach==6.2.0 (from -r requirements.txt (line 30)) + Using cached bleach-6.2.0-py3-none-any.whl.metadata (30 kB) +Collecting boltons==25.0.0 (from -r requirements.txt (line 31)) + Using cached boltons-25.0.0-py3-none-any.whl.metadata (6.5 kB) +Collecting boto==2.49.0 (from -r requirements.txt (line 32)) + Using cached boto-2.49.0-py2.py3-none-any.whl.metadata (7.3 kB) +Collecting botocore==1.37.1 (from -r requirements.txt (line 33)) + Using cached botocore-1.37.1-py3-none-any.whl.metadata (5.7 kB) +Collecting bx-python==0.13.0 (from -r requirements.txt (line 34)) + Using cached bx_python-0.13.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.1 kB) +Collecting cachecontrol==0.14.2 (from -r requirements.txt (line 35)) + Using cached cachecontrol-0.14.2-py3-none-any.whl.metadata (3.1 kB) +Collecting celery==5.5.2 (from -r requirements.txt (line 36)) + Using cached celery-5.5.2-py3-none-any.whl.metadata (22 kB) +Collecting certifi==2025.4.26 (from -r requirements.txt (line 37)) + Using cached certifi-2025.4.26-py3-none-any.whl.metadata (2.5 kB) +Collecting cffi==1.17.1 (from -r requirements.txt (line 38)) + Using cached cffi-1.17.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.5 kB) +Collecting charset-normalizer==3.4.1 (from -r requirements.txt (line 39)) + Using cached charset_normalizer-3.4.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB) +Collecting circus==0.19.0 (from -r requirements.txt (line 40)) + Using cached circus-0.19.0-py3-none-any.whl.metadata (2.1 kB) +Collecting click==8.1.8 (from -r requirements.txt (line 41)) + Using cached click-8.1.8-py3-none-any.whl.metadata (2.3 kB) +Collecting click-didyoumean==0.3.1 (from -r requirements.txt (line 42)) + Using cached click_didyoumean-0.3.1-py3-none-any.whl.metadata (3.9 kB) +Collecting click-plugins==1.1.1 (from -r requirements.txt (line 43)) + Using cached click_plugins-1.1.1-py2.py3-none-any.whl.metadata (6.4 kB) +Collecting click-repl==0.3.0 (from -r requirements.txt (line 44)) + Using cached click_repl-0.3.0-py3-none-any.whl.metadata (3.6 kB) +Collecting cloudauthz==0.6.0 (from -r requirements.txt (line 45)) + Using cached cloudauthz-0.6.0-py2.py3-none-any.whl.metadata (2.9 kB) +Collecting cloudbridge==3.2.0 (from -r requirements.txt (line 46)) + Using cached cloudbridge-3.2.0-py2.py3-none-any.whl.metadata (5.0 kB) +Collecting coloredlogs==15.0.1 (from -r requirements.txt (line 48)) + Using cached coloredlogs-15.0.1-py2.py3-none-any.whl.metadata (12 kB) +Collecting conda-package-streaming==0.11.0 (from -r requirements.txt (line 49)) + Using cached conda_package_streaming-0.11.0-py3-none-any.whl.metadata (4.5 kB) +Collecting cryptography==44.0.2 (from -r requirements.txt (line 50)) + Using cached cryptography-44.0.2-cp39-abi3-manylinux_2_28_x86_64.whl.metadata (5.7 kB) +Collecting ct3==3.4.0 (from -r requirements.txt (line 51)) + Using cached CT3-3.4.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (3.4 kB) +Collecting cwl-upgrader==1.2.12 (from -r requirements.txt (line 52)) + Using cached cwl_upgrader-1.2.12-py3-none-any.whl.metadata (2.7 kB) +Collecting cwl-utils==0.37 (from -r requirements.txt (line 53)) + Using cached cwl_utils-0.37-py3-none-any.whl.metadata (8.2 kB) +Collecting cwltool==3.1.20250110105449 (from -r requirements.txt (line 54)) + Using cached cwltool-3.1.20250110105449-py3-none-any.whl.metadata (41 kB) +Collecting defusedxml==0.7.1 (from -r requirements.txt (line 55)) + Using cached defusedxml-0.7.1-py2.py3-none-any.whl.metadata (32 kB) +Collecting deprecated==1.2.18 (from -r requirements.txt (line 56)) + Using cached Deprecated-1.2.18-py2.py3-none-any.whl.metadata (5.7 kB) +Collecting deprecation==2.1.0 (from -r requirements.txt (line 57)) + Using cached deprecation-2.1.0-py2.py3-none-any.whl.metadata (4.6 kB) +Collecting dictobj==0.4 (from -r requirements.txt (line 58)) + Using cached dictobj-0.4-py3-none-any.whl +Collecting dnspython==2.7.0 (from -r requirements.txt (line 59)) + Using cached dnspython-2.7.0-py3-none-any.whl.metadata (5.8 kB) +Collecting docopt==0.6.2 (from -r requirements.txt (line 60)) + Using cached https://wheels.galaxyproject.org/simple/docopt/docopt-0.6.2-py2.py3-none-any.whl (19 kB) +Collecting docutils==0.21.2 (from -r requirements.txt (line 61)) + Using cached docutils-0.21.2-py3-none-any.whl.metadata (2.8 kB) +Collecting dparse==0.6.4 (from -r requirements.txt (line 62)) + Using cached dparse-0.6.4-py3-none-any.whl.metadata (5.5 kB) +Collecting edam-ontology==1.25.2 (from -r requirements.txt (line 63)) + Using cached edam_ontology-1.25.2-py2.py3-none-any.whl.metadata (2.4 kB) +Collecting email-validator==2.2.0 (from -r requirements.txt (line 64)) + Using cached email_validator-2.2.0-py3-none-any.whl.metadata (25 kB) +Collecting exceptiongroup==1.2.2 (from -r requirements.txt (line 65)) + Using cached exceptiongroup-1.2.2-py3-none-any.whl.metadata (6.6 kB) +Collecting fastapi-slim==0.115.12 (from -r requirements.txt (line 66)) + Using cached fastapi_slim-0.115.12-py3-none-any.whl.metadata (27 kB) +Collecting filelock==3.18.0 (from -r requirements.txt (line 67)) + Using cached filelock-3.18.0-py3-none-any.whl.metadata (2.9 kB) +Collecting fissix==24.4.24 (from -r requirements.txt (line 68)) + Using cached fissix-24.4.24-py3-none-any.whl.metadata (2.1 kB) +Collecting frozenlist==1.6.0 (from -r requirements.txt (line 69)) + Using cached frozenlist-1.6.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (16 kB) +Collecting fs==2.4.16 (from -r requirements.txt (line 70)) + Using cached fs-2.4.16-py2.py3-none-any.whl.metadata (6.3 kB) +Collecting fsspec==2025.3.2 (from -r requirements.txt (line 71)) + Using cached fsspec-2025.3.2-py3-none-any.whl.metadata (11 kB) +Collecting future==1.0.0 (from -r requirements.txt (line 72)) + Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB) +Collecting gravity==1.1.1 (from -r requirements.txt (line 73)) + Using cached gravity-1.1.1-py3-none-any.whl.metadata (15 kB) +Collecting greenlet==3.2.1 (from -r requirements.txt (line 74)) + Using cached greenlet-3.2.1-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (4.1 kB) +Collecting gunicorn==23.0.0 (from -r requirements.txt (line 75)) + Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB) +Collecting gxformat2==0.20.0 (from -r requirements.txt (line 76)) + Using cached gxformat2-0.20.0-py2.py3-none-any.whl.metadata (13 kB) +Collecting h11==0.16.0 (from -r requirements.txt (line 77)) + Using cached h11-0.16.0-py3-none-any.whl.metadata (8.3 kB) +Collecting httpcore==1.0.9 (from -r requirements.txt (line 78)) + Using cached httpcore-1.0.9-py3-none-any.whl.metadata (21 kB) +Collecting httpx==0.28.1 (from -r requirements.txt (line 79)) + Using cached httpx-0.28.1-py3-none-any.whl.metadata (7.1 kB) +Collecting h5grove==2.3.0 (from -r requirements.txt (line 80)) + Using cached h5grove-2.3.0-py3-none-any.whl.metadata (3.6 kB) +Collecting h5py==3.13.0 (from -r requirements.txt (line 81)) + Using cached h5py-3.13.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) +Collecting humanfriendly==10.0 (from -r requirements.txt (line 82)) + Using cached humanfriendly-10.0-py2.py3-none-any.whl.metadata (9.2 kB) +Collecting idna==3.10 (from -r requirements.txt (line 83)) + Using cached idna-3.10-py3-none-any.whl.metadata (10 kB) +Collecting importlib-metadata==8.6.1 (from -r requirements.txt (line 84)) + Using cached importlib_metadata-8.6.1-py3-none-any.whl.metadata (4.7 kB) +Collecting importlib-resources==6.5.2 (from -r requirements.txt (line 85)) + Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB) +Collecting isa-rwval==0.10.11 (from -r requirements.txt (line 86)) + Using cached isa_rwval-0.10.11-py3-none-any.whl.metadata (5.0 kB) +Collecting isal==1.7.2 (from -r requirements.txt (line 87)) + Using cached isal-1.7.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB) +Collecting isodate==0.7.2 (from -r requirements.txt (line 88)) + Using cached isodate-0.7.2-py3-none-any.whl.metadata (11 kB) +Collecting jinja2==3.1.6 (from -r requirements.txt (line 89)) + Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB) +Collecting jmespath==1.0.1 (from -r requirements.txt (line 90)) + Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB) +Collecting jsonref==1.1.0 (from -r requirements.txt (line 91)) + Using cached jsonref-1.1.0-py3-none-any.whl.metadata (2.7 kB) +Collecting jsonschema==4.23.0 (from -r requirements.txt (line 92)) + Using cached jsonschema-4.23.0-py3-none-any.whl.metadata (7.9 kB) +Collecting jsonschema-specifications==2025.4.1 (from -r requirements.txt (line 93)) + Using cached jsonschema_specifications-2025.4.1-py3-none-any.whl.metadata (2.9 kB) +Collecting kombu==5.5.3 (from -r requirements.txt (line 94)) + Using cached kombu-5.5.3-py3-none-any.whl.metadata (3.5 kB) +Collecting lagom==2.7.5 (from -r requirements.txt (line 95)) + Using cached lagom-2.7.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.7 kB) +Collecting limits==4.2 (from -r requirements.txt (line 97)) + Using cached limits-4.2-py3-none-any.whl.metadata (10 kB) +Collecting lxml==5.4.0 (from -r requirements.txt (line 99)) + Using cached lxml-5.4.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (3.5 kB) +Collecting mako==1.3.10 (from -r requirements.txt (line 100)) + Using cached mako-1.3.10-py3-none-any.whl.metadata (2.9 kB) +Collecting markdown==3.8 (from -r requirements.txt (line 101)) + Using cached markdown-3.8-py3-none-any.whl.metadata (5.1 kB) +Collecting markdown-it-py==3.0.0 (from -r requirements.txt (line 102)) + Using cached markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB) +Collecting markupsafe==3.0.2 (from -r requirements.txt (line 103)) + Using cached MarkupSafe-3.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB) +Collecting mdurl==0.1.2 (from -r requirements.txt (line 104)) + Using cached mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB) +Collecting mercurial==7.0.1 (from -r requirements.txt (line 105)) + Using cached mercurial-7.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl.metadata (2.2 kB) +Collecting mistune==3.0.2 (from -r requirements.txt (line 106)) + Using cached mistune-3.0.2-py3-none-any.whl.metadata (1.7 kB) +Collecting mrcfile==1.5.4 (from -r requirements.txt (line 107)) + Using cached mrcfile-1.5.4-py2.py3-none-any.whl.metadata (7.0 kB) +Collecting msal==1.32.3 (from -r requirements.txt (line 108)) + Using cached msal-1.32.3-py3-none-any.whl.metadata (11 kB) +Collecting msgpack==1.1.0 (from -r requirements.txt (line 109)) + Using cached msgpack-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB) +Collecting multidict==6.4.3 (from -r requirements.txt (line 110)) + Using cached multidict-6.4.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) +Collecting mypy-extensions==1.1.0 (from -r requirements.txt (line 111)) + Using cached mypy_extensions-1.1.0-py3-none-any.whl.metadata (1.1 kB) +Collecting networkx==3.2.1 (from -r requirements.txt (line 112)) + Using cached networkx-3.2.1-py3-none-any.whl.metadata (5.2 kB) +Collecting nodeenv==1.9.1 (from -r requirements.txt (line 114)) + Using cached nodeenv-1.9.1-py2.py3-none-any.whl.metadata (21 kB) +Collecting numpy==2.0.2 (from -r requirements.txt (line 115)) + Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB) +Collecting oauthlib==3.2.2 (from -r requirements.txt (line 117)) + Using cached oauthlib-3.2.2-py3-none-any.whl.metadata (7.5 kB) +Collecting orjson==3.10.16 (from -r requirements.txt (line 118)) + Using cached orjson-3.10.16-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (41 kB) +Collecting oyaml==1.0 (from -r requirements.txt (line 119)) + Using cached oyaml-1.0-py2.py3-none-any.whl.metadata (1.2 kB) +Collecting packaging==24.2 (from -r requirements.txt (line 120)) + Using cached packaging-24.2-py3-none-any.whl.metadata (3.2 kB) +Collecting paramiko==3.5.1 (from -r requirements.txt (line 122)) + Using cached paramiko-3.5.1-py3-none-any.whl.metadata (4.6 kB) +Collecting parsley==1.3 (from -r requirements.txt (line 123)) + Using cached Parsley-1.3-py2.py3-none-any.whl.metadata (4.1 kB) +Collecting paste==3.10.1 (from -r requirements.txt (line 124)) + Using cached Paste-3.10.1-py3-none-any.whl.metadata (5.3 kB) +Collecting pastedeploy==3.1.0 (from -r requirements.txt (line 125)) + Using cached PasteDeploy-3.1.0-py3-none-any.whl.metadata (2.7 kB) +Collecting pebble==5.1.1 (from -r requirements.txt (line 126)) + Using cached pebble-5.1.1-py3-none-any.whl.metadata (3.8 kB) +Collecting pillow==11.2.1 (from -r requirements.txt (line 127)) + Using cached pillow-11.2.1-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (8.9 kB) +Collecting prompt-toolkit==3.0.51 (from -r requirements.txt (line 128)) + Using cached prompt_toolkit-3.0.51-py3-none-any.whl.metadata (6.4 kB) +Collecting propcache==0.3.1 (from -r requirements.txt (line 129)) + Using cached propcache-0.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (10 kB) +Collecting prov==1.5.1 (from -r requirements.txt (line 130)) + Using cached prov-1.5.1-py2.py3-none-any.whl.metadata (7.9 kB) +Collecting psutil==7.0.0 (from -r requirements.txt (line 131)) + Using cached psutil-7.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (22 kB) +Collecting pulsar-galaxy-lib==0.15.8 (from -r requirements.txt (line 132)) + Using cached pulsar_galaxy_lib-0.15.8-py3-none-any.whl.metadata (37 kB) +Collecting pycparser==2.22 (from -r requirements.txt (line 133)) + Using cached pycparser-2.22-py3-none-any.whl.metadata (943 bytes) +Collecting pycryptodome==3.22.0 (from -r requirements.txt (line 134)) + Using cached pycryptodome-3.22.0-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.4 kB) +Collecting pydantic==2.11.3 (from -r requirements.txt (line 135)) + Using cached pydantic-2.11.3-py3-none-any.whl.metadata (65 kB) +Collecting pydantic-core==2.33.1 (from -r requirements.txt (line 136)) + Using cached pydantic_core-2.33.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.8 kB) +Collecting pydantic-tes==0.2.0 (from -r requirements.txt (line 137)) + Using cached pydantic_tes-0.2.0-py2.py3-none-any.whl.metadata (3.1 kB) +Collecting pydot==2.0.0 (from -r requirements.txt (line 138)) + Using cached pydot-2.0.0-py3-none-any.whl.metadata (9.6 kB) +Collecting pyeventsystem==0.1.0 (from -r requirements.txt (line 139)) + Using cached pyeventsystem-0.1.0-py2.py3-none-any.whl.metadata (3.2 kB) +Collecting pyfaidx==0.8.1.3 (from -r requirements.txt (line 140)) + Using cached pyfaidx-0.8.1.3-py3-none-any.whl.metadata (25 kB) +Collecting pygments==2.19.1 (from -r requirements.txt (line 141)) + Using cached pygments-2.19.1-py3-none-any.whl.metadata (2.5 kB) +Collecting pyjwt==2.10.1 (from -r requirements.txt (line 142)) + Using cached PyJWT-2.10.1-py3-none-any.whl.metadata (4.0 kB) +Collecting pykwalify==1.8.0 (from -r requirements.txt (line 143)) + Using cached pykwalify-1.8.0-py2.py3-none-any.whl.metadata (5.3 kB) +Collecting pylibmagic==0.5.0 (from -r requirements.txt (line 144)) + Using cached pylibmagic-0.5.0-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.5 kB) +Collecting pynacl==1.5.0 (from -r requirements.txt (line 145)) + Using cached PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl.metadata (8.6 kB) +Collecting pyparsing==3.2.3 (from -r requirements.txt (line 146)) + Using cached pyparsing-3.2.3-py3-none-any.whl.metadata (5.0 kB) +Collecting pypng==0.20220715.0 (from -r requirements.txt (line 147)) + Using cached pypng-0.20220715.0-py3-none-any.whl.metadata (13 kB) +Collecting pysam==0.23.0 (from -r requirements.txt (line 149)) + Using cached pysam-0.23.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (1.6 kB) +Collecting python-dateutil==2.9.0.post0 (from -r requirements.txt (line 150)) + Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) +Collecting python-magic==0.4.27 (from -r requirements.txt (line 151)) + Using cached python_magic-0.4.27-py2.py3-none-any.whl.metadata (5.8 kB) +Collecting python-multipart==0.0.20 (from -r requirements.txt (line 152)) + Using cached python_multipart-0.0.20-py3-none-any.whl.metadata (1.8 kB) +Collecting python-slugify==8.0.4 (from -r requirements.txt (line 153)) + Using cached python_slugify-8.0.4-py2.py3-none-any.whl.metadata (8.5 kB) +Collecting python3-openid==3.2.0 (from -r requirements.txt (line 154)) + Using cached python3_openid-3.2.0-py3-none-any.whl.metadata (1.6 kB) +Collecting pytz==2025.2 (from -r requirements.txt (line 155)) + Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB) +Collecting pyyaml==6.0.2 (from -r requirements.txt (line 156)) + Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB) +Collecting pyzmq==26.4.0 (from -r requirements.txt (line 157)) + Using cached pyzmq-26.4.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.0 kB) +Collecting rdflib==7.1.4 (from -r requirements.txt (line 158)) + Using cached rdflib-7.1.4-py3-none-any.whl.metadata (11 kB) +Collecting referencing==0.36.2 (from -r requirements.txt (line 159)) + Using cached referencing-0.36.2-py3-none-any.whl.metadata (2.8 kB) +Collecting refgenconf==0.12.2 (from -r requirements.txt (line 160)) + Using cached refgenconf-0.12.2-py3-none-any.whl.metadata (1.5 kB) +Collecting regex==2024.11.6 (from -r requirements.txt (line 161)) + Using cached regex-2024.11.6-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (40 kB) +Collecting repoze-lru==0.7 (from -r requirements.txt (line 162)) + Using cached repoze.lru-0.7-py3-none-any.whl.metadata (1.1 kB) +Collecting requests==2.32.3 (from -r requirements.txt (line 163)) + Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB) +Collecting requests-oauthlib==2.0.0 (from -r requirements.txt (line 164)) + Using cached requests_oauthlib-2.0.0-py2.py3-none-any.whl.metadata (11 kB) +Collecting requests-toolbelt==1.0.0 (from -r requirements.txt (line 165)) + Using cached requests_toolbelt-1.0.0-py2.py3-none-any.whl.metadata (14 kB) +Collecting requests-unixsocket==0.4.1 (from -r requirements.txt (line 166)) + Using cached requests_unixsocket-0.4.1-py3-none-any.whl.metadata (3.8 kB) +Collecting rich==13.9.4 (from -r requirements.txt (line 167)) + Using cached rich-13.9.4-py3-none-any.whl.metadata (18 kB) +Collecting rich-argparse==1.7.0 (from -r requirements.txt (line 168)) + Using cached rich_argparse-1.7.0-py3-none-any.whl.metadata (14 kB) +Collecting rocrate==0.13.0 (from -r requirements.txt (line 169)) + Using cached rocrate-0.13.0-py3-none-any.whl.metadata (18 kB) +Collecting routes==2.5.1 (from -r requirements.txt (line 170)) + Using cached Routes-2.5.1-py2.py3-none-any.whl.metadata (25 kB) +Collecting rpds-py==0.24.0 (from -r requirements.txt (line 171)) + Using cached rpds_py-0.24.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.1 kB) +Collecting ruamel-yaml==0.18.10 (from -r requirements.txt (line 172)) + Using cached ruamel.yaml-0.18.10-py3-none-any.whl.metadata (23 kB) +Collecting ruamel-yaml-clib==0.2.12 (from -r requirements.txt (line 173)) + Using cached ruamel.yaml.clib-0.2.12-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.7 kB) +Collecting s3fs==2025.3.2 (from -r requirements.txt (line 174)) + Using cached s3fs-2025.3.2-py3-none-any.whl.metadata (1.9 kB) +Collecting schema-salad==8.9.20250408123006 (from -r requirements.txt (line 175)) + Using cached schema_salad-8.9.20250408123006-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl.metadata (17 kB) +Collecting setuptools==79.0.1 (from -r requirements.txt (line 176)) + Using cached setuptools-79.0.1-py3-none-any.whl.metadata (6.5 kB) +Collecting setuptools-scm==5.0.2 (from -r requirements.txt (line 177)) + Using cached setuptools_scm-5.0.2-py2.py3-none-any.whl.metadata (21 kB) +Collecting six==1.17.0 (from -r requirements.txt (line 178)) + Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB) +Collecting slowapi==0.1.9 (from -r requirements.txt (line 179)) + Using cached slowapi-0.1.9-py3-none-any.whl.metadata (3.0 kB) +Collecting sniffio==1.3.1 (from -r requirements.txt (line 180)) + Using cached sniffio-1.3.1-py3-none-any.whl.metadata (3.9 kB) +Collecting social-auth-core==4.6.0 (from -r requirements.txt (line 181)) + Using cached social_auth_core-4.6.0-py3-none-any.whl.metadata (4.1 kB) +Collecting sortedcontainers==2.4.0 (from -r requirements.txt (line 182)) + Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl.metadata (10 kB) +Collecting spython==0.3.14 (from -r requirements.txt (line 183)) + Using cached spython-0.3.14-py3-none-any.whl.metadata (8.6 kB) +Collecting sqlalchemy==2.0.40 (from -r requirements.txt (line 184)) + Using cached sqlalchemy-2.0.40-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.6 kB) +Collecting sqlitedict==2.1.0 (from -r requirements.txt (line 185)) + Using cached sqlitedict-2.1.0-py3-none-any.whl +Collecting sqlparse==0.5.3 (from -r requirements.txt (line 186)) + Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB) +Collecting starlette==0.46.2 (from -r requirements.txt (line 187)) + Using cached starlette-0.46.2-py3-none-any.whl.metadata (6.2 kB) +Collecting starlette-context==0.4.0 (from -r requirements.txt (line 188)) + Using cached starlette_context-0.4.0-py3-none-any.whl.metadata (4.1 kB) +Collecting supervisor==4.2.5 (from -r requirements.txt (line 189)) + Using cached supervisor-4.2.5-py2.py3-none-any.whl.metadata (86 kB) +Collecting svgwrite==1.4.3 (from -r requirements.txt (line 190)) + Using cached svgwrite-1.4.3-py3-none-any.whl.metadata (8.8 kB) +Collecting tenacity==9.1.2 (from -r requirements.txt (line 191)) + Using cached tenacity-9.1.2-py3-none-any.whl.metadata (1.2 kB) +Collecting text-unidecode==1.3 (from -r requirements.txt (line 192)) + Using cached text_unidecode-1.3-py2.py3-none-any.whl.metadata (2.4 kB) +Collecting tifffile==2024.8.30 (from -r requirements.txt (line 193)) + Using cached tifffile-2024.8.30-py3-none-any.whl.metadata (31 kB) +Collecting tinydb==4.8.2 (from -r requirements.txt (line 195)) + Using cached tinydb-4.8.2-py3-none-any.whl.metadata (6.7 kB) +Collecting tomli==2.2.1 (from -r requirements.txt (line 196)) + Using cached tomli-2.2.1-py3-none-any.whl.metadata (10 kB) +Collecting tornado==6.4.2 (from -r requirements.txt (line 197)) + Using cached tornado-6.4.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) +Collecting tqdm==4.67.1 (from -r requirements.txt (line 198)) + Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB) +Collecting tuspy==1.1.0 (from -r requirements.txt (line 199)) + Using cached tuspy-1.1.0-py3-none-any.whl.metadata (4.2 kB) +Collecting tuswsgi==0.5.5 (from -r requirements.txt (line 200)) + Using cached tuswsgi-0.5.5-py2.py3-none-any.whl.metadata (2.2 kB) +Collecting typing-extensions==4.13.2 (from -r requirements.txt (line 201)) + Using cached typing_extensions-4.13.2-py3-none-any.whl.metadata (3.0 kB) +Collecting typing-inspection==0.4.0 (from -r requirements.txt (line 202)) + Using cached typing_inspection-0.4.0-py3-none-any.whl.metadata (2.6 kB) +Collecting tzdata==2025.2 (from -r requirements.txt (line 203)) + Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB) +Collecting tzlocal==5.3.1 (from -r requirements.txt (line 204)) + Using cached tzlocal-5.3.1-py3-none-any.whl.metadata (7.6 kB) +Collecting ubiquerg==0.8.1 (from -r requirements.txt (line 205)) + Using cached ubiquerg-0.8.1-py2.py3-none-any.whl.metadata (2.0 kB) +Collecting urllib3==1.26.20 (from -r requirements.txt (line 206)) + Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB) +Collecting uvicorn==0.34.2 (from -r requirements.txt (line 208)) + Using cached uvicorn-0.34.2-py3-none-any.whl.metadata (6.5 kB) +Collecting uvloop==0.21.0 (from -r requirements.txt (line 209)) + Using cached uvloop-0.21.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.9 kB) +Collecting vine==5.1.0 (from -r requirements.txt (line 210)) + Using cached vine-5.1.0-py3-none-any.whl.metadata (2.7 kB) +Collecting wcwidth==0.2.13 (from -r requirements.txt (line 211)) + Using cached wcwidth-0.2.13-py2.py3-none-any.whl.metadata (14 kB) +Collecting webencodings==0.5.1 (from -r requirements.txt (line 212)) + Using cached webencodings-0.5.1-py2.py3-none-any.whl.metadata (2.1 kB) +Collecting webob==1.8.9 (from -r requirements.txt (line 213)) + Using cached WebOb-1.8.9-py2.py3-none-any.whl.metadata (11 kB) +Collecting whoosh==2.7.4 (from -r requirements.txt (line 214)) + Using cached Whoosh-2.7.4-py2.py3-none-any.whl.metadata (3.1 kB) +Collecting wrapt==1.17.2 (from -r requirements.txt (line 215)) + Using cached wrapt-1.17.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.4 kB) +Collecting yacman==0.9.3 (from -r requirements.txt (line 216)) + Using cached yacman-0.9.3-py3-none-any.whl.metadata (5.3 kB) +Collecting yarl==1.20.0 (from -r requirements.txt (line 217)) + Using cached yarl-1.20.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (72 kB) +Collecting zipp==3.21.0 (from -r requirements.txt (line 218)) + Using cached zipp-3.21.0-py3-none-any.whl.metadata (3.7 kB) +Collecting zipstream-new==1.1.8 (from -r requirements.txt (line 219)) + Using cached zipstream_new-1.1.8-py3-none-any.whl.metadata (5.3 kB) +Collecting zstandard==0.23.0 (from -r requirements.txt (line 220)) + Using cached zstandard-0.23.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB) +Using cached a2wsgi-1.10.8-py3-none-any.whl (17 kB) +Using cached adal-1.2.7-py2.py3-none-any.whl (55 kB) +Using cached PyJWT-2.10.1-py3-none-any.whl (22 kB) +Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) +Using cached requests-2.32.3-py3-none-any.whl (64 kB) +Using cached charset_normalizer-3.4.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (146 kB) +Using cached idna-3.10-py3-none-any.whl (70 kB) +Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB) +Using cached aiobotocore-2.21.1-py3-none-any.whl (78 kB) +Using cached aiohttp-3.11.18-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.6 MB) +Using cached aioitertools-0.12.0-py3-none-any.whl (24 kB) +Using cached async_timeout-5.0.1-py3-none-any.whl (6.2 kB) +Using cached botocore-1.37.1-py3-none-any.whl (13.4 MB) +Using cached jmespath-1.0.1-py3-none-any.whl (20 kB) +Using cached multidict-6.4.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (216 kB) +Using cached wrapt-1.17.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (82 kB) +Using cached yarl-1.20.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (335 kB) +Using cached aiofiles-24.1.0-py3-none-any.whl (15 kB) +Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB) +Using cached aiosignal-1.3.2-py2.py3-none-any.whl (7.6 kB) +Using cached alembic-1.15.2-py3-none-any.whl (231 kB) +Using cached amqp-5.3.1-py3-none-any.whl (50 kB) +Using cached vine-5.1.0-py3-none-any.whl (9.6 kB) +Using cached annotated_types-0.7.0-py3-none-any.whl (13 kB) +Using cached anyio-4.9.0-py3-none-any.whl (100 kB) +Using cached apispec-6.8.1-py3-none-any.whl (30 kB) +Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB) +Using cached arcp-0.2.1-py2.py3-none-any.whl (15 kB) +Using cached argcomplete-3.6.2-py3-none-any.whl (43 kB) +Using cached attmap-0.13.2-py3-none-any.whl (12 kB) +Using cached attrs-25.3.0-py3-none-any.whl (63 kB) +Using cached babel-2.17.0-py3-none-any.whl (10.2 MB) +Using cached bagit-1.8.1-py2.py3-none-any.whl (35 kB) +Using cached bagit_profile-1.3.1-py3-none-any.whl (14 kB) +Using cached bcrypt-4.3.0-cp39-abi3-manylinux_2_28_x86_64.whl (284 kB) +Using cached bdbag-1.7.3-py2.py3-none-any.whl (75 kB) +Using cached setuptools_scm-5.0.2-py2.py3-none-any.whl (29 kB) +Using cached billiard-4.2.1-py3-none-any.whl (86 kB) +Using cached bioblend-1.5.0-py3-none-any.whl (160 kB) +Using cached bleach-6.2.0-py3-none-any.whl (163 kB) +Using cached boltons-25.0.0-py3-none-any.whl (194 kB) +Using cached boto-2.49.0-py2.py3-none-any.whl (1.4 MB) +Using cached bx_python-0.13.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.5 MB) +Using cached cachecontrol-0.14.2-py3-none-any.whl (21 kB) +Using cached msgpack-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (377 kB) +Using cached celery-5.5.2-py3-none-any.whl (438 kB) +Using cached click-8.1.8-py3-none-any.whl (98 kB) +Using cached kombu-5.5.3-py3-none-any.whl (209 kB) +Using cached certifi-2025.4.26-py3-none-any.whl (159 kB) +Using cached cffi-1.17.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (445 kB) +Using cached circus-0.19.0-py3-none-any.whl (118 kB) +Using cached click_didyoumean-0.3.1-py3-none-any.whl (3.6 kB) +Using cached click_plugins-1.1.1-py2.py3-none-any.whl (7.5 kB) +Using cached click_repl-0.3.0-py3-none-any.whl (10 kB) +Using cached cloudauthz-0.6.0-py2.py3-none-any.whl (8.9 kB) +Using cached cloudbridge-3.2.0-py2.py3-none-any.whl (193 kB) +Using cached pyeventsystem-0.1.0-py2.py3-none-any.whl (15 kB) +Using cached coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB) +Using cached conda_package_streaming-0.11.0-py3-none-any.whl (17 kB) +Using cached cryptography-44.0.2-cp39-abi3-manylinux_2_28_x86_64.whl (4.2 MB) +Using cached CT3-3.4.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (671 kB) +Using cached cwl_upgrader-1.2.12-py3-none-any.whl (27 kB) +Using cached ruamel.yaml-0.18.10-py3-none-any.whl (117 kB) +Using cached cwl_utils-0.37-py3-none-any.whl (427 kB) +Using cached schema_salad-8.9.20250408123006-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl (1.6 MB) +Using cached mistune-3.0.2-py3-none-any.whl (47 kB) +Using cached rdflib-7.1.4-py3-none-any.whl (565 kB) +Using cached isodate-0.7.2-py3-none-any.whl (22 kB) +Using cached pyparsing-3.2.3-py3-none-any.whl (111 kB) +Using cached cwltool-3.1.20250110105449-py3-none-any.whl (1.7 MB) +Using cached pydot-2.0.0-py3-none-any.whl (22 kB) +Using cached defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) +Using cached Deprecated-1.2.18-py2.py3-none-any.whl (10.0 kB) +Using cached deprecation-2.1.0-py2.py3-none-any.whl (11 kB) +Using cached dnspython-2.7.0-py3-none-any.whl (313 kB) +Using cached docutils-0.21.2-py3-none-any.whl (587 kB) +Using cached dparse-0.6.4-py3-none-any.whl (11 kB) +Using cached edam_ontology-1.25.2-py2.py3-none-any.whl (262 kB) +Using cached email_validator-2.2.0-py3-none-any.whl (33 kB) +Using cached exceptiongroup-1.2.2-py3-none-any.whl (16 kB) +Using cached fastapi_slim-0.115.12-py3-none-any.whl (95 kB) +Using cached pydantic-2.11.3-py3-none-any.whl (443 kB) +Using cached starlette-0.46.2-py3-none-any.whl (72 kB) +Using cached filelock-3.18.0-py3-none-any.whl (16 kB) +Using cached fissix-24.4.24-py3-none-any.whl (188 kB) +Using cached frozenlist-1.6.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (288 kB) +Using cached fs-2.4.16-py2.py3-none-any.whl (135 kB) +Using cached six-1.17.0-py2.py3-none-any.whl (11 kB) +Using cached fsspec-2025.3.2-py3-none-any.whl (194 kB) +Using cached future-1.0.0-py3-none-any.whl (491 kB) +Using cached gravity-1.1.1-py3-none-any.whl (47 kB) +Using cached greenlet-3.2.1-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (579 kB) +Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB) +Using cached gxformat2-0.20.0-py2.py3-none-any.whl (60 kB) +Using cached h11-0.16.0-py3-none-any.whl (37 kB) +Using cached httpcore-1.0.9-py3-none-any.whl (78 kB) +Using cached httpx-0.28.1-py3-none-any.whl (73 kB) +Using cached h5grove-2.3.0-py3-none-any.whl (16 kB) +Using cached h5py-3.13.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB) +Using cached humanfriendly-10.0-py2.py3-none-any.whl (86 kB) +Using cached importlib_metadata-8.6.1-py3-none-any.whl (26 kB) +Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB) +Using cached isa_rwval-0.10.11-py3-none-any.whl (112 kB) +Using cached isal-1.7.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (260 kB) +Using cached jinja2-3.1.6-py3-none-any.whl (134 kB) +Using cached jsonref-1.1.0-py3-none-any.whl (9.4 kB) +Using cached jsonschema-4.23.0-py3-none-any.whl (88 kB) +Using cached jsonschema_specifications-2025.4.1-py3-none-any.whl (18 kB) +Using cached lagom-2.7.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (258 kB) +Using cached limits-4.2-py3-none-any.whl (60 kB) +Using cached packaging-24.2-py3-none-any.whl (65 kB) +Using cached lxml-5.4.0-cp39-cp39-manylinux_2_28_x86_64.whl (5.1 MB) +Using cached mako-1.3.10-py3-none-any.whl (78 kB) +Using cached markdown-3.8-py3-none-any.whl (106 kB) +Using cached markdown_it_py-3.0.0-py3-none-any.whl (87 kB) +Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB) +Using cached MarkupSafe-3.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (20 kB) +Using cached mercurial-7.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl (7.4 MB) +Using cached mrcfile-1.5.4-py2.py3-none-any.whl (45 kB) +Using cached msal-1.32.3-py3-none-any.whl (115 kB) +Using cached mypy_extensions-1.1.0-py3-none-any.whl (5.0 kB) +Using cached networkx-3.2.1-py3-none-any.whl (1.6 MB) +Using cached nodeenv-1.9.1-py2.py3-none-any.whl (22 kB) +Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.5 MB) +Using cached oauthlib-3.2.2-py3-none-any.whl (151 kB) +Using cached orjson-3.10.16-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (132 kB) +Using cached oyaml-1.0-py2.py3-none-any.whl (3.0 kB) +Using cached paramiko-3.5.1-py3-none-any.whl (227 kB) +Using cached Parsley-1.3-py2.py3-none-any.whl (88 kB) +Using cached Paste-3.10.1-py3-none-any.whl (289 kB) +Using cached PasteDeploy-3.1.0-py3-none-any.whl (16 kB) +Using cached pebble-5.1.1-py3-none-any.whl (34 kB) +Using cached pillow-11.2.1-cp39-cp39-manylinux_2_28_x86_64.whl (4.6 MB) +Using cached prompt_toolkit-3.0.51-py3-none-any.whl (387 kB) +Using cached propcache-0.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (209 kB) +Using cached prov-1.5.1-py2.py3-none-any.whl (426 kB) +Using cached psutil-7.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (277 kB) +Using cached pulsar_galaxy_lib-0.15.8-py3-none-any.whl (203 kB) +Using cached pycparser-2.22-py3-none-any.whl (117 kB) +Using cached pycryptodome-3.22.0-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.3 MB) +Using cached pydantic_core-2.33.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.0 MB) +Using cached pydantic_tes-0.2.0-py2.py3-none-any.whl (12 kB) +Using cached pyfaidx-0.8.1.3-py3-none-any.whl (28 kB) +Using cached pygments-2.19.1-py3-none-any.whl (1.2 MB) +Using cached pykwalify-1.8.0-py2.py3-none-any.whl (24 kB) +Using cached pylibmagic-0.5.0-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (619 kB) +Using cached PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (856 kB) +Using cached pypng-0.20220715.0-py3-none-any.whl (58 kB) +Using cached pysam-0.23.0-cp39-cp39-manylinux_2_28_x86_64.whl (25.2 MB) +Using cached python_magic-0.4.27-py2.py3-none-any.whl (13 kB) +Using cached python_multipart-0.0.20-py3-none-any.whl (24 kB) +Using cached python_slugify-8.0.4-py2.py3-none-any.whl (10 kB) +Using cached python3_openid-3.2.0-py3-none-any.whl (133 kB) +Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB) +Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (737 kB) +Using cached pyzmq-26.4.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (863 kB) +Using cached referencing-0.36.2-py3-none-any.whl (26 kB) +Using cached refgenconf-0.12.2-py3-none-any.whl (72 kB) +Using cached regex-2024.11.6-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (780 kB) +Using cached repoze.lru-0.7-py3-none-any.whl (10 kB) +Using cached requests_oauthlib-2.0.0-py2.py3-none-any.whl (24 kB) +Using cached requests_toolbelt-1.0.0-py2.py3-none-any.whl (54 kB) +Using cached requests_unixsocket-0.4.1-py3-none-any.whl (11 kB) +Using cached rich-13.9.4-py3-none-any.whl (242 kB) +Using cached typing_extensions-4.13.2-py3-none-any.whl (45 kB) +Using cached rich_argparse-1.7.0-py3-none-any.whl (25 kB) +Using cached rocrate-0.13.0-py3-none-any.whl (332 kB) +Using cached Routes-2.5.1-py2.py3-none-any.whl (40 kB) +Using cached rpds_py-0.24.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (390 kB) +Using cached ruamel.yaml.clib-0.2.12-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (724 kB) +Using cached s3fs-2025.3.2-py3-none-any.whl (30 kB) +Using cached setuptools-79.0.1-py3-none-any.whl (1.3 MB) +Using cached slowapi-0.1.9-py3-none-any.whl (14 kB) +Using cached sniffio-1.3.1-py3-none-any.whl (10 kB) +Using cached social_auth_core-4.6.0-py3-none-any.whl (424 kB) +Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB) +Using cached spython-0.3.14-py3-none-any.whl (109 kB) +Using cached sqlalchemy-2.0.40-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB) +Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB) +Using cached starlette_context-0.4.0-py3-none-any.whl (12 kB) +Using cached supervisor-4.2.5-py2.py3-none-any.whl (319 kB) +Using cached svgwrite-1.4.3-py3-none-any.whl (67 kB) +Using cached tenacity-9.1.2-py3-none-any.whl (28 kB) +Using cached text_unidecode-1.3-py2.py3-none-any.whl (78 kB) +Using cached tifffile-2024.8.30-py3-none-any.whl (227 kB) +Using cached tinydb-4.8.2-py3-none-any.whl (24 kB) +Using cached tomli-2.2.1-py3-none-any.whl (14 kB) +Using cached tornado-6.4.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (437 kB) +Using cached tqdm-4.67.1-py3-none-any.whl (78 kB) +Using cached tuspy-1.1.0-py3-none-any.whl (15 kB) +Using cached tuswsgi-0.5.5-py2.py3-none-any.whl (6.9 kB) +Using cached typing_inspection-0.4.0-py3-none-any.whl (14 kB) +Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB) +Using cached tzlocal-5.3.1-py3-none-any.whl (18 kB) +Using cached ubiquerg-0.8.1-py2.py3-none-any.whl (17 kB) +Using cached uvicorn-0.34.2-py3-none-any.whl (62 kB) +Using cached uvloop-0.21.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.8 MB) +Using cached wcwidth-0.2.13-py2.py3-none-any.whl (34 kB) +Using cached webencodings-0.5.1-py2.py3-none-any.whl (11 kB) +Using cached WebOb-1.8.9-py2.py3-none-any.whl (115 kB) +Using cached Whoosh-2.7.4-py2.py3-none-any.whl (468 kB) +Using cached yacman-0.9.3-py3-none-any.whl (26 kB) +Using cached zipp-3.21.0-py3-none-any.whl (9.6 kB) +Using cached zipstream_new-1.1.8-py3-none-any.whl (20 kB) +Using cached zstandard-0.23.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.4 MB) +Installing collected packages: zipstream-new, whoosh, webencodings, wcwidth, ubiquerg, text-unidecode, sqlitedict, spython, sortedcontainers, repoze-lru, pytz, pypng, pyeventsystem, parsley, edam-ontology, docopt, dictobj, boto, beaker, bagit, arcp, appdirs, zstandard, zipp, wrapt, webob, vine, uvloop, urllib3, tzlocal, tzdata, typing-extensions, tqdm, tornado, tomli, tinydb, tenacity, svgwrite, sqlparse, sniffio, six, setuptools, ruamel-yaml-clib, rpds-py, regex, pyzmq, pyyaml, python-slugify, python-multipart, python-magic, pysam, pyparsing, pylibmagic, pyjwt, pygments, pycryptodome, pycparser, psutil, propcache, prompt-toolkit, pillow, pebble, pastedeploy, packaging, orjson, oauthlib, numpy, nodeenv, networkx, mypy-extensions, msgpack, mistune, mercurial, mdurl, markupsafe, lxml, lagom, jsonref, jmespath, isodate, isal, idna, humanfriendly, h11, greenlet, future, fsspec, frozenlist, fissix, filelock, exceptiongroup, docutils, dnspython, defusedxml, ct3, click, charset-normalizer, certifi, boltons, bleach, billiard, bcrypt, babel, attrs, attmap, async-timeout, argcomplete, annotated-types, aiohappyeyeballs, aiofiles, uvicorn, typing-inspection, tuswsgi, tifffile, supervisor, sqlalchemy, setuptools-scm, ruamel-yaml, routes, requests, referencing, rdflib, python3-openid, python-dateutil, pydot, pydantic-core, paste, oyaml, multidict, mrcfile, markdown-it-py, mako, jinja2, isa-rwval, importlib-resources, importlib-metadata, httpcore, h5py, gunicorn, fs, email-validator, dparse, deprecation, deprecated, coloredlogs, click-repl, click-plugins, click-didyoumean, circus, cffi, bx-python, apispec, anyio, amqp, aiosignal, aioitertools, a2wsgi, yarl, starlette, rocrate, rich, requests-unixsocket, requests-toolbelt, requests-oauthlib, pynacl, pykwalify, pyfaidx, pydantic, prov, markdown, limits, kombu, jsonschema-specifications, httpx, h5grove, cryptography, conda-package-streaming, cloudbridge, cachecontrol, botocore, bagit-profile, alembic, starlette-context, social-auth-core, slowapi, rich-argparse, pydantic-tes, paramiko, jsonschema, gravity, fastapi-slim, celery, bdbag, aiohttp, adal, yacman, tuspy, schema-salad, msal, cloudauthz, aiobotocore, s3fs, refgenconf, pulsar-galaxy-lib, cwl-upgrader, bioblend, gxformat2, cwl-utils, cwltool + Attempting uninstall: setuptools + Found existing installation: setuptools 80.9.0 + Uninstalling setuptools-80.9.0: + Successfully uninstalled setuptools-80.9.0 + +Successfully installed a2wsgi-1.10.8 adal-1.2.7 aiobotocore-2.21.1 aiofiles-24.1.0 aiohappyeyeballs-2.6.1 aiohttp-3.11.18 aioitertools-0.12.0 aiosignal-1.3.2 alembic-1.15.2 amqp-5.3.1 annotated-types-0.7.0 anyio-4.9.0 apispec-6.8.1 appdirs-1.4.4 arcp-0.2.1 argcomplete-3.6.2 async-timeout-5.0.1 attmap-0.13.2 attrs-25.3.0 babel-2.17.0 bagit-1.8.1 bagit-profile-1.3.1 bcrypt-4.3.0 bdbag-1.7.3 beaker-1.13.0 billiard-4.2.1 bioblend-1.5.0 bleach-6.2.0 boltons-25.0.0 boto-2.49.0 botocore-1.37.1 bx-python-0.13.0 cachecontrol-0.14.2 celery-5.5.2 certifi-2025.4.26 cffi-1.17.1 charset-normalizer-3.4.1 circus-0.19.0 click-8.1.8 click-didyoumean-0.3.1 click-plugins-1.1.1 click-repl-0.3.0 cloudauthz-0.6.0 cloudbridge-3.2.0 coloredlogs-15.0.1 conda-package-streaming-0.11.0 cryptography-44.0.2 ct3-3.4.0 cwl-upgrader-1.2.12 cwl-utils-0.37 cwltool-3.1.20250110105449 defusedxml-0.7.1 deprecated-1.2.18 deprecation-2.1.0 dictobj-0.4 dnspython-2.7.0 docopt-0.6.2 docutils-0.21.2 dparse-0.6.4 edam-ontology-1.25.2 email-validator-2.2.0 exceptiongroup-1.2.2 fastapi-slim-0.115.12 filelock-3.18.0 fissix-24.4.24 frozenlist-1.6.0 fs-2.4.16 fsspec-2025.3.2 future-1.0.0 gravity-1.1.1 greenlet-3.2.1 gunicorn-23.0.0 gxformat2-0.20.0 h11-0.16.0 h5grove-2.3.0 h5py-3.13.0 httpcore-1.0.9 httpx-0.28.1 humanfriendly-10.0 idna-3.10 importlib-metadata-8.6.1 importlib-resources-6.5.2 isa-rwval-0.10.11 isal-1.7.2 isodate-0.7.2 jinja2-3.1.6 jmespath-1.0.1 jsonref-1.1.0 jsonschema-4.23.0 jsonschema-specifications-2025.4.1 kombu-5.5.3 lagom-2.7.5 limits-4.2 lxml-5.4.0 mako-1.3.10 markdown-3.8 markdown-it-py-3.0.0 markupsafe-3.0.2 mdurl-0.1.2 mercurial-7.0.1 mistune-3.0.2 mrcfile-1.5.4 msal-1.32.3 msgpack-1.1.0 multidict-6.4.3 mypy-extensions-1.1.0 networkx-3.2.1 nodeenv-1.9.1 numpy-2.0.2 oauthlib-3.2.2 orjson-3.10.16 oyaml-1.0 packaging-24.2 paramiko-3.5.1 parsley-1.3 paste-3.10.1 pastedeploy-3.1.0 pebble-5.1.1 pillow-11.2.1 prompt-toolkit-3.0.51 propcache-0.3.1 prov-1.5.1 psutil-7.0.0 pulsar-galaxy-lib-0.15.8 pycparser-2.22 pycryptodome-3.22.0 pydantic-2.11.3 pydantic-core-2.33.1 pydantic-tes-0.2.0 pydot-2.0.0 pyeventsystem-0.1.0 pyfaidx-0.8.1.3 pygments-2.19.1 pyjwt-2.10.1 pykwalify-1.8.0 pylibmagic-0.5.0 pynacl-1.5.0 pyparsing-3.2.3 pypng-0.20220715.0 pysam-0.23.0 python-dateutil-2.9.0.post0 python-magic-0.4.27 python-multipart-0.0.20 python-slugify-8.0.4 python3-openid-3.2.0 pytz-2025.2 pyyaml-6.0.2 pyzmq-26.4.0 rdflib-7.1.4 referencing-0.36.2 refgenconf-0.12.2 regex-2024.11.6 repoze-lru-0.7 requests-2.32.3 requests-oauthlib-2.0.0 requests-toolbelt-1.0.0 requests-unixsocket-0.4.1 rich-13.9.4 rich-argparse-1.7.0 rocrate-0.13.0 routes-2.5.1 rpds-py-0.24.0 ruamel-yaml-0.18.10 ruamel-yaml-clib-0.2.12 s3fs-2025.3.2 schema-salad-8.9.20250408123006 setuptools-79.0.1 setuptools-scm-5.0.2 six-1.17.0 slowapi-0.1.9 sniffio-1.3.1 social-auth-core-4.6.0 sortedcontainers-2.4.0 spython-0.3.14 sqlalchemy-2.0.40 sqlitedict-2.1.0 sqlparse-0.5.3 starlette-0.46.2 starlette-context-0.4.0 supervisor-4.2.5 svgwrite-1.4.3 tenacity-9.1.2 text-unidecode-1.3 tifffile-2024.8.30 tinydb-4.8.2 tomli-2.2.1 tornado-6.4.2 tqdm-4.67.1 tuspy-1.1.0 tuswsgi-0.5.5 typing-extensions-4.13.2 typing-inspection-0.4.0 tzdata-2025.2 tzlocal-5.3.1 ubiquerg-0.8.1 urllib3-1.26.20 uvicorn-0.34.2 uvloop-0.21.0 vine-5.1.0 wcwidth-0.2.13 webencodings-0.5.1 webob-1.8.9 whoosh-2.7.4 wrapt-1.17.2 yacman-0.9.3 yarl-1.20.0 zipp-3.21.0 zipstream-new-1.1.8 zstandard-0.23.0 +Trying to resolve path for the 'email_ban_file' option but it's empty/None +Installing node into /scratch/rico/planemo/gx_venv_3 with nodeenv. + * Install prebuilt node (22.13.0) ..... done. + * Appending data to /scratch/rico/planemo/gx_venv_3/bin/activate + * Appending data to /scratch/rico/planemo/gx_venv_3/bin/activate.fish +The Galaxy client has not yet been built and will be built now. +Installing yarn into /scratch/rico/planemo/gx_venv_3 with npm. + +added 1 package in 933ms +yarn install v1.22.22 +info No lockfile found. +[1/4] Resolving packages... +warning @galaxyproject/galaxy-client > babel-runtime > core-js@2.6.12: core-js@<3.23.3 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Some versions have web compatibility issues. Please, upgrade your dependencies to the actual version of core-js. +warning @galaxyproject/galaxy-client > jquery@2.2.4: This version is deprecated. Please upgrade to the latest version or find support at https://www.herodevs.com/support/jquery-nes. +warning @galaxyproject/galaxy-client > lodash.isequal@4.5.0: This package is deprecated. Use require('node:util').isDeepStrictEqual instead. +warning @galaxyproject/galaxy-client > popper.js@1.16.1: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1 +warning @galaxyproject/galaxy-client > bootstrap-vue > popper.js@1.16.1: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1 +warning @galaxyproject/galaxy-client > lucide-vue@0.344.0: Package no longer supported. Contact Support at https://www.npmjs.com/support for more info. +warning @galaxyproject/galaxy-client > vue@2.7.16: Vue 2 has reached EOL and is no longer actively maintained. See https://v2.vuejs.org/eol/ for more details. +warning @galaxyproject/galaxy-client > @johmun/vue-tags-input > vue@2.7.16: Vue 2 has reached EOL and is no longer actively maintained. See https://v2.vuejs.org/eol/ for more details. +warning @galaxyproject/galaxy-client > rxjs-spy > circular-json@0.5.9: CircularJSON is in maintenance only, flatted is its successor. +warning @galaxyproject/galaxy-client > rxjs-spy-devtools-plugin > rxjs-spy > circular-json@0.5.9: CircularJSON is in maintenance only, flatted is its successor. +warning @galaxyproject/galaxy-client > rxjs-spy > rxjs-report-usage > glob@7.2.3: Glob versions prior to v9 are no longer supported +warning @galaxyproject/galaxy-client > rxjs-spy > rxjs-report-usage > glob > inflight@1.0.6: This module is not supported, and leaks memory. Do not use it. Check out lru-cache if you want a good and tested way to coalesce async requests by a key value, which is much more comprehensive and powerful. +[2/4] Fetching packages... +[3/4] Linking dependencies... +warning " > @galaxyproject/galaxy-client@24.2.4" has unmet peer dependency "postcss@^8.4.6". +warning "@galaxyproject/galaxy-client > @hirez_io/observer-spy@2.2.0" has unmet peer dependency "typescript@>=2.8.1". +warning "@galaxyproject/galaxy-client > vue-rx@6.2.0" has incorrect peer dependency "rxjs@^6.0.0". +[4/4] Building fresh packages... +success Saved lockfile. +Done in 213.34s. +yarn run v1.22.22 +$ cpy './node_modules/@galaxyproject/galaxy-client/dist/*' './static/dist' +Done in 0.58s. +Starting Galaxy with command [cd /scratch/rico/galaxy && if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/scratch/rico/planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /scratch/rico/.venv/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /scratch/rico/.venv/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && /scratch/rico/galaxy/run.sh $COMMON_STARTUP_ARGS --server-name main] +galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input +Activated a virtualenv for Galaxy +/scratch/rico/planemo/gx_venv_3 +Activating virtualenv at /scratch/rico/planemo/gx_venv_3 +Requirement already satisfied: pip>=20.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (25.1.1) +Requirement already satisfied: wheel in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (0.45.1) +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple +Ignoring colorama: markers 'sys_platform == "win32"' don't match your environment +Ignoring legacy-cgi: markers 'python_full_version >= "3.13"' don't match your environment +Ignoring limits: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring networkx: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring numpy: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring packaging: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring pyreadline3: markers 'sys_platform == "win32"' don't match your environment +Ignoring tifffile: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring urllib3: markers 'python_full_version >= "3.10"' don't match your environment +Requirement already satisfied: a2wsgi==1.10.8 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.10.8) +Requirement already satisfied: adal==1.2.7 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7) +Requirement already satisfied: aiobotocore==2.21.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (2.21.1) +Requirement already satisfied: aiofiles==24.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (24.1.0) +Requirement already satisfied: aiohappyeyeballs==2.6.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (2.6.1) +Requirement already satisfied: aiohttp==3.11.18 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (3.11.18) +Requirement already satisfied: aioitertools==0.12.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 9)) (0.12.0) +Requirement already satisfied: aiosignal==1.3.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 10)) (1.3.2) +Requirement already satisfied: alembic==1.15.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 11)) (1.15.2) +Requirement already satisfied: amqp==5.3.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 12)) (5.3.1) +Requirement already satisfied: annotated-types==0.7.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 13)) (0.7.0) +Requirement already satisfied: anyio==4.9.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 14)) (4.9.0) +Requirement already satisfied: apispec==6.8.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 15)) (6.8.1) +Requirement already satisfied: appdirs==1.4.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 16)) (1.4.4) +Requirement already satisfied: arcp==0.2.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 17)) (0.2.1) +Requirement already satisfied: argcomplete==3.6.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 18)) (3.6.2) +Requirement already satisfied: async-timeout==5.0.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 19)) (5.0.1) +Requirement already satisfied: attmap==0.13.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 20)) (0.13.2) +Requirement already satisfied: attrs==25.3.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 21)) (25.3.0) +Requirement already satisfied: babel==2.17.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 22)) (2.17.0) +Requirement already satisfied: bagit==1.8.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 23)) (1.8.1) +Requirement already satisfied: bagit-profile==1.3.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 24)) (1.3.1) +Requirement already satisfied: bcrypt==4.3.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 25)) (4.3.0) +Requirement already satisfied: bdbag==1.7.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 26)) (1.7.3) +Requirement already satisfied: beaker==1.13.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 27)) (1.13.0) +Requirement already satisfied: billiard==4.2.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 28)) (4.2.1) +Requirement already satisfied: bioblend==1.5.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 29)) (1.5.0) +Requirement already satisfied: bleach==6.2.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 30)) (6.2.0) +Requirement already satisfied: boltons==25.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 31)) (25.0.0) +Requirement already satisfied: boto==2.49.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 32)) (2.49.0) +Requirement already satisfied: botocore==1.37.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 33)) (1.37.1) +Requirement already satisfied: bx-python==0.13.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 34)) (0.13.0) +Requirement already satisfied: cachecontrol==0.14.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 35)) (0.14.2) +Requirement already satisfied: celery==5.5.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 36)) (5.5.2) +Requirement already satisfied: certifi==2025.4.26 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 37)) (2025.4.26) +Requirement already satisfied: cffi==1.17.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 38)) (1.17.1) +Requirement already satisfied: charset-normalizer==3.4.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 39)) (3.4.1) +Requirement already satisfied: circus==0.19.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 40)) (0.19.0) +Requirement already satisfied: click==8.1.8 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 41)) (8.1.8) +Requirement already satisfied: click-didyoumean==0.3.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 42)) (0.3.1) +Requirement already satisfied: click-plugins==1.1.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 43)) (1.1.1) +Requirement already satisfied: click-repl==0.3.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 44)) (0.3.0) +Requirement already satisfied: cloudauthz==0.6.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 45)) (0.6.0) +Requirement already satisfied: cloudbridge==3.2.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 46)) (3.2.0) +Requirement already satisfied: coloredlogs==15.0.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 48)) (15.0.1) +Requirement already satisfied: conda-package-streaming==0.11.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 49)) (0.11.0) +Requirement already satisfied: cryptography==44.0.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 50)) (44.0.2) +Requirement already satisfied: ct3==3.4.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 51)) (3.4.0) +Requirement already satisfied: cwl-upgrader==1.2.12 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 52)) (1.2.12) +Requirement already satisfied: cwl-utils==0.37 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 53)) (0.37) +Requirement already satisfied: cwltool==3.1.20250110105449 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 54)) (3.1.20250110105449) +Requirement already satisfied: defusedxml==0.7.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 55)) (0.7.1) +Requirement already satisfied: deprecated==1.2.18 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 56)) (1.2.18) +Requirement already satisfied: deprecation==2.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 57)) (2.1.0) +Requirement already satisfied: dictobj==0.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 58)) (0.4) +Requirement already satisfied: dnspython==2.7.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 59)) (2.7.0) +Requirement already satisfied: docopt==0.6.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 60)) (0.6.2) +Requirement already satisfied: docutils==0.21.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 61)) (0.21.2) +Requirement already satisfied: dparse==0.6.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 62)) (0.6.4) +Requirement already satisfied: edam-ontology==1.25.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 63)) (1.25.2) +Requirement already satisfied: email-validator==2.2.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 64)) (2.2.0) +Requirement already satisfied: exceptiongroup==1.2.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 65)) (1.2.2) +Requirement already satisfied: fastapi-slim==0.115.12 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 66)) (0.115.12) +Requirement already satisfied: filelock==3.18.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 67)) (3.18.0) +Requirement already satisfied: fissix==24.4.24 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 68)) (24.4.24) +Requirement already satisfied: frozenlist==1.6.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 69)) (1.6.0) +Requirement already satisfied: fs==2.4.16 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 70)) (2.4.16) +Requirement already satisfied: fsspec==2025.3.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 71)) (2025.3.2) +Requirement already satisfied: future==1.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 72)) (1.0.0) +Requirement already satisfied: gravity==1.1.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 73)) (1.1.1) +Requirement already satisfied: greenlet==3.2.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 74)) (3.2.1) +Requirement already satisfied: gunicorn==23.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 75)) (23.0.0) +Requirement already satisfied: gxformat2==0.20.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 76)) (0.20.0) +Requirement already satisfied: h11==0.16.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 77)) (0.16.0) +Requirement already satisfied: httpcore==1.0.9 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 78)) (1.0.9) +Requirement already satisfied: httpx==0.28.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 79)) (0.28.1) +Requirement already satisfied: h5grove==2.3.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 80)) (2.3.0) +Requirement already satisfied: h5py==3.13.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 81)) (3.13.0) +Requirement already satisfied: humanfriendly==10.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 82)) (10.0) +Requirement already satisfied: idna==3.10 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 83)) (3.10) +Requirement already satisfied: importlib-metadata==8.6.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 84)) (8.6.1) +Requirement already satisfied: importlib-resources==6.5.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 85)) (6.5.2) +Requirement already satisfied: isa-rwval==0.10.11 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 86)) (0.10.11) +Requirement already satisfied: isal==1.7.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 87)) (1.7.2) +Requirement already satisfied: isodate==0.7.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 88)) (0.7.2) +Requirement already satisfied: jinja2==3.1.6 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 89)) (3.1.6) +Requirement already satisfied: jmespath==1.0.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 90)) (1.0.1) +Requirement already satisfied: jsonref==1.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 91)) (1.1.0) +Requirement already satisfied: jsonschema==4.23.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 92)) (4.23.0) +Requirement already satisfied: jsonschema-specifications==2025.4.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 93)) (2025.4.1) +Requirement already satisfied: kombu==5.5.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 94)) (5.5.3) +Requirement already satisfied: lagom==2.7.5 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 95)) (2.7.5) +Requirement already satisfied: limits==4.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 97)) (4.2) +Requirement already satisfied: lxml==5.4.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 99)) (5.4.0) +Requirement already satisfied: mako==1.3.10 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 100)) (1.3.10) +Requirement already satisfied: markdown==3.8 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 101)) (3.8) +Requirement already satisfied: markdown-it-py==3.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 102)) (3.0.0) +Requirement already satisfied: markupsafe==3.0.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 103)) (3.0.2) +Requirement already satisfied: mdurl==0.1.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 104)) (0.1.2) +Requirement already satisfied: mercurial==7.0.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 105)) (7.0.1) +Requirement already satisfied: mistune==3.0.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 106)) (3.0.2) +Requirement already satisfied: mrcfile==1.5.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 107)) (1.5.4) +Requirement already satisfied: msal==1.32.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 108)) (1.32.3) +Requirement already satisfied: msgpack==1.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 109)) (1.1.0) +Requirement already satisfied: multidict==6.4.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 110)) (6.4.3) +Requirement already satisfied: mypy-extensions==1.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 111)) (1.1.0) +Requirement already satisfied: networkx==3.2.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 112)) (3.2.1) +Requirement already satisfied: nodeenv==1.9.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 114)) (1.9.1) +Requirement already satisfied: numpy==2.0.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 115)) (2.0.2) +Requirement already satisfied: oauthlib==3.2.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 117)) (3.2.2) +Requirement already satisfied: orjson==3.10.16 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 118)) (3.10.16) +Requirement already satisfied: oyaml==1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 119)) (1.0) +Requirement already satisfied: packaging==24.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 120)) (24.2) +Requirement already satisfied: paramiko==3.5.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 122)) (3.5.1) +Requirement already satisfied: parsley==1.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 123)) (1.3) +Requirement already satisfied: paste==3.10.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 124)) (3.10.1) +Requirement already satisfied: pastedeploy==3.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 125)) (3.1.0) +Requirement already satisfied: pebble==5.1.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 126)) (5.1.1) +Requirement already satisfied: pillow==11.2.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 127)) (11.2.1) +Requirement already satisfied: prompt-toolkit==3.0.51 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 128)) (3.0.51) +Requirement already satisfied: propcache==0.3.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 129)) (0.3.1) +Requirement already satisfied: prov==1.5.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 130)) (1.5.1) +Requirement already satisfied: psutil==7.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 131)) (7.0.0) +Requirement already satisfied: pulsar-galaxy-lib==0.15.8 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 132)) (0.15.8) +Requirement already satisfied: pycparser==2.22 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 133)) (2.22) +Requirement already satisfied: pycryptodome==3.22.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 134)) (3.22.0) +Requirement already satisfied: pydantic==2.11.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 135)) (2.11.3) +Requirement already satisfied: pydantic-core==2.33.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 136)) (2.33.1) +Requirement already satisfied: pydantic-tes==0.2.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 137)) (0.2.0) +Requirement already satisfied: pydot==2.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 138)) (2.0.0) +Requirement already satisfied: pyeventsystem==0.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 139)) (0.1.0) +Requirement already satisfied: pyfaidx==0.8.1.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 140)) (0.8.1.3) +Requirement already satisfied: pygments==2.19.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 141)) (2.19.1) +Requirement already satisfied: pyjwt==2.10.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 142)) (2.10.1) +Requirement already satisfied: pykwalify==1.8.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 143)) (1.8.0) +Requirement already satisfied: pylibmagic==0.5.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 144)) (0.5.0) +Requirement already satisfied: pynacl==1.5.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 145)) (1.5.0) +Requirement already satisfied: pyparsing==3.2.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 146)) (3.2.3) +Requirement already satisfied: pypng==0.20220715.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 147)) (0.20220715.0) +Requirement already satisfied: pysam==0.23.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 149)) (0.23.0) +Requirement already satisfied: python-dateutil==2.9.0.post0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 150)) (2.9.0.post0) +Requirement already satisfied: python-magic==0.4.27 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 151)) (0.4.27) +Requirement already satisfied: python-multipart==0.0.20 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 152)) (0.0.20) +Requirement already satisfied: python-slugify==8.0.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 153)) (8.0.4) +Requirement already satisfied: python3-openid==3.2.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 154)) (3.2.0) +Requirement already satisfied: pytz==2025.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 155)) (2025.2) +Requirement already satisfied: pyyaml==6.0.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 156)) (6.0.2) +Requirement already satisfied: pyzmq==26.4.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 157)) (26.4.0) +Requirement already satisfied: rdflib==7.1.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 158)) (7.1.4) +Requirement already satisfied: referencing==0.36.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 159)) (0.36.2) +Requirement already satisfied: refgenconf==0.12.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 160)) (0.12.2) +Requirement already satisfied: regex==2024.11.6 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 161)) (2024.11.6) +Requirement already satisfied: repoze-lru==0.7 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 162)) (0.7) +Requirement already satisfied: requests==2.32.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 163)) (2.32.3) +Requirement already satisfied: requests-oauthlib==2.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 164)) (2.0.0) +Requirement already satisfied: requests-toolbelt==1.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 165)) (1.0.0) +Requirement already satisfied: requests-unixsocket==0.4.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 166)) (0.4.1) +Requirement already satisfied: rich==13.9.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 167)) (13.9.4) +Requirement already satisfied: rich-argparse==1.7.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 168)) (1.7.0) +Requirement already satisfied: rocrate==0.13.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 169)) (0.13.0) +Requirement already satisfied: routes==2.5.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 170)) (2.5.1) +Requirement already satisfied: rpds-py==0.24.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 171)) (0.24.0) +Requirement already satisfied: ruamel-yaml==0.18.10 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 172)) (0.18.10) +Requirement already satisfied: ruamel-yaml-clib==0.2.12 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 173)) (0.2.12) +Requirement already satisfied: s3fs==2025.3.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 174)) (2025.3.2) +Requirement already satisfied: schema-salad==8.9.20250408123006 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 175)) (8.9.20250408123006) +Requirement already satisfied: setuptools==79.0.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 176)) (79.0.1) +Requirement already satisfied: setuptools-scm==5.0.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 177)) (5.0.2) +Requirement already satisfied: six==1.17.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 178)) (1.17.0) +Requirement already satisfied: slowapi==0.1.9 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 179)) (0.1.9) +Requirement already satisfied: sniffio==1.3.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 180)) (1.3.1) +Requirement already satisfied: social-auth-core==4.6.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 181)) (4.6.0) +Requirement already satisfied: sortedcontainers==2.4.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 182)) (2.4.0) +Requirement already satisfied: spython==0.3.14 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 183)) (0.3.14) +Requirement already satisfied: sqlalchemy==2.0.40 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 184)) (2.0.40) +Requirement already satisfied: sqlitedict==2.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 185)) (2.1.0) +Requirement already satisfied: sqlparse==0.5.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 186)) (0.5.3) +Requirement already satisfied: starlette==0.46.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 187)) (0.46.2) +Requirement already satisfied: starlette-context==0.4.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 188)) (0.4.0) +Requirement already satisfied: supervisor==4.2.5 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 189)) (4.2.5) +Requirement already satisfied: svgwrite==1.4.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 190)) (1.4.3) +Requirement already satisfied: tenacity==9.1.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 191)) (9.1.2) +Requirement already satisfied: text-unidecode==1.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 192)) (1.3) +Requirement already satisfied: tifffile==2024.8.30 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 193)) (2024.8.30) +Requirement already satisfied: tinydb==4.8.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 195)) (4.8.2) +Requirement already satisfied: tomli==2.2.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 196)) (2.2.1) +Requirement already satisfied: tornado==6.4.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 197)) (6.4.2) +Requirement already satisfied: tqdm==4.67.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 198)) (4.67.1) +Requirement already satisfied: tuspy==1.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 199)) (1.1.0) +Requirement already satisfied: tuswsgi==0.5.5 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 200)) (0.5.5) +Requirement already satisfied: typing-extensions==4.13.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 201)) (4.13.2) +Requirement already satisfied: typing-inspection==0.4.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 202)) (0.4.0) +Requirement already satisfied: tzdata==2025.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 203)) (2025.2) +Requirement already satisfied: tzlocal==5.3.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 204)) (5.3.1) +Requirement already satisfied: ubiquerg==0.8.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 205)) (0.8.1) +Requirement already satisfied: urllib3==1.26.20 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 206)) (1.26.20) +Requirement already satisfied: uvicorn==0.34.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 208)) (0.34.2) +Requirement already satisfied: uvloop==0.21.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 209)) (0.21.0) +Requirement already satisfied: vine==5.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 210)) (5.1.0) +Requirement already satisfied: wcwidth==0.2.13 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 211)) (0.2.13) +Requirement already satisfied: webencodings==0.5.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 212)) (0.5.1) +Requirement already satisfied: webob==1.8.9 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 213)) (1.8.9) +Requirement already satisfied: whoosh==2.7.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 214)) (2.7.4) +Requirement already satisfied: wrapt==1.17.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 215)) (1.17.2) +Requirement already satisfied: yacman==0.9.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 216)) (0.9.3) +Requirement already satisfied: yarl==1.20.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 217)) (1.20.0) +Requirement already satisfied: zipp==3.21.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 218)) (3.21.0) +Requirement already satisfied: zipstream-new==1.1.8 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 219)) (1.1.8) +Requirement already satisfied: zstandard==0.23.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 220)) (0.23.0) +Option master_api_key has been deprecated in favor of bootstrap_admin_api_key +Trying to resolve path for the 'email_ban_file' option but it's empty/None +Trying to resolve path for the 'data_manager_config_file' option but it's empty/None +/scratch/rico/galaxy/lib/galaxy/dependencies/__init__.py:77: FutureWarning: Truth-testing of elements was a source of confusion and will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. + if plugins_elem: +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple +Collecting watchdog (from -r /dev/stdin (line 1)) + Using cached watchdog-6.0.0-py3-none-manylinux2014_x86_64.whl.metadata (44 kB) +Using cached watchdog-6.0.0-py3-none-manylinux2014_x86_64.whl (79 kB) +Installing collected packages: watchdog +Successfully installed watchdog-6.0.0 +The Galaxy client has not yet been built and will be built now. +Option master_api_key has been deprecated in favor of bootstrap_admin_api_key +Trying to resolve path for the 'email_ban_file' option but it's empty/None +Trying to resolve path for the 'data_manager_config_file' option but it's empty/None +yarn install v1.22.22 +[1/4] Resolving packages... +success Already up-to-date. +Done in 6.00s. +yarn run v1.22.22 +$ cpy './node_modules/@galaxyproject/galaxy-client/dist/*' './static/dist' +Done in 0.55s. +Activating virtualenv at /scratch/rico/planemo/gx_venv_3 +Adding service gunicorn +supervisord is not running +Adding service celery +supervisord is not running +Adding service celery-beat +supervisord is not running +Executing: galaxy +Removing supervisor configs: /scratch/rico/tmp/tmp1o92xtdc/gravity/supervisor/supervisord.conf.d/_default_.d/celery-beat_celery-beat.conf, /scratch/rico/tmp/tmp1o92xtdc/gravity/supervisor/supervisord.conf.d/_default_.d/celery_celery.conf, /scratch/rico/tmp/tmp1o92xtdc/gravity/supervisor/supervisord.conf.d/_default_.d/gunicorn_gunicorn.conf +Removing empty instance dir: /scratch/rico/tmp/tmp1o92xtdc/gravity/supervisor/supervisord.conf.d/_default_.d +Working directory: /scratch/rico/galaxy +Executing: PYTHONPATH=lib GALAXY_CONFIG_FILE=/scratch/rico/tmp/tmp1o92xtdc/galaxy.yml gunicorn 'galaxy.webapps.galaxy.fast_factory:factory()' --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b 127.0.0.1:9090 --workers=1 --config python:galaxy.web_stack.gunicorn_config --preload +Working directory: /scratch/rico/galaxy +Executing: PYTHONPATH=lib GALAXY_CONFIG_FILE=/scratch/rico/tmp/tmp1o92xtdc/galaxy.yml celery --app galaxy.celery worker --concurrency 2 --loglevel DEBUG --pool threads --queues celery,galaxy.internal,galaxy.external +Working directory: /scratch/rico/galaxy +Executing: PYTHONPATH=lib GALAXY_CONFIG_FILE=/scratch/rico/tmp/tmp1o92xtdc/galaxy.yml celery --app galaxy.celery beat --loglevel DEBUG --schedule /scratch/rico/tmp/tmp1o92xtdc/gravity/celery-beat-schedule +Option master_api_key has been deprecated in favor of bootstrap_admin_api_key +Trying to resolve path for the 'email_ban_file' option but it's empty/None +Trying to resolve path for the 'data_manager_config_file' option but it's empty/None +Option master_api_key has been deprecated in favor of bootstrap_admin_api_key +Trying to resolve path for the 'email_ban_file' option but it's empty/None +Trying to resolve path for the 'data_manager_config_file' option but it's empty/None +Option master_api_key has been deprecated in favor of bootstrap_admin_api_key +Trying to resolve path for the 'email_ban_file' option but it's empty/None +Trying to resolve path for the 'data_manager_config_file' option but it's empty/None +[2025-07-24 11:19:46,372: DEBUG/MainProcess] | Worker: Preparing bootsteps. +[2025-07-24 11:19:46,374: DEBUG/MainProcess] | Worker: Building graph... +[2025-07-24 11:19:46,374: DEBUG/MainProcess] | Worker: New boot order: {StateDB, Timer, Hub, Pool, Autoscaler, Beat, Consumer} +[2025-07-24 11:19:46,378: DEBUG/MainProcess] | Consumer: Preparing bootsteps. +[2025-07-24 11:19:46,378: DEBUG/MainProcess] | Consumer: Building graph... +[2025-07-24 11:19:46,380: DEBUG/MainProcess] Setting default socket timeout to 30 +[2025-07-24 11:19:46,380: INFO/MainProcess] beat: Starting... +[2025-07-24 11:19:46,405: DEBUG/MainProcess] | Consumer: New boot order: {Connection, Events, Mingle, Tasks, DelayedDelivery, Control, Heart, Agent, Gossip, event loop} + + -------------- celery@laila v5.5.2 (immunity) +--- ***** ----- +-- ******* ---- Linux-5.10.0-35-amd64-x86_64-with-glibc2.31 2025-07-24 11:19:46 +- *** --- * --- +- ** ---------- [config] +- ** ---------- .> app: galaxy:0x7fc6a17951c0 +- ** ---------- .> transport: sqlalchemy+sqlite:////scratch/rico/tmp/tmp1o92xtdc/galaxy.sqlite +- ** ---------- .> results: sqlite:////scratch/rico/galaxy/database/results.sqlite +- *** --- * --- .> concurrency: 2 (thread) +-- ******* ---- .> task events: OFF (enable -E to monitor tasks in this worker) +--- ***** ----- + -------------- [queues] + .> celery exchange=celery(direct) key=celery + .> galaxy.external exchange=galaxy.external(direct) key=galaxy.external + .> galaxy.internal exchange=galaxy.internal(direct) key=galaxy.internal + +[tasks] + . celery.accumulate + . celery.backend_cleanup + . celery.chain + . celery.chord + . celery.chord_unlock + . celery.chunks + . celery.group + . celery.map + . celery.starmap + . galaxy.change_datatype + . galaxy.clean_object_store_caches + . galaxy.cleanup_expired_notifications + . galaxy.cleanup_jwds + . galaxy.cleanup_short_term_storage + . galaxy.compute_dataset_hash + . galaxy.dispatch_pending_notifications + . galaxy.export_history + . galaxy.fetch_data + . galaxy.finish_job + . galaxy.import_data_bundle + . galaxy.import_model_store + . galaxy.materialize + . galaxy.prepare_dataset_collection_download + . galaxy.prepare_history_content_download + . galaxy.prepare_history_download + . galaxy.prepare_invocation_download + . galaxy.prepare_pdf_download + . galaxy.prune_history_audit_table + . galaxy.purge_datasets + . galaxy.purge_hda + . galaxy.recalculate_user_disk_usage + . galaxy.send_notification_to_recipients_async + . galaxy.set_job_metadata + . galaxy.set_metadata + . galaxy.setup_fetch_data + . galaxy.touch + . galaxy.write_history_content_to + . galaxy.write_history_to + . galaxy.write_invocation_to + +[2025-07-24 11:19:46,444: DEBUG/MainProcess] | Worker: Starting Pool +[2025-07-24 11:19:46,444: DEBUG/MainProcess] ^-- substep ok +[2025-07-24 11:19:46,444: DEBUG/MainProcess] | Worker: Starting Consumer +[2025-07-24 11:19:46,444: DEBUG/MainProcess] | Consumer: Starting Connection +[2025-07-24 11:19:46,449: INFO/MainProcess] Connected to sqlalchemy+sqlite:////scratch/rico/tmp/tmp1o92xtdc/galaxy.sqlite +[2025-07-24 11:19:46,449: DEBUG/MainProcess] ^-- substep ok +[2025-07-24 11:19:46,449: DEBUG/MainProcess] | Consumer: Starting Events +[2025-07-24 11:19:46,449: DEBUG/MainProcess] ^-- substep ok +[2025-07-24 11:19:46,449: DEBUG/MainProcess] | Consumer: Starting Tasks +[2025-07-24 11:19:46,465: DEBUG/MainProcess] Current schedule: +<ScheduleEntry: prune-history-audit-table galaxy.prune_history_audit_table() <freq: 1.00 hour> +<ScheduleEntry: clean-object-store-caches galaxy.clean_object_store_caches() <freq: 10.00 minutes> +<ScheduleEntry: cleanup-short-term-storage galaxy.cleanup_short_term_storage() <freq: 1.00 hour> +<ScheduleEntry: celery.backend_cleanup celery.backend_cleanup() <crontab: 0 4 * * * (m/h/dM/MY/d)> +[2025-07-24 11:19:46,465: DEBUG/MainProcess] beat: Ticking with max interval->5.00 minutes +[2025-07-24 11:19:46,466: DEBUG/MainProcess] beat: Waking up in 5.00 minutes. +[2025-07-24 11:19:46,495: DEBUG/MainProcess] ^-- substep ok +[2025-07-24 11:19:46,495: DEBUG/MainProcess] | Consumer: Starting Heart +[2025-07-24 11:19:46,496: DEBUG/MainProcess] ^-- substep ok +[2025-07-24 11:19:46,496: DEBUG/MainProcess] | Consumer: Starting event loop +[2025-07-24 11:19:46,496: INFO/MainProcess] celery@laila ready. +DEBUG:yacman.yacman:Patching yaml loader +DEBUG:yacman.yacman1:Using yacman version 0.9.3 +DEBUG:yacman.yacman_future:Using yacman version 0.9.3 +DEBUG:galaxy.app:python path is: /scratch/rico/galaxy, /scratch/rico/planemo/gx_venv_3/bin, /scratch/rico/galaxy/lib, /usr/local/lib/python39.zip, /usr/local/lib/python3.9, /usr/local/lib/python3.9/lib-dynload, /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages, /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages/setuptools/_vendor +DEBUG:galaxy.config:Configuration directory is /scratch/rico/tmp/tmp1o92xtdc +DEBUG:galaxy.config:Data directory is /scratch/rico/galaxy/database +DEBUG:galaxy.config:Managed config directory is /scratch/rico/tmp/tmp1o92xtdc +WARNING:galaxy.config:Option master_api_key has been deprecated in favor of bootstrap_admin_api_key +WARNING:galaxy.config:Trying to resolve path for the 'email_ban_file' option but it's empty/None +WARNING:galaxy.config:Trying to resolve path for the 'data_manager_config_file' option but it's empty/None +DEBUG:galaxy.config:No extra version JSON file detected at /scratch/rico/galaxy/version.json +INFO:alembic.runtime.migration:Context impl SQLiteImpl. +INFO:alembic.runtime.migration:Will assume non-transactional DDL. +INFO:alembic.runtime.migration:Running stamp_revision -> c716ee82337b +DEBUG:alembic.runtime.migration:new branch insert c716ee82337b +INFO:alembic.runtime.migration:Context impl SQLiteImpl. +INFO:alembic.runtime.migration:Will assume non-transactional DDL. +INFO:alembic.runtime.migration:Running stamp_revision -> d4a650f47a3c +DEBUG:alembic.runtime.migration:new branch insert d4a650f47a3c +INFO:galaxy.app:Install database targeting Galaxy's database configuration. +WARNING:galaxy.security.vault:No vault configured. We recommend defining the vault_config_file setting in galaxy.yml +DEBUG:galaxy.web_stack:GunicornApplicationStack initialized +galaxy.web_stack.handlers INFO 2025-07-24 11:19:48,995 [pN:main,p:2330407,tN:MainThread] JobConfiguration: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on <handlers> to override the default +galaxy.jobs INFO 2025-07-24 11:19:48,995 [pN:main,p:2330407,tN:MainThread] Job handler assignment methods set to: db-skip-locked +galaxy.queue_worker INFO 2025-07-24 11:19:49,640 [pN:main,p:2330407,tN:MainThread] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////scratch/rico/tmp/tmp1o92xtdc/galaxy.sqlite?isolation_level=IMMEDIATE +galaxy.tool_util.data INFO 2025-07-24 11:19:49,654 [pN:main,p:2330407,tN:MainThread] Could not find tool data /scratch/rico/galaxy/tool-data/all_fasta.loc, reading sample +galaxy.visualization.genomes ERROR 2025-07-24 11:19:49,659 [pN:main,p:2330407,tN:MainThread] Error reading twobit.loc +Traceback (most recent call last): + File "/scratch/rico/galaxy/lib/galaxy/visualization/genomes.py", line 226, in reload_genomes + with open(twobit_path) as f: +FileNotFoundError: [Errno 2] No such file or directory: '/scratch/rico/galaxy/tool-data/twobit.loc' +galaxy.util WARNING 2025-07-24 11:19:49,725 [pN:main,p:2330407,tN:MainThread] directory not found: /scratch/rico/galaxy/config/plugins/activities +galaxy.tools WARNING 2025-07-24 11:19:49,726 [pN:main,p:2330407,tN:MainThread] The default shed tool config file (/scratch/rico/tmp/tmp1o92xtdc/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2025-07-24 11:19:49,726 [pN:main,p:2330407,tN:MainThread] Parsing the tool configuration /scratch/rico/tmp/tmp1o92xtdc/tool_conf.xml +galaxy.tools WARNING 2025-07-24 11:19:50,113 [pN:main,p:2330407,tN:MainThread] The default shed tool config file (/scratch/rico/tmp/tmp1o92xtdc/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2025-07-24 11:19:50,113 [pN:main,p:2330407,tN:MainThread] Parsing the tool configuration /scratch/rico/tmp/tmp1o92xtdc/shed_tools_conf.xml +galaxy.tools WARNING 2025-07-24 11:19:50,113 [pN:main,p:2330407,tN:MainThread] The default shed tool config file (/scratch/rico/tmp/tmp1o92xtdc/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2025-07-24 11:19:50,113 [pN:main,p:2330407,tN:MainThread] Parsing the tool configuration /scratch/rico/tmp/tmp1o92xtdc/empty_tool_conf.xml +galaxy.tools.search WARNING 2025-07-24 11:19:54,461 [pN:main,p:2330407,tN:MainThread] Index at '/scratch/rico/galaxy/database/tool_search_index/default' uses outdated schema, creating a new index +galaxy.tools.search WARNING 2025-07-24 11:19:54,465 [pN:main,p:2330407,tN:MainThread] Index at '/scratch/rico/galaxy/database/tool_search_index/ontology:edam_operations' uses outdated schema, creating a new index +galaxy.tools.search WARNING 2025-07-24 11:19:54,467 [pN:main,p:2330407,tN:MainThread] Index at '/scratch/rico/galaxy/database/tool_search_index/ontology:edam_topics' uses outdated schema, creating a new index +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,477 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,479 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "bam_iobio". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,486 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "intermine_simple_display". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,488 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,491 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,498 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,499 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "q2view_display". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,499 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "q2view_display". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,503 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,504 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "vcf_iobio". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,506 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,507 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,507 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "biom_simple_display". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,507 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "icn3d_simple_display". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,508 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "icn3d_simple_display". +galaxy.datatypes.display_applications.application ERROR 2025-07-24 11:19:54,508 [pN:main,p:2330407,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "icn3d_simple_display". +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,979 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: aceeditor +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,980 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,980 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: aladin +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,981 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: alignment +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,982 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,982 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz +galaxy.visualization.plugins.config_parser INFO 2025-07-24 11:19:54,983 [pN:main,p:2330407,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,983 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: csg +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,984 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,984 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna +/scratch/rico/galaxy/lib/galaxy/visualization/plugins/config_parser.py:170: FutureWarning: Truth-testing of elements was a source of confusion and will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. + if (tracks_section := xml_tree.find("tracks") or xml_tree.find("groups")) is not None: +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,985 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: example +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,986 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: fits_graph_viewer +galaxy.visualization.plugins.config_parser INFO 2025-07-24 11:19:54,986 [pN:main,p:2330407,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,986 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,987 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: h5web +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,988 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap +galaxy.visualization.plugins.config_parser INFO 2025-07-24 11:19:54,989 [pN:main,p:2330407,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,989 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace +galaxy.visualization.plugins.config_parser INFO 2025-07-24 11:19:54,989 [pN:main,p:2330407,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,989 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,992 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,994 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,996 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:54,998 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,000 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,000 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: jupyterlite +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,001 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: kepler +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,002 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: molstar +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,002 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: msa +galaxy.visualization.plugins.config_parser INFO 2025-07-24 11:19:55,003 [pN:main,p:2330407,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,003 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,004 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,005 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: niivue +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,005 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: nora +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,007 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,009 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,011 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,013 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,015 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,017 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,020 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,022 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,023 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,025 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,027 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,029 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,031 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,032 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,033 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,033 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: pca +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,034 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,035 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: plotly +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,036 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: plotly_box +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,036 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: plotly_histogram +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,037 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: plotly_surface +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,037 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: plyr +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,038 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: pv +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,039 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,039 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: tabulator +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,040 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: tiffviewer +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,040 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,041 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: ts_visjs +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,041 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,042 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: venn +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,043 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: vitessce +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,043 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: vizarr +galaxy.visualization.plugins.registry INFO 2025-07-24 11:19:55,044 [pN:main,p:2330407,tN:MainThread] VisualizationsRegistry, loaded plugin: vtk +galaxy.tours._impl INFO 2025-07-24 11:19:55,064 [pN:main,p:2330407,tN:MainThread] Loaded tour 'core.galaxy_ui' +galaxy.tours._impl INFO 2025-07-24 11:19:55,082 [pN:main,p:2330407,tN:MainThread] Loaded tour 'core.deferred' +galaxy.tours._impl INFO 2025-07-24 11:19:55,095 [pN:main,p:2330407,tN:MainThread] Loaded tour 'core.history' +galaxy.tours._impl INFO 2025-07-24 11:19:55,101 [pN:main,p:2330407,tN:MainThread] Loaded tour 'core.visualizations' +galaxy.tours._impl INFO 2025-07-24 11:19:55,112 [pN:main,p:2330407,tN:MainThread] Loaded tour 'core.windows' +galaxy.workflow.scheduling_manager INFO 2025-07-24 11:19:55,135 [pN:main,p:2330407,tN:MainThread] No workflow schedulers plugin config file defined, using default scheduler. +galaxy.web_stack.handlers INFO 2025-07-24 11:19:55,136 [pN:main,p:2330407,tN:MainThread] WorkflowSchedulingManager: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on <handlers> to override the default +galaxy.app INFO 2025-07-24 11:19:55,145 [pN:main,p:2330407,tN:MainThread] Galaxy app startup finished (8078.308 ms) +[2025-07-24 11:20:05 -0400] [2330407] [INFO] Starting gunicorn 23.0.0 +[2025-07-24 11:20:05 -0400] [2330407] [INFO] Listening at: http://127.0.0.1:9090 (2330407) +[2025-07-24 11:20:05 -0400] [2330407] [INFO] Using worker: galaxy.webapps.galaxy.workers.Worker +[2025-07-24 11:20:05 -0400] [2330658] [INFO] Booting worker with pid: 2330658 +galaxy.jobs.handler INFO 2025-07-24 11:20:05,153 [pN:main.1,p:2330658,tN:WorkflowRequestMonitor.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method for handler 'main.1', tag(s): None, _default_ +galaxy.jobs INFO 2025-07-24 11:20:05,154 [pN:main.1,p:2330658,tN:Thread-2] Handler 'main.1' will load all configured runner plugins +galaxy.jobs.handler INFO 2025-07-24 11:20:05,233 [pN:main.1,p:2330658,tN:JobHandlerQueue.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method for handler 'main.1', tag(s): +galaxy.jobs.handler INFO 2025-07-24 11:20:05,233 [pN:main.1,p:2330658,tN:Thread-2] job handler queue started +galaxy.jobs.handler INFO 2025-07-24 11:20:05,236 [pN:main.1,p:2330658,tN:Thread-2] job handler stop queue started +galaxy.queue_worker INFO 2025-07-24 11:20:05,242 [pN:main.1,p:2330658,tN:Thread-2] Binding and starting galaxy control worker for main.1 +[2025-07-24 11:20:05 -0400] [2330658] [INFO] Started server process [2330658] +[2025-07-24 11:20:05 -0400] [2330658] [INFO] Waiting for application startup. +[2025-07-24 11:20:05 -0400] [2330658] [INFO] Application startup complete. +galaxy.util WARNING 2025-07-24 11:20:05,268 [pN:main.1,p:2330658,tN:Thread-2] directory not found: /scratch/rico/galaxy/config/plugins/activities +galaxy.tools WARNING 2025-07-24 11:20:05,271 [pN:main.1,p:2330658,tN:Thread-2] The default shed tool config file (/scratch/rico/tmp/tmp1o92xtdc/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2025-07-24 11:20:05,271 [pN:main.1,p:2330658,tN:Thread-2] Parsing the tool configuration /scratch/rico/tmp/tmp1o92xtdc/tool_conf.xml +galaxy.tools WARNING 2025-07-24 11:20:05,273 [pN:main.1,p:2330658,tN:Thread-2] The default shed tool config file (/scratch/rico/tmp/tmp1o92xtdc/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2025-07-24 11:20:05,273 [pN:main.1,p:2330658,tN:Thread-2] Parsing the tool configuration /scratch/rico/tmp/tmp1o92xtdc/shed_tools_conf.xml +galaxy.tools WARNING 2025-07-24 11:20:05,275 [pN:main.1,p:2330658,tN:Thread-2] The default shed tool config file (/scratch/rico/tmp/tmp1o92xtdc/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2025-07-24 11:20:05,276 [pN:main.1,p:2330658,tN:Thread-2] Parsing the tool configuration /scratch/rico/tmp/tmp1o92xtdc/empty_tool_conf.xml +Exception in thread database_heartbeart_main.1.thread: +Traceback (most recent call last): + File "/usr/local/lib/python3.9/threading.py", line 980, in _bootstrap_inner + self.run() + File "/usr/local/lib/python3.9/threading.py", line 917, in run + self._target(*self._args, **self._kwargs) + File "/scratch/rico/galaxy/lib/galaxy/model/database_heartbeat.py", line 104, in send_database_heartbeat + self.update_watcher_designation() + File "/scratch/rico/galaxy/lib/galaxy/model/database_heartbeat.py", line 99, in update_watcher_designation + self.is_config_watcher = is_config_watcher + File "/scratch/rico/galaxy/lib/galaxy/model/database_heartbeat.py", line 81, in is_config_watcher + callback(self._is_config_watcher) + File "/scratch/rico/galaxy/lib/galaxy/config_watchers.py", line 73, in change_state + self.start() + File "/scratch/rico/galaxy/lib/galaxy/config_watchers.py", line 81, in start +galaxy.queue_worker INFO 2025-07-24 11:20:05,443 [pN:main.1,p:2330658,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. + [self.data_manager_config_watcher.watch_file(config) for config in self.data_manager_configs] + File "/scratch/rico/galaxy/lib/galaxy/config_watchers.py", line 81, in <listcomp> + [self.data_manager_config_watcher.watch_file(config) for config in self.data_manager_configs] + File "/scratch/rico/galaxy/lib/galaxy/tool_util/toolbox/watcher.py", line 159, in watch_file + self.monitor(tool_conf_file) + File "/scratch/rico/galaxy/lib/galaxy/tool_util/toolbox/watcher.py", line 153, in monitor + if os.path.exists(path): + File "/usr/local/lib/python3.9/genericpath.py", line 19, in exists + os.stat(path) +TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType +galaxy.queue_worker INFO 2025-07-24 11:20:05,491 [pN:main.1,p:2330658,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. +galaxy.web_stack INFO 2025-07-24 11:20:05,504 [pN:main.1,p:2330658,tN:Thread-2] Galaxy server instance 'main.1' is running +[92m +Serving on http://127.0.0.1:9090 +[0m +galaxy.queue_worker INFO 2025-07-24 11:20:05,517 [pN:main.1,p:2330658,tN:Thread-1] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker INFO 2025-07-24 11:20:05,917 [pN:main.1,p:2330658,tN:Thread-1] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. +uvicorn.access INFO 2025-07-24 11:20:09,846 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET / HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:09,882 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /static/dist/base.css?v=1753370386 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:09,883 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34294 - "GET /static/style/jquery-ui/smoothness/jquery-ui.css?v=1753370386 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:09,884 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34300 - "GET /static/dist/libs.bundled.js?v=1753370386 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:09,903 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34294 - "GET /static/dist/analysis.bundled.js?v=1753370386 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:11,580 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /api/configuration HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:11,635 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /static/dist/1551f4f60c37af51121f.woff2 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:11,636 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34300 - "GET /api/users/current HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:11,654 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34300 - "GET /static/dist/7c05f33b4fe5f8132439.woff2 HTTP/1.1" 304 +uvicorn.access INFO 2025-07-24 11:20:11,660 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34294 - "GET /api/webhooks HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:11,703 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /static/dist/b07ad0e0d01ba4d56c1a.woff2 HTTP/1.1" 304 +uvicorn.access INFO 2025-07-24 11:20:11,717 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34322 - "GET /welcome HTTP/1.1" 302 +uvicorn.access INFO 2025-07-24 11:20:11,742 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34294 - "GET /static/favicon.svg HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:11,771 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34322 - "GET /static/welcome.html HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:11,845 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34322 - "GET /static/dist/base.css HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:11,845 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34310 - "GET /api/tool_panels HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:11,846 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34330 - "GET /history/current_history_json HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:11,849 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34300 - "GET /api/histories/count HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:11,868 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /api/webhooks HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:11,994 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34300 - "GET /api/histories?view=summary&order=update_time&offset=0&limit=10 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:11,996 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34330 - "GET /api/datatypes?extension_only=false HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:12,091 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34310 - "GET /api/genomes HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:12,220 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34294 - "GET /api/histories/9e690f7bf8043dee/contents?v=dev&limit=1000&q=update_time-ge&qv=2025-07-24T15:20:10.358Z HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:12,223 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34300 - "GET /api/histories/count HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:12,236 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /api/histories/9e690f7bf8043dee/contents?v=dev&order=hid&offset=0&limit=100&q=deleted&qv=false&q=visible&qv=true HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:12,275 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34300 - "GET /api/users/75b4a35f9b4c0d00 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:12,303 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /api/tools?in_panel=False HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:12,338 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /api/tool_panels/default HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:14,196 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET / HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,482 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52610 - "GET /api/webhooks HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,487 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52640 - "GET /api/tool_panels HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,523 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /history/current_history_json?since=2025-07-24T15:20:11.638000 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,524 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52650 - "GET /welcome HTTP/1.1" 302 +uvicorn.access INFO 2025-07-24 11:20:15,561 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52630 - "GET /api/configuration HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,573 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52618 - "GET /api/users/current HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,607 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52640 - "GET /history/current_history_json HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,615 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52610 - "GET /api/webhooks HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,689 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /api/histories/22ae0e71d134acd7/contents?v=dev&order=hid&offset=0&limit=100&q=deleted&qv=false&q=visible&qv=true HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,787 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52610 - "GET /api/datatypes?extension_only=false HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,789 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52630 - "GET /api/histories/count HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,809 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52618 - "GET /api/histories/22ae0e71d134acd7/contents?v=dev&limit=1000&q=update_time-ge&qv=2025-07-24T15:20:12.159Z HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,943 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52640 - "GET /api/genomes HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,948 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52650 - "GET /api/histories/22ae0e71d134acd7/contents?v=dev&limit=1000&q=update_time-ge&qv=2025-07-24T15:20:14.600Z HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,958 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /api/histories/22ae0e71d134acd7/contents?v=dev&order=hid&offset=0&limit=100&q=deleted&qv=false&q=visible&qv=true HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,967 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52618 - "GET /api/users/75b4a35f9b4c0d00 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:15,999 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52630 - "GET /api/histories?view=summary&order=update_time&offset=0&limit=10 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:16,104 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52630 - "GET /api/users/75b4a35f9b4c0d00 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:16,121 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52618 - "GET /api/histories/count HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:16,164 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52618 - "GET /api/tools?in_panel=False HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:16,199 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52618 - "GET /api/tool_panels/default HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:17,456 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52618 - "GET /api/histories/22ae0e71d134acd7/contents?v=dev&order=hid&offset=0&limit=100&q=deleted&qv=false&q=visible&qv=true HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:17,863 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /static/dist/616.bundled.js HTTP/1.1" 304 +uvicorn.access INFO 2025-07-24 11:20:17,873 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52618 - "GET /history/current_history_json?since=2025-07-24T15:20:11.677000 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:17,897 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52630 - "GET /api/entry_points?running=true HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:17,902 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /static/dist/libs.bundled.js HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:19,423 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /history/current_history_json?since=2025-07-24T15:20:11.677000 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:20,119 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /api/tools/ncbi_egapx/build?version=latest&tool_version=latest HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:20,170 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /static/dist/441.bundled.js HTTP/1.1" 304 +uvicorn.access INFO 2025-07-24 11:20:20,217 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52658 - "GET /api/datatypes/types_and_mapping?upload_only=false HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:20,265 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52672 - "GET /%24PATH_TO_IMAGES/Pipeline_sm_ncRNA_CAGE_80pct.png HTTP/1.1" 404 +uvicorn.access INFO 2025-07-24 11:20:20,272 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /api/tools/ncbi_egapx/citations HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:20,273 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52674 - "GET /static/dist/f80d5ce4e2dd8f120516.png HTTP/1.1" 304 +uvicorn.access INFO 2025-07-24 11:20:20,305 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:52674 - "GET /static/dist/cite.bundled.js HTTP/1.1" 304 +uvicorn.access INFO 2025-07-24 11:20:20,308 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /static/dist/435.bundled.js HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:20,915 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:34288 - "GET /history/current_history_json?since=2025-07-24T15:20:11.677000 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:23,431 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:41740 - "GET /history/current_history_json?since=2025-07-24T15:20:11.677000 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:23,948 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:41740 - "GET /history/current_history_json?since=2025-07-24T15:20:11.677000 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:26,983 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:41744 - "GET /history/current_history_json?since=2025-07-24T15:20:11.677000 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:27,414 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:41744 - "GET /history/current_history_json?since=2025-07-24T15:20:11.677000 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:27,931 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:41744 - "GET /api/entry_points?running=true HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:30,017 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:41752 - "GET /history/current_history_json?since=2025-07-24T15:20:11.677000 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:33,053 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:41766 - "GET /history/current_history_json?since=2025-07-24T15:20:11.677000 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:36,087 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:41638 - "GET /history/current_history_json?since=2025-07-24T15:20:11.677000 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:37,972 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:41638 - "GET /api/entry_points?running=true HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:39,126 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:41638 - "GET /history/current_history_json?since=2025-07-24T15:20:11.677000 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:42,174 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:41644 - "GET /history/current_history_json?since=2025-07-24T15:20:11.677000 HTTP/1.1" 200 +uvicorn.access INFO 2025-07-24 11:20:45,222 [pN:main.1,p:2330658,tN:MainThread] 127.0.0.1:56024 - "GET /history/current_history_json?since=2025-07-24T15:20:11.677000 HTTP/1.1" 200
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test.bash Mon Jul 28 14:35:28 2025 +0000 @@ -0,0 +1,70 @@ +#!/usr/bin/env bash + +set -o errexit +set -o nounset +set -o pipefail +#set -o xtrace + +export TMP=/scratch/rico/tmp + +#source "/scratch/rico/new/env.bash" + +export PLANEMO_GLOBAL_WORKSPACE=/scratch/rico/planemo +export PLANEMO_GLOBAL_CONFIG_PATH=${PLANEMO_GLOBAL_WORKSPACE}/.planemo.yml +CLEAN=0 +CLEAN=1 + +if [ -e "/scratch/rico/galaxy" ]; then + z_time=$(stat --format="%Z" "/scratch/rico/galaxy") + + w_time=$(stat --format="%W" "/scratch/rico/galaxy") + if [ $w_time -ne 0 ]; then + if [ $w_time -lt $z_time ]; then + z_time="$w_time" + fi + fi + + now=$(date +%s) + delta=$(( now - z_time )) + if [ $delta -ge 86400 ]; then + CLEAN=1 + fi +else + CLEAN=1 +fi + +if [ $CLEAN -ne 0 ]; then + rm -rf /scratch/rico/galaxy + rm -rf "$PLANEMO_GLOBAL_WORKSPACE" + rm -rf /scratch/rico/.npm + mkdir /scratch/rico/.npm +fi + +rm -rf /tmp/tmp* "$TMP/tmp*" + +export GALAXY_SLOTS=64 +export GALAXY_MEMORY_MB=262144 + +if [ $CLEAN -ne 0 ]; then + planemo test \ + --galaxy_root /scratch/rico/galaxy \ + --docker \ + --no_cleanup \ + 2>&1 \ + | tee test.out +else + planemo test \ + --galaxy_root /scratch/rico/galaxy \ + --docker \ + --no_docker_sudo \ + --no_cleanup \ + 2>&1 \ + | tee test.out +fi + +# Galaxy upload tool fails when using planemo server on galaxy release branch 24 +# +# rm -rf /scratch/rico/galaxy; planemo serve --galaxy_branch release_23.2 --galaxy_root /scratch/rico/galaxy +# rm -rf /scratch/rico/galaxy; planemo serve --galaxy_branch release_24.0 --galaxy_root /scratch/rico/galaxy + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test.out Mon Jul 28 14:35:28 2025 +0000 @@ -0,0 +1,1928 @@ +git clone --mirror https://github.com/galaxyproject/galaxy /scratch/rico/planemo/gx_repo +Cloning into bare repository '/scratch/rico/planemo/gx_repo'... +git clone --branch master --depth 1 file:///scratch/rico/planemo/gx_repo /scratch/rico/galaxy +Cloning into '/scratch/rico/galaxy'... +Updating files: 61% (4764/7701) Updating files: 62% (4775/7701) Updating files: 63% (4852/7701) Updating files: 64% (4929/7701) Updating files: 65% (5006/7701) Updating files: 66% (5083/7701) Updating files: 67% (5160/7701) Updating files: 68% (5237/7701) Updating files: 69% (5314/7701) Updating files: 70% (5391/7701) Updating files: 71% (5468/7701) Updating files: 72% (5545/7701) Updating files: 73% (5622/7701) Updating files: 74% (5699/7701) Updating files: 75% (5776/7701) Updating files: 76% (5853/7701) Updating files: 77% (5930/7701) Updating files: 78% (6007/7701) Updating files: 79% (6084/7701) Updating files: 80% (6161/7701) Updating files: 81% (6238/7701) Updating files: 82% (6315/7701) Updating files: 83% (6392/7701) Updating files: 84% (6469/7701) Updating files: 85% (6546/7701) Updating files: 86% (6623/7701) Updating files: 87% (6700/7701) Updating files: 88% (6777/7701) Updating files: 89% (6854/7701) Updating files: 90% (6931/7701) Updating files: 91% (7008/7701) Updating files: 92% (7085/7701) Updating files: 93% (7162/7701) Updating files: 94% (7239/7701) Updating files: 95% (7316/7701) Updating files: 96% (7393/7701) Updating files: 97% (7470/7701) Updating files: 98% (7547/7701) Updating files: 99% (7624/7701) Updating files: 100% (7701/7701) Updating files: 100% (7701/7701), done. +if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/scratch/rico/planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /scratch/rico/.venv/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /scratch/rico/.venv/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS} +galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input +created virtual environment CPython3.9.19.final.0-64 in 4165ms + creator CPython3Posix(dest=/scratch/rico/planemo/gx_venv_3, clear=False, no_vcs_ignore=False, global=False) + seeder FromAppData(download=False, pip=bundle, setuptools=bundle, via=copy, app_data_dir=/afs/bx.psu.edu/home/rico/.local/share/virtualenv) + added seed packages: pip==25.1.1, setuptools==80.9.0 + activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator +Created virtualenv +Activated a virtualenv for Galaxy +/scratch/rico/planemo/gx_venv_3 +Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample +Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample +Activating virtualenv at /scratch/rico/planemo/gx_venv_3 +Requirement already satisfied: pip>=20.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (25.1.1) +Collecting wheel + Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB) +Using cached wheel-0.45.1-py3-none-any.whl (72 kB) +Installing collected packages: wheel +Successfully installed wheel-0.45.1 +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple +Ignoring colorama: markers 'sys_platform == "win32"' don't match your environment +Ignoring legacy-cgi: markers 'python_full_version >= "3.13"' don't match your environment +Ignoring limits: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring networkx: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring numpy: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring packaging: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring pyreadline3: markers 'sys_platform == "win32"' don't match your environment +Ignoring tifffile: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring urllib3: markers 'python_full_version >= "3.10"' don't match your environment +Collecting a2wsgi==1.10.8 (from -r requirements.txt (line 3)) + Using cached a2wsgi-1.10.8-py3-none-any.whl.metadata (3.9 kB) +Collecting adal==1.2.7 (from -r requirements.txt (line 4)) + Using cached adal-1.2.7-py2.py3-none-any.whl.metadata (6.9 kB) +Collecting aiobotocore==2.21.1 (from -r requirements.txt (line 5)) + Using cached aiobotocore-2.21.1-py3-none-any.whl.metadata (24 kB) +Collecting aiofiles==24.1.0 (from -r requirements.txt (line 6)) + Using cached aiofiles-24.1.0-py3-none-any.whl.metadata (10 kB) +Collecting aiohappyeyeballs==2.6.1 (from -r requirements.txt (line 7)) + Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB) +Collecting aiohttp==3.11.18 (from -r requirements.txt (line 8)) + Using cached aiohttp-3.11.18-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.7 kB) +Collecting aioitertools==0.12.0 (from -r requirements.txt (line 9)) + Using cached aioitertools-0.12.0-py3-none-any.whl.metadata (3.8 kB) +Collecting aiosignal==1.3.2 (from -r requirements.txt (line 10)) + Using cached aiosignal-1.3.2-py2.py3-none-any.whl.metadata (3.8 kB) +Collecting alembic==1.15.2 (from -r requirements.txt (line 11)) + Using cached alembic-1.15.2-py3-none-any.whl.metadata (7.3 kB) +Collecting amqp==5.3.1 (from -r requirements.txt (line 12)) + Using cached amqp-5.3.1-py3-none-any.whl.metadata (8.9 kB) +Collecting annotated-types==0.7.0 (from -r requirements.txt (line 13)) + Using cached annotated_types-0.7.0-py3-none-any.whl.metadata (15 kB) +Collecting anyio==4.9.0 (from -r requirements.txt (line 14)) + Using cached anyio-4.9.0-py3-none-any.whl.metadata (4.7 kB) +Collecting apispec==6.8.1 (from -r requirements.txt (line 15)) + Using cached apispec-6.8.1-py3-none-any.whl.metadata (10 kB) +Collecting appdirs==1.4.4 (from -r requirements.txt (line 16)) + Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB) +Collecting arcp==0.2.1 (from -r requirements.txt (line 17)) + Using cached arcp-0.2.1-py2.py3-none-any.whl.metadata (7.6 kB) +Collecting argcomplete==3.6.2 (from -r requirements.txt (line 18)) + Using cached argcomplete-3.6.2-py3-none-any.whl.metadata (16 kB) +Collecting async-timeout==5.0.1 (from -r requirements.txt (line 19)) + Using cached async_timeout-5.0.1-py3-none-any.whl.metadata (5.1 kB) +Collecting attmap==0.13.2 (from -r requirements.txt (line 20)) + Using cached attmap-0.13.2-py3-none-any.whl.metadata (1.1 kB) +Collecting attrs==25.3.0 (from -r requirements.txt (line 21)) + Using cached attrs-25.3.0-py3-none-any.whl.metadata (10 kB) +Collecting babel==2.17.0 (from -r requirements.txt (line 22)) + Using cached babel-2.17.0-py3-none-any.whl.metadata (2.0 kB) +Collecting bagit==1.8.1 (from -r requirements.txt (line 23)) + Using cached bagit-1.8.1-py2.py3-none-any.whl.metadata (8.3 kB) +Collecting bagit-profile==1.3.1 (from -r requirements.txt (line 24)) + Using cached bagit_profile-1.3.1-py3-none-any.whl.metadata (3.2 kB) +Collecting bcrypt==4.3.0 (from -r requirements.txt (line 25)) + Using cached bcrypt-4.3.0-cp39-abi3-manylinux_2_28_x86_64.whl.metadata (10 kB) +Collecting bdbag==1.7.3 (from -r requirements.txt (line 26)) + Using cached bdbag-1.7.3-py2.py3-none-any.whl.metadata (7.8 kB) +Collecting beaker==1.13.0 (from -r requirements.txt (line 27)) + Using cached Beaker-1.13.0-py3-none-any.whl +Collecting billiard==4.2.1 (from -r requirements.txt (line 28)) + Using cached billiard-4.2.1-py3-none-any.whl.metadata (4.4 kB) +Collecting bioblend==1.5.0 (from -r requirements.txt (line 29)) + Using cached bioblend-1.5.0-py3-none-any.whl.metadata (2.3 kB) +Collecting bleach==6.2.0 (from -r requirements.txt (line 30)) + Using cached bleach-6.2.0-py3-none-any.whl.metadata (30 kB) +Collecting boltons==25.0.0 (from -r requirements.txt (line 31)) + Using cached boltons-25.0.0-py3-none-any.whl.metadata (6.5 kB) +Collecting boto==2.49.0 (from -r requirements.txt (line 32)) + Using cached boto-2.49.0-py2.py3-none-any.whl.metadata (7.3 kB) +Collecting botocore==1.37.1 (from -r requirements.txt (line 33)) + Using cached botocore-1.37.1-py3-none-any.whl.metadata (5.7 kB) +Collecting bx-python==0.13.0 (from -r requirements.txt (line 34)) + Using cached bx_python-0.13.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.1 kB) +Collecting cachecontrol==0.14.2 (from -r requirements.txt (line 35)) + Using cached cachecontrol-0.14.2-py3-none-any.whl.metadata (3.1 kB) +Collecting celery==5.5.2 (from -r requirements.txt (line 36)) + Using cached celery-5.5.2-py3-none-any.whl.metadata (22 kB) +Collecting certifi==2025.4.26 (from -r requirements.txt (line 37)) + Using cached certifi-2025.4.26-py3-none-any.whl.metadata (2.5 kB) +Collecting cffi==1.17.1 (from -r requirements.txt (line 38)) + Using cached cffi-1.17.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.5 kB) +Collecting charset-normalizer==3.4.1 (from -r requirements.txt (line 39)) + Using cached charset_normalizer-3.4.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB) +Collecting circus==0.19.0 (from -r requirements.txt (line 40)) + Using cached circus-0.19.0-py3-none-any.whl.metadata (2.1 kB) +Collecting click==8.1.8 (from -r requirements.txt (line 41)) + Using cached click-8.1.8-py3-none-any.whl.metadata (2.3 kB) +Collecting click-didyoumean==0.3.1 (from -r requirements.txt (line 42)) + Using cached click_didyoumean-0.3.1-py3-none-any.whl.metadata (3.9 kB) +Collecting click-plugins==1.1.1 (from -r requirements.txt (line 43)) + Using cached click_plugins-1.1.1-py2.py3-none-any.whl.metadata (6.4 kB) +Collecting click-repl==0.3.0 (from -r requirements.txt (line 44)) + Using cached click_repl-0.3.0-py3-none-any.whl.metadata (3.6 kB) +Collecting cloudauthz==0.6.0 (from -r requirements.txt (line 45)) + Using cached cloudauthz-0.6.0-py2.py3-none-any.whl.metadata (2.9 kB) +Collecting cloudbridge==3.2.0 (from -r requirements.txt (line 46)) + Using cached cloudbridge-3.2.0-py2.py3-none-any.whl.metadata (5.0 kB) +Collecting coloredlogs==15.0.1 (from -r requirements.txt (line 48)) + Using cached coloredlogs-15.0.1-py2.py3-none-any.whl.metadata (12 kB) +Collecting conda-package-streaming==0.11.0 (from -r requirements.txt (line 49)) + Using cached conda_package_streaming-0.11.0-py3-none-any.whl.metadata (4.5 kB) +Collecting cryptography==44.0.2 (from -r requirements.txt (line 50)) + Using cached cryptography-44.0.2-cp39-abi3-manylinux_2_28_x86_64.whl.metadata (5.7 kB) +Collecting ct3==3.4.0 (from -r requirements.txt (line 51)) + Using cached CT3-3.4.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (3.4 kB) +Collecting cwl-upgrader==1.2.12 (from -r requirements.txt (line 52)) + Using cached cwl_upgrader-1.2.12-py3-none-any.whl.metadata (2.7 kB) +Collecting cwl-utils==0.37 (from -r requirements.txt (line 53)) + Using cached cwl_utils-0.37-py3-none-any.whl.metadata (8.2 kB) +Collecting cwltool==3.1.20250110105449 (from -r requirements.txt (line 54)) + Using cached cwltool-3.1.20250110105449-py3-none-any.whl.metadata (41 kB) +Collecting defusedxml==0.7.1 (from -r requirements.txt (line 55)) + Using cached defusedxml-0.7.1-py2.py3-none-any.whl.metadata (32 kB) +Collecting deprecated==1.2.18 (from -r requirements.txt (line 56)) + Using cached Deprecated-1.2.18-py2.py3-none-any.whl.metadata (5.7 kB) +Collecting deprecation==2.1.0 (from -r requirements.txt (line 57)) + Using cached deprecation-2.1.0-py2.py3-none-any.whl.metadata (4.6 kB) +Collecting dictobj==0.4 (from -r requirements.txt (line 58)) + Using cached dictobj-0.4-py3-none-any.whl +Collecting dnspython==2.7.0 (from -r requirements.txt (line 59)) + Using cached dnspython-2.7.0-py3-none-any.whl.metadata (5.8 kB) +Collecting docopt==0.6.2 (from -r requirements.txt (line 60)) + Using cached https://wheels.galaxyproject.org/simple/docopt/docopt-0.6.2-py2.py3-none-any.whl (19 kB) +Collecting docutils==0.21.2 (from -r requirements.txt (line 61)) + Using cached docutils-0.21.2-py3-none-any.whl.metadata (2.8 kB) +Collecting dparse==0.6.4 (from -r requirements.txt (line 62)) + Using cached dparse-0.6.4-py3-none-any.whl.metadata (5.5 kB) +Collecting edam-ontology==1.25.2 (from -r requirements.txt (line 63)) + Using cached edam_ontology-1.25.2-py2.py3-none-any.whl.metadata (2.4 kB) +Collecting email-validator==2.2.0 (from -r requirements.txt (line 64)) + Using cached email_validator-2.2.0-py3-none-any.whl.metadata (25 kB) +Collecting exceptiongroup==1.2.2 (from -r requirements.txt (line 65)) + Using cached exceptiongroup-1.2.2-py3-none-any.whl.metadata (6.6 kB) +Collecting fastapi-slim==0.115.12 (from -r requirements.txt (line 66)) + Using cached fastapi_slim-0.115.12-py3-none-any.whl.metadata (27 kB) +Collecting filelock==3.18.0 (from -r requirements.txt (line 67)) + Using cached filelock-3.18.0-py3-none-any.whl.metadata (2.9 kB) +Collecting fissix==24.4.24 (from -r requirements.txt (line 68)) + Using cached fissix-24.4.24-py3-none-any.whl.metadata (2.1 kB) +Collecting frozenlist==1.6.0 (from -r requirements.txt (line 69)) + Using cached frozenlist-1.6.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (16 kB) +Collecting fs==2.4.16 (from -r requirements.txt (line 70)) + Using cached fs-2.4.16-py2.py3-none-any.whl.metadata (6.3 kB) +Collecting fsspec==2025.3.2 (from -r requirements.txt (line 71)) + Using cached fsspec-2025.3.2-py3-none-any.whl.metadata (11 kB) +Collecting future==1.0.0 (from -r requirements.txt (line 72)) + Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB) +Collecting gravity==1.1.1 (from -r requirements.txt (line 73)) + Using cached gravity-1.1.1-py3-none-any.whl.metadata (15 kB) +Collecting greenlet==3.2.1 (from -r requirements.txt (line 74)) + Using cached greenlet-3.2.1-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (4.1 kB) +Collecting gunicorn==23.0.0 (from -r requirements.txt (line 75)) + Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB) +Collecting gxformat2==0.20.0 (from -r requirements.txt (line 76)) + Using cached gxformat2-0.20.0-py2.py3-none-any.whl.metadata (13 kB) +Collecting h11==0.16.0 (from -r requirements.txt (line 77)) + Using cached h11-0.16.0-py3-none-any.whl.metadata (8.3 kB) +Collecting httpcore==1.0.9 (from -r requirements.txt (line 78)) + Using cached httpcore-1.0.9-py3-none-any.whl.metadata (21 kB) +Collecting httpx==0.28.1 (from -r requirements.txt (line 79)) + Using cached httpx-0.28.1-py3-none-any.whl.metadata (7.1 kB) +Collecting h5grove==2.3.0 (from -r requirements.txt (line 80)) + Using cached h5grove-2.3.0-py3-none-any.whl.metadata (3.6 kB) +Collecting h5py==3.13.0 (from -r requirements.txt (line 81)) + Using cached h5py-3.13.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) +Collecting humanfriendly==10.0 (from -r requirements.txt (line 82)) + Using cached humanfriendly-10.0-py2.py3-none-any.whl.metadata (9.2 kB) +Collecting idna==3.10 (from -r requirements.txt (line 83)) + Using cached idna-3.10-py3-none-any.whl.metadata (10 kB) +Collecting importlib-metadata==8.6.1 (from -r requirements.txt (line 84)) + Using cached importlib_metadata-8.6.1-py3-none-any.whl.metadata (4.7 kB) +Collecting importlib-resources==6.5.2 (from -r requirements.txt (line 85)) + Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB) +Collecting isa-rwval==0.10.11 (from -r requirements.txt (line 86)) + Using cached isa_rwval-0.10.11-py3-none-any.whl.metadata (5.0 kB) +Collecting isal==1.7.2 (from -r requirements.txt (line 87)) + Using cached isal-1.7.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB) +Collecting isodate==0.7.2 (from -r requirements.txt (line 88)) + Using cached isodate-0.7.2-py3-none-any.whl.metadata (11 kB) +Collecting jinja2==3.1.6 (from -r requirements.txt (line 89)) + Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB) +Collecting jmespath==1.0.1 (from -r requirements.txt (line 90)) + Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB) +Collecting jsonref==1.1.0 (from -r requirements.txt (line 91)) + Using cached jsonref-1.1.0-py3-none-any.whl.metadata (2.7 kB) +Collecting jsonschema==4.23.0 (from -r requirements.txt (line 92)) + Using cached jsonschema-4.23.0-py3-none-any.whl.metadata (7.9 kB) +Collecting jsonschema-specifications==2025.4.1 (from -r requirements.txt (line 93)) + Using cached jsonschema_specifications-2025.4.1-py3-none-any.whl.metadata (2.9 kB) +Collecting kombu==5.5.3 (from -r requirements.txt (line 94)) + Using cached kombu-5.5.3-py3-none-any.whl.metadata (3.5 kB) +Collecting lagom==2.7.5 (from -r requirements.txt (line 95)) + Using cached lagom-2.7.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.7 kB) +Collecting limits==4.2 (from -r requirements.txt (line 97)) + Using cached limits-4.2-py3-none-any.whl.metadata (10 kB) +Collecting lxml==5.4.0 (from -r requirements.txt (line 99)) + Using cached lxml-5.4.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (3.5 kB) +Collecting mako==1.3.10 (from -r requirements.txt (line 100)) + Using cached mako-1.3.10-py3-none-any.whl.metadata (2.9 kB) +Collecting markdown==3.8 (from -r requirements.txt (line 101)) + Using cached markdown-3.8-py3-none-any.whl.metadata (5.1 kB) +Collecting markdown-it-py==3.0.0 (from -r requirements.txt (line 102)) + Using cached markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB) +Collecting markupsafe==3.0.2 (from -r requirements.txt (line 103)) + Using cached MarkupSafe-3.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB) +Collecting mdurl==0.1.2 (from -r requirements.txt (line 104)) + Using cached mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB) +Collecting mercurial==7.0.1 (from -r requirements.txt (line 105)) + Using cached mercurial-7.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl.metadata (2.2 kB) +Collecting mistune==3.0.2 (from -r requirements.txt (line 106)) + Using cached mistune-3.0.2-py3-none-any.whl.metadata (1.7 kB) +Collecting mrcfile==1.5.4 (from -r requirements.txt (line 107)) + Using cached mrcfile-1.5.4-py2.py3-none-any.whl.metadata (7.0 kB) +Collecting msal==1.32.3 (from -r requirements.txt (line 108)) + Using cached msal-1.32.3-py3-none-any.whl.metadata (11 kB) +Collecting msgpack==1.1.0 (from -r requirements.txt (line 109)) + Using cached msgpack-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB) +Collecting multidict==6.4.3 (from -r requirements.txt (line 110)) + Using cached multidict-6.4.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) +Collecting mypy-extensions==1.1.0 (from -r requirements.txt (line 111)) + Using cached mypy_extensions-1.1.0-py3-none-any.whl.metadata (1.1 kB) +Collecting networkx==3.2.1 (from -r requirements.txt (line 112)) + Using cached networkx-3.2.1-py3-none-any.whl.metadata (5.2 kB) +Collecting nodeenv==1.9.1 (from -r requirements.txt (line 114)) + Using cached nodeenv-1.9.1-py2.py3-none-any.whl.metadata (21 kB) +Collecting numpy==2.0.2 (from -r requirements.txt (line 115)) + Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB) +Collecting oauthlib==3.2.2 (from -r requirements.txt (line 117)) + Using cached oauthlib-3.2.2-py3-none-any.whl.metadata (7.5 kB) +Collecting orjson==3.10.16 (from -r requirements.txt (line 118)) + Using cached orjson-3.10.16-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (41 kB) +Collecting oyaml==1.0 (from -r requirements.txt (line 119)) + Using cached oyaml-1.0-py2.py3-none-any.whl.metadata (1.2 kB) +Collecting packaging==24.2 (from -r requirements.txt (line 120)) + Using cached packaging-24.2-py3-none-any.whl.metadata (3.2 kB) +Collecting paramiko==3.5.1 (from -r requirements.txt (line 122)) + Using cached paramiko-3.5.1-py3-none-any.whl.metadata (4.6 kB) +Collecting parsley==1.3 (from -r requirements.txt (line 123)) + Using cached Parsley-1.3-py2.py3-none-any.whl.metadata (4.1 kB) +Collecting paste==3.10.1 (from -r requirements.txt (line 124)) + Using cached Paste-3.10.1-py3-none-any.whl.metadata (5.3 kB) +Collecting pastedeploy==3.1.0 (from -r requirements.txt (line 125)) + Using cached PasteDeploy-3.1.0-py3-none-any.whl.metadata (2.7 kB) +Collecting pebble==5.1.1 (from -r requirements.txt (line 126)) + Using cached pebble-5.1.1-py3-none-any.whl.metadata (3.8 kB) +Collecting pillow==11.2.1 (from -r requirements.txt (line 127)) + Using cached pillow-11.2.1-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (8.9 kB) +Collecting prompt-toolkit==3.0.51 (from -r requirements.txt (line 128)) + Using cached prompt_toolkit-3.0.51-py3-none-any.whl.metadata (6.4 kB) +Collecting propcache==0.3.1 (from -r requirements.txt (line 129)) + Using cached propcache-0.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (10 kB) +Collecting prov==1.5.1 (from -r requirements.txt (line 130)) + Using cached prov-1.5.1-py2.py3-none-any.whl.metadata (7.9 kB) +Collecting psutil==7.0.0 (from -r requirements.txt (line 131)) + Using cached psutil-7.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (22 kB) +Collecting pulsar-galaxy-lib==0.15.8 (from -r requirements.txt (line 132)) + Using cached pulsar_galaxy_lib-0.15.8-py3-none-any.whl.metadata (37 kB) +Collecting pycparser==2.22 (from -r requirements.txt (line 133)) + Using cached pycparser-2.22-py3-none-any.whl.metadata (943 bytes) +Collecting pycryptodome==3.22.0 (from -r requirements.txt (line 134)) + Using cached pycryptodome-3.22.0-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.4 kB) +Collecting pydantic==2.11.3 (from -r requirements.txt (line 135)) + Using cached pydantic-2.11.3-py3-none-any.whl.metadata (65 kB) +Collecting pydantic-core==2.33.1 (from -r requirements.txt (line 136)) + Using cached pydantic_core-2.33.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.8 kB) +Collecting pydantic-tes==0.2.0 (from -r requirements.txt (line 137)) + Using cached pydantic_tes-0.2.0-py2.py3-none-any.whl.metadata (3.1 kB) +Collecting pydot==2.0.0 (from -r requirements.txt (line 138)) + Using cached pydot-2.0.0-py3-none-any.whl.metadata (9.6 kB) +Collecting pyeventsystem==0.1.0 (from -r requirements.txt (line 139)) + Using cached pyeventsystem-0.1.0-py2.py3-none-any.whl.metadata (3.2 kB) +Collecting pyfaidx==0.8.1.3 (from -r requirements.txt (line 140)) + Using cached pyfaidx-0.8.1.3-py3-none-any.whl.metadata (25 kB) +Collecting pygments==2.19.1 (from -r requirements.txt (line 141)) + Using cached pygments-2.19.1-py3-none-any.whl.metadata (2.5 kB) +Collecting pyjwt==2.10.1 (from -r requirements.txt (line 142)) + Using cached PyJWT-2.10.1-py3-none-any.whl.metadata (4.0 kB) +Collecting pykwalify==1.8.0 (from -r requirements.txt (line 143)) + Using cached pykwalify-1.8.0-py2.py3-none-any.whl.metadata (5.3 kB) +Collecting pylibmagic==0.5.0 (from -r requirements.txt (line 144)) + Using cached pylibmagic-0.5.0-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.5 kB) +Collecting pynacl==1.5.0 (from -r requirements.txt (line 145)) + Using cached PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl.metadata (8.6 kB) +Collecting pyparsing==3.2.3 (from -r requirements.txt (line 146)) + Using cached pyparsing-3.2.3-py3-none-any.whl.metadata (5.0 kB) +Collecting pypng==0.20220715.0 (from -r requirements.txt (line 147)) + Using cached pypng-0.20220715.0-py3-none-any.whl.metadata (13 kB) +Collecting pysam==0.23.0 (from -r requirements.txt (line 149)) + Using cached pysam-0.23.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (1.6 kB) +Collecting python-dateutil==2.9.0.post0 (from -r requirements.txt (line 150)) + Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) +Collecting python-magic==0.4.27 (from -r requirements.txt (line 151)) + Using cached python_magic-0.4.27-py2.py3-none-any.whl.metadata (5.8 kB) +Collecting python-multipart==0.0.20 (from -r requirements.txt (line 152)) + Using cached python_multipart-0.0.20-py3-none-any.whl.metadata (1.8 kB) +Collecting python-slugify==8.0.4 (from -r requirements.txt (line 153)) + Using cached python_slugify-8.0.4-py2.py3-none-any.whl.metadata (8.5 kB) +Collecting python3-openid==3.2.0 (from -r requirements.txt (line 154)) + Using cached python3_openid-3.2.0-py3-none-any.whl.metadata (1.6 kB) +Collecting pytz==2025.2 (from -r requirements.txt (line 155)) + Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB) +Collecting pyyaml==6.0.2 (from -r requirements.txt (line 156)) + Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB) +Collecting pyzmq==26.4.0 (from -r requirements.txt (line 157)) + Using cached pyzmq-26.4.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.0 kB) +Collecting rdflib==7.1.4 (from -r requirements.txt (line 158)) + Using cached rdflib-7.1.4-py3-none-any.whl.metadata (11 kB) +Collecting referencing==0.36.2 (from -r requirements.txt (line 159)) + Using cached referencing-0.36.2-py3-none-any.whl.metadata (2.8 kB) +Collecting refgenconf==0.12.2 (from -r requirements.txt (line 160)) + Using cached refgenconf-0.12.2-py3-none-any.whl.metadata (1.5 kB) +Collecting regex==2024.11.6 (from -r requirements.txt (line 161)) + Using cached regex-2024.11.6-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (40 kB) +Collecting repoze-lru==0.7 (from -r requirements.txt (line 162)) + Using cached repoze.lru-0.7-py3-none-any.whl.metadata (1.1 kB) +Collecting requests==2.32.3 (from -r requirements.txt (line 163)) + Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB) +Collecting requests-oauthlib==2.0.0 (from -r requirements.txt (line 164)) + Using cached requests_oauthlib-2.0.0-py2.py3-none-any.whl.metadata (11 kB) +Collecting requests-toolbelt==1.0.0 (from -r requirements.txt (line 165)) + Using cached requests_toolbelt-1.0.0-py2.py3-none-any.whl.metadata (14 kB) +Collecting requests-unixsocket==0.4.1 (from -r requirements.txt (line 166)) + Using cached requests_unixsocket-0.4.1-py3-none-any.whl.metadata (3.8 kB) +Collecting rich==13.9.4 (from -r requirements.txt (line 167)) + Using cached rich-13.9.4-py3-none-any.whl.metadata (18 kB) +Collecting rich-argparse==1.7.0 (from -r requirements.txt (line 168)) + Using cached rich_argparse-1.7.0-py3-none-any.whl.metadata (14 kB) +Collecting rocrate==0.13.0 (from -r requirements.txt (line 169)) + Using cached rocrate-0.13.0-py3-none-any.whl.metadata (18 kB) +Collecting routes==2.5.1 (from -r requirements.txt (line 170)) + Using cached Routes-2.5.1-py2.py3-none-any.whl.metadata (25 kB) +Collecting rpds-py==0.24.0 (from -r requirements.txt (line 171)) + Using cached rpds_py-0.24.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.1 kB) +Collecting ruamel-yaml==0.18.10 (from -r requirements.txt (line 172)) + Using cached ruamel.yaml-0.18.10-py3-none-any.whl.metadata (23 kB) +Collecting ruamel-yaml-clib==0.2.12 (from -r requirements.txt (line 173)) + Using cached ruamel.yaml.clib-0.2.12-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.7 kB) +Collecting s3fs==2025.3.2 (from -r requirements.txt (line 174)) + Using cached s3fs-2025.3.2-py3-none-any.whl.metadata (1.9 kB) +Collecting schema-salad==8.9.20250408123006 (from -r requirements.txt (line 175)) + Using cached schema_salad-8.9.20250408123006-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl.metadata (17 kB) +Collecting setuptools==79.0.1 (from -r requirements.txt (line 176)) + Using cached setuptools-79.0.1-py3-none-any.whl.metadata (6.5 kB) +Collecting setuptools-scm==5.0.2 (from -r requirements.txt (line 177)) + Using cached setuptools_scm-5.0.2-py2.py3-none-any.whl.metadata (21 kB) +Collecting six==1.17.0 (from -r requirements.txt (line 178)) + Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB) +Collecting slowapi==0.1.9 (from -r requirements.txt (line 179)) + Using cached slowapi-0.1.9-py3-none-any.whl.metadata (3.0 kB) +Collecting sniffio==1.3.1 (from -r requirements.txt (line 180)) + Using cached sniffio-1.3.1-py3-none-any.whl.metadata (3.9 kB) +Collecting social-auth-core==4.6.0 (from -r requirements.txt (line 181)) + Using cached social_auth_core-4.6.0-py3-none-any.whl.metadata (4.1 kB) +Collecting sortedcontainers==2.4.0 (from -r requirements.txt (line 182)) + Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl.metadata (10 kB) +Collecting spython==0.3.14 (from -r requirements.txt (line 183)) + Using cached spython-0.3.14-py3-none-any.whl.metadata (8.6 kB) +Collecting sqlalchemy==2.0.40 (from -r requirements.txt (line 184)) + Using cached sqlalchemy-2.0.40-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.6 kB) +Collecting sqlitedict==2.1.0 (from -r requirements.txt (line 185)) + Using cached sqlitedict-2.1.0-py3-none-any.whl +Collecting sqlparse==0.5.3 (from -r requirements.txt (line 186)) + Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB) +Collecting starlette==0.46.2 (from -r requirements.txt (line 187)) + Using cached starlette-0.46.2-py3-none-any.whl.metadata (6.2 kB) +Collecting starlette-context==0.4.0 (from -r requirements.txt (line 188)) + Using cached starlette_context-0.4.0-py3-none-any.whl.metadata (4.1 kB) +Collecting supervisor==4.2.5 (from -r requirements.txt (line 189)) + Using cached supervisor-4.2.5-py2.py3-none-any.whl.metadata (86 kB) +Collecting svgwrite==1.4.3 (from -r requirements.txt (line 190)) + Using cached svgwrite-1.4.3-py3-none-any.whl.metadata (8.8 kB) +Collecting tenacity==9.1.2 (from -r requirements.txt (line 191)) + Using cached tenacity-9.1.2-py3-none-any.whl.metadata (1.2 kB) +Collecting text-unidecode==1.3 (from -r requirements.txt (line 192)) + Using cached text_unidecode-1.3-py2.py3-none-any.whl.metadata (2.4 kB) +Collecting tifffile==2024.8.30 (from -r requirements.txt (line 193)) + Using cached tifffile-2024.8.30-py3-none-any.whl.metadata (31 kB) +Collecting tinydb==4.8.2 (from -r requirements.txt (line 195)) + Using cached tinydb-4.8.2-py3-none-any.whl.metadata (6.7 kB) +Collecting tomli==2.2.1 (from -r requirements.txt (line 196)) + Using cached tomli-2.2.1-py3-none-any.whl.metadata (10 kB) +Collecting tornado==6.4.2 (from -r requirements.txt (line 197)) + Using cached tornado-6.4.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) +Collecting tqdm==4.67.1 (from -r requirements.txt (line 198)) + Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB) +Collecting tuspy==1.1.0 (from -r requirements.txt (line 199)) + Using cached tuspy-1.1.0-py3-none-any.whl.metadata (4.2 kB) +Collecting tuswsgi==0.5.5 (from -r requirements.txt (line 200)) + Using cached tuswsgi-0.5.5-py2.py3-none-any.whl.metadata (2.2 kB) +Collecting typing-extensions==4.13.2 (from -r requirements.txt (line 201)) + Using cached typing_extensions-4.13.2-py3-none-any.whl.metadata (3.0 kB) +Collecting typing-inspection==0.4.0 (from -r requirements.txt (line 202)) + Using cached typing_inspection-0.4.0-py3-none-any.whl.metadata (2.6 kB) +Collecting tzdata==2025.2 (from -r requirements.txt (line 203)) + Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB) +Collecting tzlocal==5.3.1 (from -r requirements.txt (line 204)) + Using cached tzlocal-5.3.1-py3-none-any.whl.metadata (7.6 kB) +Collecting ubiquerg==0.8.1 (from -r requirements.txt (line 205)) + Using cached ubiquerg-0.8.1-py2.py3-none-any.whl.metadata (2.0 kB) +Collecting urllib3==1.26.20 (from -r requirements.txt (line 206)) + Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB) +Collecting uvicorn==0.34.2 (from -r requirements.txt (line 208)) + Using cached uvicorn-0.34.2-py3-none-any.whl.metadata (6.5 kB) +Collecting uvloop==0.21.0 (from -r requirements.txt (line 209)) + Using cached uvloop-0.21.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.9 kB) +Collecting vine==5.1.0 (from -r requirements.txt (line 210)) + Using cached vine-5.1.0-py3-none-any.whl.metadata (2.7 kB) +Collecting wcwidth==0.2.13 (from -r requirements.txt (line 211)) + Using cached wcwidth-0.2.13-py2.py3-none-any.whl.metadata (14 kB) +Collecting webencodings==0.5.1 (from -r requirements.txt (line 212)) + Using cached webencodings-0.5.1-py2.py3-none-any.whl.metadata (2.1 kB) +Collecting webob==1.8.9 (from -r requirements.txt (line 213)) + Using cached WebOb-1.8.9-py2.py3-none-any.whl.metadata (11 kB) +Collecting whoosh==2.7.4 (from -r requirements.txt (line 214)) + Using cached Whoosh-2.7.4-py2.py3-none-any.whl.metadata (3.1 kB) +Collecting wrapt==1.17.2 (from -r requirements.txt (line 215)) + Using cached wrapt-1.17.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.4 kB) +Collecting yacman==0.9.3 (from -r requirements.txt (line 216)) + Using cached yacman-0.9.3-py3-none-any.whl.metadata (5.3 kB) +Collecting yarl==1.20.0 (from -r requirements.txt (line 217)) + Using cached yarl-1.20.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (72 kB) +Collecting zipp==3.21.0 (from -r requirements.txt (line 218)) + Using cached zipp-3.21.0-py3-none-any.whl.metadata (3.7 kB) +Collecting zipstream-new==1.1.8 (from -r requirements.txt (line 219)) + Using cached zipstream_new-1.1.8-py3-none-any.whl.metadata (5.3 kB) +Collecting zstandard==0.23.0 (from -r requirements.txt (line 220)) + Using cached zstandard-0.23.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB) +Using cached a2wsgi-1.10.8-py3-none-any.whl (17 kB) +Using cached adal-1.2.7-py2.py3-none-any.whl (55 kB) +Using cached PyJWT-2.10.1-py3-none-any.whl (22 kB) +Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) +Using cached requests-2.32.3-py3-none-any.whl (64 kB) +Using cached charset_normalizer-3.4.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (146 kB) +Using cached idna-3.10-py3-none-any.whl (70 kB) +Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB) +Using cached aiobotocore-2.21.1-py3-none-any.whl (78 kB) +Using cached aiohttp-3.11.18-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.6 MB) +Using cached aioitertools-0.12.0-py3-none-any.whl (24 kB) +Using cached async_timeout-5.0.1-py3-none-any.whl (6.2 kB) +Using cached botocore-1.37.1-py3-none-any.whl (13.4 MB) +Using cached jmespath-1.0.1-py3-none-any.whl (20 kB) +Using cached multidict-6.4.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (216 kB) +Using cached wrapt-1.17.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (82 kB) +Using cached yarl-1.20.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (335 kB) +Using cached aiofiles-24.1.0-py3-none-any.whl (15 kB) +Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB) +Using cached aiosignal-1.3.2-py2.py3-none-any.whl (7.6 kB) +Using cached alembic-1.15.2-py3-none-any.whl (231 kB) +Using cached amqp-5.3.1-py3-none-any.whl (50 kB) +Using cached vine-5.1.0-py3-none-any.whl (9.6 kB) +Using cached annotated_types-0.7.0-py3-none-any.whl (13 kB) +Using cached anyio-4.9.0-py3-none-any.whl (100 kB) +Using cached apispec-6.8.1-py3-none-any.whl (30 kB) +Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB) +Using cached arcp-0.2.1-py2.py3-none-any.whl (15 kB) +Using cached argcomplete-3.6.2-py3-none-any.whl (43 kB) +Using cached attmap-0.13.2-py3-none-any.whl (12 kB) +Using cached attrs-25.3.0-py3-none-any.whl (63 kB) +Using cached babel-2.17.0-py3-none-any.whl (10.2 MB) +Using cached bagit-1.8.1-py2.py3-none-any.whl (35 kB) +Using cached bagit_profile-1.3.1-py3-none-any.whl (14 kB) +Using cached bcrypt-4.3.0-cp39-abi3-manylinux_2_28_x86_64.whl (284 kB) +Using cached bdbag-1.7.3-py2.py3-none-any.whl (75 kB) +Using cached setuptools_scm-5.0.2-py2.py3-none-any.whl (29 kB) +Using cached billiard-4.2.1-py3-none-any.whl (86 kB) +Using cached bioblend-1.5.0-py3-none-any.whl (160 kB) +Using cached bleach-6.2.0-py3-none-any.whl (163 kB) +Using cached boltons-25.0.0-py3-none-any.whl (194 kB) +Using cached boto-2.49.0-py2.py3-none-any.whl (1.4 MB) +Using cached bx_python-0.13.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.5 MB) +Using cached cachecontrol-0.14.2-py3-none-any.whl (21 kB) +Using cached msgpack-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (377 kB) +Using cached celery-5.5.2-py3-none-any.whl (438 kB) +Using cached click-8.1.8-py3-none-any.whl (98 kB) +Using cached kombu-5.5.3-py3-none-any.whl (209 kB) +Using cached certifi-2025.4.26-py3-none-any.whl (159 kB) +Using cached cffi-1.17.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (445 kB) +Using cached circus-0.19.0-py3-none-any.whl (118 kB) +Using cached click_didyoumean-0.3.1-py3-none-any.whl (3.6 kB) +Using cached click_plugins-1.1.1-py2.py3-none-any.whl (7.5 kB) +Using cached click_repl-0.3.0-py3-none-any.whl (10 kB) +Using cached cloudauthz-0.6.0-py2.py3-none-any.whl (8.9 kB) +Using cached cloudbridge-3.2.0-py2.py3-none-any.whl (193 kB) +Using cached pyeventsystem-0.1.0-py2.py3-none-any.whl (15 kB) +Using cached coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB) +Using cached conda_package_streaming-0.11.0-py3-none-any.whl (17 kB) +Using cached cryptography-44.0.2-cp39-abi3-manylinux_2_28_x86_64.whl (4.2 MB) +Using cached CT3-3.4.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (671 kB) +Using cached cwl_upgrader-1.2.12-py3-none-any.whl (27 kB) +Using cached ruamel.yaml-0.18.10-py3-none-any.whl (117 kB) +Using cached cwl_utils-0.37-py3-none-any.whl (427 kB) +Using cached schema_salad-8.9.20250408123006-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl (1.6 MB) +Using cached mistune-3.0.2-py3-none-any.whl (47 kB) +Using cached rdflib-7.1.4-py3-none-any.whl (565 kB) +Using cached isodate-0.7.2-py3-none-any.whl (22 kB) +Using cached pyparsing-3.2.3-py3-none-any.whl (111 kB) +Using cached cwltool-3.1.20250110105449-py3-none-any.whl (1.7 MB) +Using cached pydot-2.0.0-py3-none-any.whl (22 kB) +Using cached defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) +Using cached Deprecated-1.2.18-py2.py3-none-any.whl (10.0 kB) +Using cached deprecation-2.1.0-py2.py3-none-any.whl (11 kB) +Using cached dnspython-2.7.0-py3-none-any.whl (313 kB) +Using cached docutils-0.21.2-py3-none-any.whl (587 kB) +Using cached dparse-0.6.4-py3-none-any.whl (11 kB) +Using cached edam_ontology-1.25.2-py2.py3-none-any.whl (262 kB) +Using cached email_validator-2.2.0-py3-none-any.whl (33 kB) +Using cached exceptiongroup-1.2.2-py3-none-any.whl (16 kB) +Using cached fastapi_slim-0.115.12-py3-none-any.whl (95 kB) +Using cached pydantic-2.11.3-py3-none-any.whl (443 kB) +Using cached starlette-0.46.2-py3-none-any.whl (72 kB) +Using cached filelock-3.18.0-py3-none-any.whl (16 kB) +Using cached fissix-24.4.24-py3-none-any.whl (188 kB) +Using cached frozenlist-1.6.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (288 kB) +Using cached fs-2.4.16-py2.py3-none-any.whl (135 kB) +Using cached six-1.17.0-py2.py3-none-any.whl (11 kB) +Using cached fsspec-2025.3.2-py3-none-any.whl (194 kB) +Using cached future-1.0.0-py3-none-any.whl (491 kB) +Using cached gravity-1.1.1-py3-none-any.whl (47 kB) +Using cached greenlet-3.2.1-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (579 kB) +Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB) +Using cached gxformat2-0.20.0-py2.py3-none-any.whl (60 kB) +Using cached h11-0.16.0-py3-none-any.whl (37 kB) +Using cached httpcore-1.0.9-py3-none-any.whl (78 kB) +Using cached httpx-0.28.1-py3-none-any.whl (73 kB) +Using cached h5grove-2.3.0-py3-none-any.whl (16 kB) +Using cached h5py-3.13.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB) +Using cached humanfriendly-10.0-py2.py3-none-any.whl (86 kB) +Using cached importlib_metadata-8.6.1-py3-none-any.whl (26 kB) +Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB) +Using cached isa_rwval-0.10.11-py3-none-any.whl (112 kB) +Using cached isal-1.7.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (260 kB) +Using cached jinja2-3.1.6-py3-none-any.whl (134 kB) +Using cached jsonref-1.1.0-py3-none-any.whl (9.4 kB) +Using cached jsonschema-4.23.0-py3-none-any.whl (88 kB) +Using cached jsonschema_specifications-2025.4.1-py3-none-any.whl (18 kB) +Using cached lagom-2.7.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (258 kB) +Using cached limits-4.2-py3-none-any.whl (60 kB) +Using cached packaging-24.2-py3-none-any.whl (65 kB) +Using cached lxml-5.4.0-cp39-cp39-manylinux_2_28_x86_64.whl (5.1 MB) +Using cached mako-1.3.10-py3-none-any.whl (78 kB) +Using cached markdown-3.8-py3-none-any.whl (106 kB) +Using cached markdown_it_py-3.0.0-py3-none-any.whl (87 kB) +Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB) +Using cached MarkupSafe-3.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (20 kB) +Using cached mercurial-7.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl (7.4 MB) +Using cached mrcfile-1.5.4-py2.py3-none-any.whl (45 kB) +Using cached msal-1.32.3-py3-none-any.whl (115 kB) +Using cached mypy_extensions-1.1.0-py3-none-any.whl (5.0 kB) +Using cached networkx-3.2.1-py3-none-any.whl (1.6 MB) +Using cached nodeenv-1.9.1-py2.py3-none-any.whl (22 kB) +Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.5 MB) +Using cached oauthlib-3.2.2-py3-none-any.whl (151 kB) +Using cached orjson-3.10.16-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (132 kB) +Using cached oyaml-1.0-py2.py3-none-any.whl (3.0 kB) +Using cached paramiko-3.5.1-py3-none-any.whl (227 kB) +Using cached Parsley-1.3-py2.py3-none-any.whl (88 kB) +Using cached Paste-3.10.1-py3-none-any.whl (289 kB) +Using cached PasteDeploy-3.1.0-py3-none-any.whl (16 kB) +Using cached pebble-5.1.1-py3-none-any.whl (34 kB) +Using cached pillow-11.2.1-cp39-cp39-manylinux_2_28_x86_64.whl (4.6 MB) +Using cached prompt_toolkit-3.0.51-py3-none-any.whl (387 kB) +Using cached propcache-0.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (209 kB) +Using cached prov-1.5.1-py2.py3-none-any.whl (426 kB) +Using cached psutil-7.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (277 kB) +Using cached pulsar_galaxy_lib-0.15.8-py3-none-any.whl (203 kB) +Using cached pycparser-2.22-py3-none-any.whl (117 kB) +Using cached pycryptodome-3.22.0-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.3 MB) +Using cached pydantic_core-2.33.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.0 MB) +Using cached pydantic_tes-0.2.0-py2.py3-none-any.whl (12 kB) +Using cached pyfaidx-0.8.1.3-py3-none-any.whl (28 kB) +Using cached pygments-2.19.1-py3-none-any.whl (1.2 MB) +Using cached pykwalify-1.8.0-py2.py3-none-any.whl (24 kB) +Using cached pylibmagic-0.5.0-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (619 kB) +Using cached PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (856 kB) +Using cached pypng-0.20220715.0-py3-none-any.whl (58 kB) +Using cached pysam-0.23.0-cp39-cp39-manylinux_2_28_x86_64.whl (25.2 MB) +Using cached python_magic-0.4.27-py2.py3-none-any.whl (13 kB) +Using cached python_multipart-0.0.20-py3-none-any.whl (24 kB) +Using cached python_slugify-8.0.4-py2.py3-none-any.whl (10 kB) +Using cached python3_openid-3.2.0-py3-none-any.whl (133 kB) +Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB) +Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (737 kB) +Using cached pyzmq-26.4.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (863 kB) +Using cached referencing-0.36.2-py3-none-any.whl (26 kB) +Using cached refgenconf-0.12.2-py3-none-any.whl (72 kB) +Using cached regex-2024.11.6-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (780 kB) +Using cached repoze.lru-0.7-py3-none-any.whl (10 kB) +Using cached requests_oauthlib-2.0.0-py2.py3-none-any.whl (24 kB) +Using cached requests_toolbelt-1.0.0-py2.py3-none-any.whl (54 kB) +Using cached requests_unixsocket-0.4.1-py3-none-any.whl (11 kB) +Using cached rich-13.9.4-py3-none-any.whl (242 kB) +Using cached typing_extensions-4.13.2-py3-none-any.whl (45 kB) +Using cached rich_argparse-1.7.0-py3-none-any.whl (25 kB) +Using cached rocrate-0.13.0-py3-none-any.whl (332 kB) +Using cached Routes-2.5.1-py2.py3-none-any.whl (40 kB) +Using cached rpds_py-0.24.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (390 kB) +Using cached ruamel.yaml.clib-0.2.12-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (724 kB) +Using cached s3fs-2025.3.2-py3-none-any.whl (30 kB) +Using cached setuptools-79.0.1-py3-none-any.whl (1.3 MB) +Using cached slowapi-0.1.9-py3-none-any.whl (14 kB) +Using cached sniffio-1.3.1-py3-none-any.whl (10 kB) +Using cached social_auth_core-4.6.0-py3-none-any.whl (424 kB) +Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB) +Using cached spython-0.3.14-py3-none-any.whl (109 kB) +Using cached sqlalchemy-2.0.40-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB) +Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB) +Using cached starlette_context-0.4.0-py3-none-any.whl (12 kB) +Using cached supervisor-4.2.5-py2.py3-none-any.whl (319 kB) +Using cached svgwrite-1.4.3-py3-none-any.whl (67 kB) +Using cached tenacity-9.1.2-py3-none-any.whl (28 kB) +Using cached text_unidecode-1.3-py2.py3-none-any.whl (78 kB) +Using cached tifffile-2024.8.30-py3-none-any.whl (227 kB) +Using cached tinydb-4.8.2-py3-none-any.whl (24 kB) +Using cached tomli-2.2.1-py3-none-any.whl (14 kB) +Using cached tornado-6.4.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (437 kB) +Using cached tqdm-4.67.1-py3-none-any.whl (78 kB) +Using cached tuspy-1.1.0-py3-none-any.whl (15 kB) +Using cached tuswsgi-0.5.5-py2.py3-none-any.whl (6.9 kB) +Using cached typing_inspection-0.4.0-py3-none-any.whl (14 kB) +Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB) +Using cached tzlocal-5.3.1-py3-none-any.whl (18 kB) +Using cached ubiquerg-0.8.1-py2.py3-none-any.whl (17 kB) +Using cached uvicorn-0.34.2-py3-none-any.whl (62 kB) +Using cached uvloop-0.21.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.8 MB) +Using cached wcwidth-0.2.13-py2.py3-none-any.whl (34 kB) +Using cached webencodings-0.5.1-py2.py3-none-any.whl (11 kB) +Using cached WebOb-1.8.9-py2.py3-none-any.whl (115 kB) +Using cached Whoosh-2.7.4-py2.py3-none-any.whl (468 kB) +Using cached yacman-0.9.3-py3-none-any.whl (26 kB) +Using cached zipp-3.21.0-py3-none-any.whl (9.6 kB) +Using cached zipstream_new-1.1.8-py3-none-any.whl (20 kB) +Using cached zstandard-0.23.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.4 MB) +Installing collected packages: zipstream-new, whoosh, webencodings, wcwidth, ubiquerg, text-unidecode, sqlitedict, spython, sortedcontainers, repoze-lru, pytz, pypng, pyeventsystem, parsley, edam-ontology, docopt, dictobj, boto, beaker, bagit, arcp, appdirs, zstandard, zipp, wrapt, webob, vine, uvloop, urllib3, tzlocal, tzdata, typing-extensions, tqdm, tornado, tomli, tinydb, tenacity, svgwrite, sqlparse, sniffio, six, setuptools, ruamel-yaml-clib, rpds-py, regex, pyzmq, pyyaml, python-slugify, python-multipart, python-magic, pysam, pyparsing, pylibmagic, pyjwt, pygments, pycryptodome, pycparser, psutil, propcache, prompt-toolkit, pillow, pebble, pastedeploy, packaging, orjson, oauthlib, numpy, nodeenv, networkx, mypy-extensions, msgpack, mistune, mercurial, mdurl, markupsafe, lxml, lagom, jsonref, jmespath, isodate, isal, idna, humanfriendly, h11, greenlet, future, fsspec, frozenlist, fissix, filelock, exceptiongroup, docutils, dnspython, defusedxml, ct3, click, charset-normalizer, certifi, boltons, bleach, billiard, bcrypt, babel, attrs, attmap, async-timeout, argcomplete, annotated-types, aiohappyeyeballs, aiofiles, uvicorn, typing-inspection, tuswsgi, tifffile, supervisor, sqlalchemy, setuptools-scm, ruamel-yaml, routes, requests, referencing, rdflib, python3-openid, python-dateutil, pydot, pydantic-core, paste, oyaml, multidict, mrcfile, markdown-it-py, mako, jinja2, isa-rwval, importlib-resources, importlib-metadata, httpcore, h5py, gunicorn, fs, email-validator, dparse, deprecation, deprecated, coloredlogs, click-repl, click-plugins, click-didyoumean, circus, cffi, bx-python, apispec, anyio, amqp, aiosignal, aioitertools, a2wsgi, yarl, starlette, rocrate, rich, requests-unixsocket, requests-toolbelt, requests-oauthlib, pynacl, pykwalify, pyfaidx, pydantic, prov, markdown, limits, kombu, jsonschema-specifications, httpx, h5grove, cryptography, conda-package-streaming, cloudbridge, cachecontrol, botocore, bagit-profile, alembic, starlette-context, social-auth-core, slowapi, rich-argparse, pydantic-tes, paramiko, jsonschema, gravity, fastapi-slim, celery, bdbag, aiohttp, adal, yacman, tuspy, schema-salad, msal, cloudauthz, aiobotocore, s3fs, refgenconf, pulsar-galaxy-lib, cwl-upgrader, bioblend, gxformat2, cwl-utils, cwltool + Attempting uninstall: setuptools + Found existing installation: setuptools 80.9.0 + Uninstalling setuptools-80.9.0: + Successfully uninstalled setuptools-80.9.0 + +Successfully installed a2wsgi-1.10.8 adal-1.2.7 aiobotocore-2.21.1 aiofiles-24.1.0 aiohappyeyeballs-2.6.1 aiohttp-3.11.18 aioitertools-0.12.0 aiosignal-1.3.2 alembic-1.15.2 amqp-5.3.1 annotated-types-0.7.0 anyio-4.9.0 apispec-6.8.1 appdirs-1.4.4 arcp-0.2.1 argcomplete-3.6.2 async-timeout-5.0.1 attmap-0.13.2 attrs-25.3.0 babel-2.17.0 bagit-1.8.1 bagit-profile-1.3.1 bcrypt-4.3.0 bdbag-1.7.3 beaker-1.13.0 billiard-4.2.1 bioblend-1.5.0 bleach-6.2.0 boltons-25.0.0 boto-2.49.0 botocore-1.37.1 bx-python-0.13.0 cachecontrol-0.14.2 celery-5.5.2 certifi-2025.4.26 cffi-1.17.1 charset-normalizer-3.4.1 circus-0.19.0 click-8.1.8 click-didyoumean-0.3.1 click-plugins-1.1.1 click-repl-0.3.0 cloudauthz-0.6.0 cloudbridge-3.2.0 coloredlogs-15.0.1 conda-package-streaming-0.11.0 cryptography-44.0.2 ct3-3.4.0 cwl-upgrader-1.2.12 cwl-utils-0.37 cwltool-3.1.20250110105449 defusedxml-0.7.1 deprecated-1.2.18 deprecation-2.1.0 dictobj-0.4 dnspython-2.7.0 docopt-0.6.2 docutils-0.21.2 dparse-0.6.4 edam-ontology-1.25.2 email-validator-2.2.0 exceptiongroup-1.2.2 fastapi-slim-0.115.12 filelock-3.18.0 fissix-24.4.24 frozenlist-1.6.0 fs-2.4.16 fsspec-2025.3.2 future-1.0.0 gravity-1.1.1 greenlet-3.2.1 gunicorn-23.0.0 gxformat2-0.20.0 h11-0.16.0 h5grove-2.3.0 h5py-3.13.0 httpcore-1.0.9 httpx-0.28.1 humanfriendly-10.0 idna-3.10 importlib-metadata-8.6.1 importlib-resources-6.5.2 isa-rwval-0.10.11 isal-1.7.2 isodate-0.7.2 jinja2-3.1.6 jmespath-1.0.1 jsonref-1.1.0 jsonschema-4.23.0 jsonschema-specifications-2025.4.1 kombu-5.5.3 lagom-2.7.5 limits-4.2 lxml-5.4.0 mako-1.3.10 markdown-3.8 markdown-it-py-3.0.0 markupsafe-3.0.2 mdurl-0.1.2 mercurial-7.0.1 mistune-3.0.2 mrcfile-1.5.4 msal-1.32.3 msgpack-1.1.0 multidict-6.4.3 mypy-extensions-1.1.0 networkx-3.2.1 nodeenv-1.9.1 numpy-2.0.2 oauthlib-3.2.2 orjson-3.10.16 oyaml-1.0 packaging-24.2 paramiko-3.5.1 parsley-1.3 paste-3.10.1 pastedeploy-3.1.0 pebble-5.1.1 pillow-11.2.1 prompt-toolkit-3.0.51 propcache-0.3.1 prov-1.5.1 psutil-7.0.0 pulsar-galaxy-lib-0.15.8 pycparser-2.22 pycryptodome-3.22.0 pydantic-2.11.3 pydantic-core-2.33.1 pydantic-tes-0.2.0 pydot-2.0.0 pyeventsystem-0.1.0 pyfaidx-0.8.1.3 pygments-2.19.1 pyjwt-2.10.1 pykwalify-1.8.0 pylibmagic-0.5.0 pynacl-1.5.0 pyparsing-3.2.3 pypng-0.20220715.0 pysam-0.23.0 python-dateutil-2.9.0.post0 python-magic-0.4.27 python-multipart-0.0.20 python-slugify-8.0.4 python3-openid-3.2.0 pytz-2025.2 pyyaml-6.0.2 pyzmq-26.4.0 rdflib-7.1.4 referencing-0.36.2 refgenconf-0.12.2 regex-2024.11.6 repoze-lru-0.7 requests-2.32.3 requests-oauthlib-2.0.0 requests-toolbelt-1.0.0 requests-unixsocket-0.4.1 rich-13.9.4 rich-argparse-1.7.0 rocrate-0.13.0 routes-2.5.1 rpds-py-0.24.0 ruamel-yaml-0.18.10 ruamel-yaml-clib-0.2.12 s3fs-2025.3.2 schema-salad-8.9.20250408123006 setuptools-79.0.1 setuptools-scm-5.0.2 six-1.17.0 slowapi-0.1.9 sniffio-1.3.1 social-auth-core-4.6.0 sortedcontainers-2.4.0 spython-0.3.14 sqlalchemy-2.0.40 sqlitedict-2.1.0 sqlparse-0.5.3 starlette-0.46.2 starlette-context-0.4.0 supervisor-4.2.5 svgwrite-1.4.3 tenacity-9.1.2 text-unidecode-1.3 tifffile-2024.8.30 tinydb-4.8.2 tomli-2.2.1 tornado-6.4.2 tqdm-4.67.1 tuspy-1.1.0 tuswsgi-0.5.5 typing-extensions-4.13.2 typing-inspection-0.4.0 tzdata-2025.2 tzlocal-5.3.1 ubiquerg-0.8.1 urllib3-1.26.20 uvicorn-0.34.2 uvloop-0.21.0 vine-5.1.0 wcwidth-0.2.13 webencodings-0.5.1 webob-1.8.9 whoosh-2.7.4 wrapt-1.17.2 yacman-0.9.3 yarl-1.20.0 zipp-3.21.0 zipstream-new-1.1.8 zstandard-0.23.0 +Trying to resolve path for the 'email_ban_file' option but it's empty/None +Installing node into /scratch/rico/planemo/gx_venv_3 with nodeenv. + * Install prebuilt node (22.13.0) ..... done. + * Appending data to /scratch/rico/planemo/gx_venv_3/bin/activate + * Appending data to /scratch/rico/planemo/gx_venv_3/bin/activate.fish +The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable. +Starting Galaxy with command [cd /scratch/rico/galaxy && if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/scratch/rico/planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /scratch/rico/.venv/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /scratch/rico/.venv/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && /scratch/rico/galaxy/run.sh $COMMON_STARTUP_ARGS --daemon] +galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input +Activated a virtualenv for Galaxy +/scratch/rico/planemo/gx_venv_3 +Activating virtualenv at /scratch/rico/planemo/gx_venv_3 +Requirement already satisfied: pip>=20.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (25.1.1) +Requirement already satisfied: wheel in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (0.45.1) +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple +Ignoring colorama: markers 'sys_platform == "win32"' don't match your environment +Ignoring legacy-cgi: markers 'python_full_version >= "3.13"' don't match your environment +Ignoring limits: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring networkx: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring numpy: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring packaging: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring pyreadline3: markers 'sys_platform == "win32"' don't match your environment +Ignoring tifffile: markers 'python_full_version >= "3.10"' don't match your environment +Ignoring urllib3: markers 'python_full_version >= "3.10"' don't match your environment +Requirement already satisfied: a2wsgi==1.10.8 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.10.8) +Requirement already satisfied: adal==1.2.7 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7) +Requirement already satisfied: aiobotocore==2.21.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (2.21.1) +Requirement already satisfied: aiofiles==24.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (24.1.0) +Requirement already satisfied: aiohappyeyeballs==2.6.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (2.6.1) +Requirement already satisfied: aiohttp==3.11.18 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (3.11.18) +Requirement already satisfied: aioitertools==0.12.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 9)) (0.12.0) +Requirement already satisfied: aiosignal==1.3.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 10)) (1.3.2) +Requirement already satisfied: alembic==1.15.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 11)) (1.15.2) +Requirement already satisfied: amqp==5.3.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 12)) (5.3.1) +Requirement already satisfied: annotated-types==0.7.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 13)) (0.7.0) +Requirement already satisfied: anyio==4.9.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 14)) (4.9.0) +Requirement already satisfied: apispec==6.8.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 15)) (6.8.1) +Requirement already satisfied: appdirs==1.4.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 16)) (1.4.4) +Requirement already satisfied: arcp==0.2.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 17)) (0.2.1) +Requirement already satisfied: argcomplete==3.6.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 18)) (3.6.2) +Requirement already satisfied: async-timeout==5.0.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 19)) (5.0.1) +Requirement already satisfied: attmap==0.13.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 20)) (0.13.2) +Requirement already satisfied: attrs==25.3.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 21)) (25.3.0) +Requirement already satisfied: babel==2.17.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 22)) (2.17.0) +Requirement already satisfied: bagit==1.8.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 23)) (1.8.1) +Requirement already satisfied: bagit-profile==1.3.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 24)) (1.3.1) +Requirement already satisfied: bcrypt==4.3.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 25)) (4.3.0) +Requirement already satisfied: bdbag==1.7.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 26)) (1.7.3) +Requirement already satisfied: beaker==1.13.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 27)) (1.13.0) +Requirement already satisfied: billiard==4.2.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 28)) (4.2.1) +Requirement already satisfied: bioblend==1.5.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 29)) (1.5.0) +Requirement already satisfied: bleach==6.2.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 30)) (6.2.0) +Requirement already satisfied: boltons==25.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 31)) (25.0.0) +Requirement already satisfied: boto==2.49.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 32)) (2.49.0) +Requirement already satisfied: botocore==1.37.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 33)) (1.37.1) +Requirement already satisfied: bx-python==0.13.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 34)) (0.13.0) +Requirement already satisfied: cachecontrol==0.14.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 35)) (0.14.2) +Requirement already satisfied: celery==5.5.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 36)) (5.5.2) +Requirement already satisfied: certifi==2025.4.26 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 37)) (2025.4.26) +Requirement already satisfied: cffi==1.17.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 38)) (1.17.1) +Requirement already satisfied: charset-normalizer==3.4.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 39)) (3.4.1) +Requirement already satisfied: circus==0.19.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 40)) (0.19.0) +Requirement already satisfied: click==8.1.8 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 41)) (8.1.8) +Requirement already satisfied: click-didyoumean==0.3.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 42)) (0.3.1) +Requirement already satisfied: click-plugins==1.1.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 43)) (1.1.1) +Requirement already satisfied: click-repl==0.3.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 44)) (0.3.0) +Requirement already satisfied: cloudauthz==0.6.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 45)) (0.6.0) +Requirement already satisfied: cloudbridge==3.2.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 46)) (3.2.0) +Requirement already satisfied: coloredlogs==15.0.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 48)) (15.0.1) +Requirement already satisfied: conda-package-streaming==0.11.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 49)) (0.11.0) +Requirement already satisfied: cryptography==44.0.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 50)) (44.0.2) +Requirement already satisfied: ct3==3.4.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 51)) (3.4.0) +Requirement already satisfied: cwl-upgrader==1.2.12 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 52)) (1.2.12) +Requirement already satisfied: cwl-utils==0.37 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 53)) (0.37) +Requirement already satisfied: cwltool==3.1.20250110105449 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 54)) (3.1.20250110105449) +Requirement already satisfied: defusedxml==0.7.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 55)) (0.7.1) +Requirement already satisfied: deprecated==1.2.18 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 56)) (1.2.18) +Requirement already satisfied: deprecation==2.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 57)) (2.1.0) +Requirement already satisfied: dictobj==0.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 58)) (0.4) +Requirement already satisfied: dnspython==2.7.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 59)) (2.7.0) +Requirement already satisfied: docopt==0.6.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 60)) (0.6.2) +Requirement already satisfied: docutils==0.21.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 61)) (0.21.2) +Requirement already satisfied: dparse==0.6.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 62)) (0.6.4) +Requirement already satisfied: edam-ontology==1.25.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 63)) (1.25.2) +Requirement already satisfied: email-validator==2.2.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 64)) (2.2.0) +Requirement already satisfied: exceptiongroup==1.2.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 65)) (1.2.2) +Requirement already satisfied: fastapi-slim==0.115.12 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 66)) (0.115.12) +Requirement already satisfied: filelock==3.18.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 67)) (3.18.0) +Requirement already satisfied: fissix==24.4.24 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 68)) (24.4.24) +Requirement already satisfied: frozenlist==1.6.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 69)) (1.6.0) +Requirement already satisfied: fs==2.4.16 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 70)) (2.4.16) +Requirement already satisfied: fsspec==2025.3.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 71)) (2025.3.2) +Requirement already satisfied: future==1.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 72)) (1.0.0) +Requirement already satisfied: gravity==1.1.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 73)) (1.1.1) +Requirement already satisfied: greenlet==3.2.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 74)) (3.2.1) +Requirement already satisfied: gunicorn==23.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 75)) (23.0.0) +Requirement already satisfied: gxformat2==0.20.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 76)) (0.20.0) +Requirement already satisfied: h11==0.16.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 77)) (0.16.0) +Requirement already satisfied: httpcore==1.0.9 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 78)) (1.0.9) +Requirement already satisfied: httpx==0.28.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 79)) (0.28.1) +Requirement already satisfied: h5grove==2.3.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 80)) (2.3.0) +Requirement already satisfied: h5py==3.13.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 81)) (3.13.0) +Requirement already satisfied: humanfriendly==10.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 82)) (10.0) +Requirement already satisfied: idna==3.10 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 83)) (3.10) +Requirement already satisfied: importlib-metadata==8.6.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 84)) (8.6.1) +Requirement already satisfied: importlib-resources==6.5.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 85)) (6.5.2) +Requirement already satisfied: isa-rwval==0.10.11 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 86)) (0.10.11) +Requirement already satisfied: isal==1.7.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 87)) (1.7.2) +Requirement already satisfied: isodate==0.7.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 88)) (0.7.2) +Requirement already satisfied: jinja2==3.1.6 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 89)) (3.1.6) +Requirement already satisfied: jmespath==1.0.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 90)) (1.0.1) +Requirement already satisfied: jsonref==1.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 91)) (1.1.0) +Requirement already satisfied: jsonschema==4.23.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 92)) (4.23.0) +Requirement already satisfied: jsonschema-specifications==2025.4.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 93)) (2025.4.1) +Requirement already satisfied: kombu==5.5.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 94)) (5.5.3) +Requirement already satisfied: lagom==2.7.5 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 95)) (2.7.5) +Requirement already satisfied: limits==4.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 97)) (4.2) +Requirement already satisfied: lxml==5.4.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 99)) (5.4.0) +Requirement already satisfied: mako==1.3.10 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 100)) (1.3.10) +Requirement already satisfied: markdown==3.8 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 101)) (3.8) +Requirement already satisfied: markdown-it-py==3.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 102)) (3.0.0) +Requirement already satisfied: markupsafe==3.0.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 103)) (3.0.2) +Requirement already satisfied: mdurl==0.1.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 104)) (0.1.2) +Requirement already satisfied: mercurial==7.0.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 105)) (7.0.1) +Requirement already satisfied: mistune==3.0.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 106)) (3.0.2) +Requirement already satisfied: mrcfile==1.5.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 107)) (1.5.4) +Requirement already satisfied: msal==1.32.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 108)) (1.32.3) +Requirement already satisfied: msgpack==1.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 109)) (1.1.0) +Requirement already satisfied: multidict==6.4.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 110)) (6.4.3) +Requirement already satisfied: mypy-extensions==1.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 111)) (1.1.0) +Requirement already satisfied: networkx==3.2.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 112)) (3.2.1) +Requirement already satisfied: nodeenv==1.9.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 114)) (1.9.1) +Requirement already satisfied: numpy==2.0.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 115)) (2.0.2) +Requirement already satisfied: oauthlib==3.2.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 117)) (3.2.2) +Requirement already satisfied: orjson==3.10.16 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 118)) (3.10.16) +Requirement already satisfied: oyaml==1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 119)) (1.0) +Requirement already satisfied: packaging==24.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 120)) (24.2) +Requirement already satisfied: paramiko==3.5.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 122)) (3.5.1) +Requirement already satisfied: parsley==1.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 123)) (1.3) +Requirement already satisfied: paste==3.10.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 124)) (3.10.1) +Requirement already satisfied: pastedeploy==3.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 125)) (3.1.0) +Requirement already satisfied: pebble==5.1.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 126)) (5.1.1) +Requirement already satisfied: pillow==11.2.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 127)) (11.2.1) +Requirement already satisfied: prompt-toolkit==3.0.51 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 128)) (3.0.51) +Requirement already satisfied: propcache==0.3.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 129)) (0.3.1) +Requirement already satisfied: prov==1.5.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 130)) (1.5.1) +Requirement already satisfied: psutil==7.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 131)) (7.0.0) +Requirement already satisfied: pulsar-galaxy-lib==0.15.8 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 132)) (0.15.8) +Requirement already satisfied: pycparser==2.22 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 133)) (2.22) +Requirement already satisfied: pycryptodome==3.22.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 134)) (3.22.0) +Requirement already satisfied: pydantic==2.11.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 135)) (2.11.3) +Requirement already satisfied: pydantic-core==2.33.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 136)) (2.33.1) +Requirement already satisfied: pydantic-tes==0.2.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 137)) (0.2.0) +Requirement already satisfied: pydot==2.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 138)) (2.0.0) +Requirement already satisfied: pyeventsystem==0.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 139)) (0.1.0) +Requirement already satisfied: pyfaidx==0.8.1.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 140)) (0.8.1.3) +Requirement already satisfied: pygments==2.19.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 141)) (2.19.1) +Requirement already satisfied: pyjwt==2.10.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 142)) (2.10.1) +Requirement already satisfied: pykwalify==1.8.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 143)) (1.8.0) +Requirement already satisfied: pylibmagic==0.5.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 144)) (0.5.0) +Requirement already satisfied: pynacl==1.5.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 145)) (1.5.0) +Requirement already satisfied: pyparsing==3.2.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 146)) (3.2.3) +Requirement already satisfied: pypng==0.20220715.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 147)) (0.20220715.0) +Requirement already satisfied: pysam==0.23.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 149)) (0.23.0) +Requirement already satisfied: python-dateutil==2.9.0.post0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 150)) (2.9.0.post0) +Requirement already satisfied: python-magic==0.4.27 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 151)) (0.4.27) +Requirement already satisfied: python-multipart==0.0.20 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 152)) (0.0.20) +Requirement already satisfied: python-slugify==8.0.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 153)) (8.0.4) +Requirement already satisfied: python3-openid==3.2.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 154)) (3.2.0) +Requirement already satisfied: pytz==2025.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 155)) (2025.2) +Requirement already satisfied: pyyaml==6.0.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 156)) (6.0.2) +Requirement already satisfied: pyzmq==26.4.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 157)) (26.4.0) +Requirement already satisfied: rdflib==7.1.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 158)) (7.1.4) +Requirement already satisfied: referencing==0.36.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 159)) (0.36.2) +Requirement already satisfied: refgenconf==0.12.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 160)) (0.12.2) +Requirement already satisfied: regex==2024.11.6 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 161)) (2024.11.6) +Requirement already satisfied: repoze-lru==0.7 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 162)) (0.7) +Requirement already satisfied: requests==2.32.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 163)) (2.32.3) +Requirement already satisfied: requests-oauthlib==2.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 164)) (2.0.0) +Requirement already satisfied: requests-toolbelt==1.0.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 165)) (1.0.0) +Requirement already satisfied: requests-unixsocket==0.4.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 166)) (0.4.1) +Requirement already satisfied: rich==13.9.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 167)) (13.9.4) +Requirement already satisfied: rich-argparse==1.7.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 168)) (1.7.0) +Requirement already satisfied: rocrate==0.13.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 169)) (0.13.0) +Requirement already satisfied: routes==2.5.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 170)) (2.5.1) +Requirement already satisfied: rpds-py==0.24.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 171)) (0.24.0) +Requirement already satisfied: ruamel-yaml==0.18.10 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 172)) (0.18.10) +Requirement already satisfied: ruamel-yaml-clib==0.2.12 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 173)) (0.2.12) +Requirement already satisfied: s3fs==2025.3.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 174)) (2025.3.2) +Requirement already satisfied: schema-salad==8.9.20250408123006 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 175)) (8.9.20250408123006) +Requirement already satisfied: setuptools==79.0.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 176)) (79.0.1) +Requirement already satisfied: setuptools-scm==5.0.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 177)) (5.0.2) +Requirement already satisfied: six==1.17.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 178)) (1.17.0) +Requirement already satisfied: slowapi==0.1.9 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 179)) (0.1.9) +Requirement already satisfied: sniffio==1.3.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 180)) (1.3.1) +Requirement already satisfied: social-auth-core==4.6.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 181)) (4.6.0) +Requirement already satisfied: sortedcontainers==2.4.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 182)) (2.4.0) +Requirement already satisfied: spython==0.3.14 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 183)) (0.3.14) +Requirement already satisfied: sqlalchemy==2.0.40 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 184)) (2.0.40) +Requirement already satisfied: sqlitedict==2.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 185)) (2.1.0) +Requirement already satisfied: sqlparse==0.5.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 186)) (0.5.3) +Requirement already satisfied: starlette==0.46.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 187)) (0.46.2) +Requirement already satisfied: starlette-context==0.4.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 188)) (0.4.0) +Requirement already satisfied: supervisor==4.2.5 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 189)) (4.2.5) +Requirement already satisfied: svgwrite==1.4.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 190)) (1.4.3) +Requirement already satisfied: tenacity==9.1.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 191)) (9.1.2) +Requirement already satisfied: text-unidecode==1.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 192)) (1.3) +Requirement already satisfied: tifffile==2024.8.30 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 193)) (2024.8.30) +Requirement already satisfied: tinydb==4.8.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 195)) (4.8.2) +Requirement already satisfied: tomli==2.2.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 196)) (2.2.1) +Requirement already satisfied: tornado==6.4.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 197)) (6.4.2) +Requirement already satisfied: tqdm==4.67.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 198)) (4.67.1) +Requirement already satisfied: tuspy==1.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 199)) (1.1.0) +Requirement already satisfied: tuswsgi==0.5.5 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 200)) (0.5.5) +Requirement already satisfied: typing-extensions==4.13.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 201)) (4.13.2) +Requirement already satisfied: typing-inspection==0.4.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 202)) (0.4.0) +Requirement already satisfied: tzdata==2025.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 203)) (2025.2) +Requirement already satisfied: tzlocal==5.3.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 204)) (5.3.1) +Requirement already satisfied: ubiquerg==0.8.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 205)) (0.8.1) +Requirement already satisfied: urllib3==1.26.20 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 206)) (1.26.20) +Requirement already satisfied: uvicorn==0.34.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 208)) (0.34.2) +Requirement already satisfied: uvloop==0.21.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 209)) (0.21.0) +Requirement already satisfied: vine==5.1.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 210)) (5.1.0) +Requirement already satisfied: wcwidth==0.2.13 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 211)) (0.2.13) +Requirement already satisfied: webencodings==0.5.1 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 212)) (0.5.1) +Requirement already satisfied: webob==1.8.9 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 213)) (1.8.9) +Requirement already satisfied: whoosh==2.7.4 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 214)) (2.7.4) +Requirement already satisfied: wrapt==1.17.2 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 215)) (1.17.2) +Requirement already satisfied: yacman==0.9.3 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 216)) (0.9.3) +Requirement already satisfied: yarl==1.20.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 217)) (1.20.0) +Requirement already satisfied: zipp==3.21.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 218)) (3.21.0) +Requirement already satisfied: zipstream-new==1.1.8 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 219)) (1.1.8) +Requirement already satisfied: zstandard==0.23.0 in /scratch/rico/planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 220)) (0.23.0) +Option master_api_key has been deprecated in favor of bootstrap_admin_api_key +Trying to resolve path for the 'email_ban_file' option but it's empty/None +Trying to resolve path for the 'data_manager_config_file' option but it's empty/None +/scratch/rico/galaxy/lib/galaxy/dependencies/__init__.py:77: FutureWarning: Truth-testing of elements was a source of confusion and will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. + if plugins_elem: +Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple +Collecting watchdog (from -r /dev/stdin (line 1)) + Using cached watchdog-6.0.0-py3-none-manylinux2014_x86_64.whl.metadata (44 kB) +Using cached watchdog-6.0.0-py3-none-manylinux2014_x86_64.whl (79 kB) +Installing collected packages: watchdog +Successfully installed watchdog-6.0.0 +The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable. +Activating virtualenv at /scratch/rico/planemo/gx_venv_3 +Executing: galaxyctl start +Adding service gunicorn +supervisord is not running +Adding service celery +supervisord is not running +Adding service celery-beat +supervisord is not running +celery STARTING +celery-beat STARTING +gunicorn STARTING +Log files are in /scratch/rico/tmp/tmp9ssqcs9d/gravity/log +galaxy.visualization.genomes ERROR 2025-07-23 15:16:09,732 [pN:main,p:2070463,tN:MainThread] Error reading twobit.loc +Traceback (most recent call last): + File "/scratch/rico/galaxy/lib/galaxy/visualization/genomes.py", line 226, in reload_genomes + with open(twobit_path) as f: +FileNotFoundError: [Errno 2] No such file or directory: '/scratch/rico/galaxy/tool-data/twobit.loc' +galaxy.util WARNING 2025-07-23 15:16:09,774 [pN:main,p:2070463,tN:MainThread] directory not found: /scratch/rico/galaxy/config/plugins/activities +galaxy.tools WARNING 2025-07-23 15:16:09,774 [pN:main,p:2070463,tN:MainThread] The default shed tool config file (/scratch/rico/tmp/tmp9ssqcs9d/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2025-07-23 15:16:09,774 [pN:main,p:2070463,tN:MainThread] Parsing the tool configuration /scratch/rico/tmp/tmp9ssqcs9d/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:09,774 [pN:main,p:2070463,tN:MainThread] Tool path for tool configuration /scratch/rico/tmp/tmp9ssqcs9d/tool_conf.xml is None +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:09,784 [pN:main,p:2070463,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:09,957 [pN:main,p:2070463,tN:MainThread] Loaded tool id: ncbi_egapx, version: 0.4.1+galaxy1 into tool panel.. +galaxy.tools WARNING 2025-07-23 15:16:09,957 [pN:main,p:2070463,tN:MainThread] The default shed tool config file (/scratch/rico/tmp/tmp9ssqcs9d/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2025-07-23 15:16:09,957 [pN:main,p:2070463,tN:MainThread] Parsing the tool configuration /scratch/rico/tmp/tmp9ssqcs9d/shed_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:09,958 [pN:main,p:2070463,tN:MainThread] Tool path for shed tool configuration /scratch/rico/tmp/tmp9ssqcs9d/shed_tools_conf.xml is /scratch/rico/tmp/tmp9ssqcs9d/shed_tools +galaxy.tools WARNING 2025-07-23 15:16:09,958 [pN:main,p:2070463,tN:MainThread] The default shed tool config file (/scratch/rico/tmp/tmp9ssqcs9d/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2025-07-23 15:16:09,958 [pN:main,p:2070463,tN:MainThread] Parsing the tool configuration /scratch/rico/tmp/tmp9ssqcs9d/empty_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:09,958 [pN:main,p:2070463,tN:MainThread] Tool path for tool configuration /scratch/rico/tmp/tmp9ssqcs9d/empty_tool_conf.xml is None +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:09,958 [pN:main,p:2070463,tN:MainThread] Reading tools from config files finished (184.403 ms) +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:09,959 [pN:main,p:2070463,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2025-07-23 15:16:09,959 [pN:main,p:2070463,tN:MainThread] Loading EDAM tool panel finished (1.071 ms) +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:09,960 [pN:main,p:2070463,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2025-07-23 15:16:09,960 [pN:main,p:2070463,tN:MainThread] Loading EDAM tool panel finished (0.875 ms) +galaxy.tool_util.toolbox.integrated_panel DEBUG 2025-07-23 15:16:09,960 [pN:main,p:2070463,tN:MainThread] Writing integrated tool panel config file to '/scratch/rico/tmp/tmp9ssqcs9d/integrated_tool_panel_conf.xml' +galaxy.tools.search WARNING 2025-07-23 15:16:14,081 [pN:main,p:2070463,tN:MainThread] Index at '/scratch/rico/galaxy/database/tool_search_index/default' uses outdated schema, creating a new index +galaxy.tools.search WARNING 2025-07-23 15:16:14,085 [pN:main,p:2070463,tN:MainThread] Index at '/scratch/rico/galaxy/database/tool_search_index/ontology:edam_operations' uses outdated schema, creating a new index +galaxy.tools.search WARNING 2025-07-23 15:16:14,087 [pN:main,p:2070463,tN:MainThread] Index at '/scratch/rico/galaxy/database/tool_search_index/ontology:edam_topics' uses outdated schema, creating a new index +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,095 [pN:main,p:2070463,tN:MainThread] Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,096 [pN:main,p:2070463,tN:MainThread] Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,098 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,099 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igv_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,100 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igb_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,100 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "bam_iobio". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,101 [pN:main,p:2070463,tN:MainThread] Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,101 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igb_cram' for datatype 'cram', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,102 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igb_bed' for datatype 'bed', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,103 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,104 [pN:main,p:2070463,tN:MainThread] Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,105 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,106 [pN:main,p:2070463,tN:MainThread] Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,107 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,108 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,109 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "intermine_simple_display". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,109 [pN:main,p:2070463,tN:MainThread] Loaded display application 'intermine_simple' for datatype 'intermine_tabular', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,110 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,110 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,113 [pN:main,p:2070463,tN:MainThread] Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,114 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,114 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igv_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,115 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,117 [pN:main,p:2070463,tN:MainThread] Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,120 [pN:main,p:2070463,tN:MainThread] Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,120 [pN:main,p:2070463,tN:MainThread] Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,122 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,122 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,122 [pN:main,p:2070463,tN:MainThread] Loaded display application 'avivator' for datatype 'tiff', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,123 [pN:main,p:2070463,tN:MainThread] Loaded display application 'avivator' for datatype 'ome.tiff', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,123 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "q2view_display". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,123 [pN:main,p:2070463,tN:MainThread] Loaded display application 'q2view' for datatype 'qza', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,124 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "q2view_display". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,124 [pN:main,p:2070463,tN:MainThread] Loaded display application 'q2view' for datatype 'qzv', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,125 [pN:main,p:2070463,tN:MainThread] Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,125 [pN:main,p:2070463,tN:MainThread] Loaded display application 'minerva_tabular' for datatype 'tabular', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,127 [pN:main,p:2070463,tN:MainThread] Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,128 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,128 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,129 [pN:main,p:2070463,tN:MainThread] Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,129 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "vcf_iobio". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,129 [pN:main,p:2070463,tN:MainThread] Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,130 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igb_wig' for datatype 'wig', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,131 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,131 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,132 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,132 [pN:main,p:2070463,tN:MainThread] Loaded display application 'igv_genbank' for datatype 'genbank', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,132 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "biom_simple_display". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,133 [pN:main,p:2070463,tN:MainThread] Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,133 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "icn3d_simple_display". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,133 [pN:main,p:2070463,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'sdf', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,133 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "icn3d_simple_display". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,134 [pN:main,p:2070463,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'mol2', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2025-07-23 15:16:14,134 [pN:main,p:2070463,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named "icn3d_simple_display". +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,134 [pN:main,p:2070463,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'pdb', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,134 [pN:main,p:2070463,tN:MainThread] Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,135 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,135 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,135 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,135 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,135 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,135 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,135 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,135 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,136 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,137 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,137 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,137 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,137 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,137 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'fasta.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,137 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'a3m' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,137 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,137 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,137 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,137 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,138 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.bz2' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,138 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.bz2' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,138 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,138 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,138 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gtf.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,138 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gtf.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,140 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,140 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,140 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,140 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,140 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'sequences' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,141 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,141 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,141 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,141 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,141 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,141 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,141 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,141 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,141 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,141 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,141 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,141 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,141 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,142 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,142 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,142 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,144 [pN:main,p:2070463,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'mothur.align' +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,149 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,152 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,155 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,157 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,159 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,161 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,163 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,165 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,166 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,168 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,170 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,173 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,174 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,176 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,180 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,182 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,184 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,185 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,187 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,188 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,190 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,193 [pN:main,p:2070463,tN:MainThread] Loaded converter: ucsc_bigbedtobed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,196 [pN:main,p:2070463,tN:MainThread] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,200 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,203 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,204 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,206 [pN:main,p:2070463,tN:MainThread] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,207 [pN:main,p:2070463,tN:MainThread] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,209 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,210 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,212 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,213 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,215 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,216 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,218 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,220 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,222 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,224 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,226 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,227 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,229 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,231 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,233 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,235 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,236 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,238 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,240 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,242 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,243 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,246 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,248 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,249 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,251 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,253 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,255 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,256 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,265 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,266 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,268 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,269 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,273 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,275 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,278 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,280 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,281 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,283 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,284 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,286 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,289 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,290 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,292 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,293 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,295 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,298 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,301 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,302 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,304 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,305 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_archive_to_directory +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,307 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_archive_to_directory +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,309 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_archive_to_directory +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,311 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_archive_to_directory +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,313 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,315 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,316 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,319 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,320 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,323 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,325 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,327 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,329 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,331 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,333 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,334 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,336 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,338 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,342 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,343 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,345 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,347 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,350 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,351 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,355 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,358 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,359 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,361 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,362 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,364 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,365 [pN:main,p:2070463,tN:MainThread] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,367 [pN:main,p:2070463,tN:MainThread] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,369 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,371 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,374 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,376 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,378 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,380 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,382 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,384 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,386 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,387 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,389 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,391 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,392 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,394 [pN:main,p:2070463,tN:MainThread] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,395 [pN:main,p:2070463,tN:MainThread] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,396 [pN:main,p:2070463,tN:MainThread] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,397 [pN:main,p:2070463,tN:MainThread] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,400 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,401 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,404 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,406 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,414 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,422 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,429 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,431 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,439 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,441 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,448 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,456 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,464 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,471 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,479 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,486 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,488 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,496 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,503 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,511 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,519 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,526 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,534 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,542 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,550 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,557 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,565 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,566 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,574 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,576 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,584 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,592 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,599 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,601 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,604 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,607 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,610 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,613 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,616 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,618 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,620 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,621 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,623 [pN:main,p:2070463,tN:MainThread] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:14,627 [pN:main,p:2070463,tN:MainThread] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2025-07-23 15:16:14,631 [pN:main,p:2070463,tN:MainThread] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2025-07-23 15:16:14,632 [pN:main,p:2070463,tN:MainThread] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2025-07-23 15:16:14,634 [pN:main,p:2070463,tN:MainThread] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2025-07-23 15:16:14,635 [pN:main,p:2070463,tN:MainThread] Loaded data fetch tool: __DATA_FETCH__ +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,636 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: aceeditor +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,637 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,638 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: aladin +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,638 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: alignment +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,639 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,640 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz +galaxy.visualization.plugins.config_parser INFO 2025-07-23 15:16:14,640 [pN:main,p:2070463,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,641 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: csg +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,641 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,642 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,643 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: example +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,644 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: fits_graph_viewer +galaxy.visualization.plugins.config_parser INFO 2025-07-23 15:16:14,644 [pN:main,p:2070463,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,644 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,645 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: h5web +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,646 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap +galaxy.visualization.plugins.config_parser INFO 2025-07-23 15:16:14,647 [pN:main,p:2070463,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,647 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace +galaxy.visualization.plugins.config_parser INFO 2025-07-23 15:16:14,648 [pN:main,p:2070463,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,648 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,650 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,652 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,654 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,656 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,658 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,659 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: jupyterlite +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,660 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: kepler +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,661 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: molstar +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,661 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: msa +galaxy.visualization.plugins.config_parser INFO 2025-07-23 15:16:14,662 [pN:main,p:2070463,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,662 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,663 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,664 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: niivue +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,665 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: nora +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,667 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,669 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,671 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,673 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,675 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,677 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,679 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,682 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,683 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,685 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,687 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,690 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,692 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,693 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,693 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,694 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: pca +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,695 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,695 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: plotly +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,696 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: plotly_box +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,697 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: plotly_histogram +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,697 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: plotly_surface +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,698 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: plyr +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,699 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: pv +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,700 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,700 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: tabulator +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,701 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: tiffviewer +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,701 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,702 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: ts_visjs +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,703 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,703 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: venn +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,704 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: vitessce +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,705 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: vizarr +galaxy.visualization.plugins.registry INFO 2025-07-23 15:16:14,705 [pN:main,p:2070463,tN:MainThread] VisualizationsRegistry, loaded plugin: vtk +galaxy.tours._impl INFO 2025-07-23 15:16:14,727 [pN:main,p:2070463,tN:MainThread] Loaded tour 'core.galaxy_ui' +galaxy.tours._impl INFO 2025-07-23 15:16:14,745 [pN:main,p:2070463,tN:MainThread] Loaded tour 'core.deferred' +galaxy.tours._impl INFO 2025-07-23 15:16:14,761 [pN:main,p:2070463,tN:MainThread] Loaded tour 'core.history' +galaxy.tours._impl INFO 2025-07-23 15:16:14,768 [pN:main,p:2070463,tN:MainThread] Loaded tour 'core.visualizations' +galaxy.tours._impl INFO 2025-07-23 15:16:14,779 [pN:main,p:2070463,tN:MainThread] Loaded tour 'core.windows' +galaxy.workflow.scheduling_manager INFO 2025-07-23 15:16:14,803 [pN:main,p:2070463,tN:MainThread] No workflow schedulers plugin config file defined, using default scheduler. +galaxy.web_stack.handlers INFO 2025-07-23 15:16:14,803 [pN:main,p:2070463,tN:MainThread] WorkflowSchedulingManager: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on <handlers> to override the default +galaxy.workflow.scheduling_manager DEBUG 2025-07-23 15:16:14,803 [pN:main,p:2070463,tN:MainThread] Starting workflow schedulers +galaxy.app INFO 2025-07-23 15:16:14,812 [pN:main,p:2070463,tN:MainThread] Galaxy app startup finished (6466.375 ms) +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,841 [pN:main,p:2070463,tN:MainThread] Enabling 'user' controller, class: User +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,844 [pN:main,p:2070463,tN:MainThread] Enabling 'data_manager' controller, class: DataManager +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,846 [pN:main,p:2070463,tN:MainThread] Enabling 'async' controller, class: ASync +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,848 [pN:main,p:2070463,tN:MainThread] Enabling 'tag' controller, class: TagsController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,856 [pN:main,p:2070463,tN:MainThread] Enabling 'page' controller, class: PageController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,858 [pN:main,p:2070463,tN:MainThread] Enabling 'root' controller, class: RootController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,860 [pN:main,p:2070463,tN:MainThread] Enabling 'tool_runner' controller, class: ToolRunner +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,860 [pN:main,p:2070463,tN:MainThread] Enabling 'error' controller, class: Error +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,865 [pN:main,p:2070463,tN:MainThread] Enabling 'forms' controller, class: Forms +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,908 [pN:main,p:2070463,tN:MainThread] Enabling 'admin_toolshed' controller, class: AdminGalaxy +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,908 [pN:main,p:2070463,tN:MainThread] Enabling 'admin_toolshed' controller, class: AdminToolshed +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,912 [pN:main,p:2070463,tN:MainThread] Enabling 'visualization' controller, class: VisualizationController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,913 [pN:main,p:2070463,tN:MainThread] Enabling 'shed_tool_static' controller, class: ShedToolStatic +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,915 [pN:main,p:2070463,tN:MainThread] Enabling 'authnz' controller, class: JSAppLauncher +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,916 [pN:main,p:2070463,tN:MainThread] Enabling 'authnz' controller, class: OIDC +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,923 [pN:main,p:2070463,tN:MainThread] Enabling 'workflow' controller, class: WorkflowController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,949 [pN:main,p:2070463,tN:MainThread] Enabling 'history' controller, class: HistoryController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,999 [pN:main,p:2070463,tN:MainThread] Enabling 'dataset' controller, class: DatasetInterface +galaxy.web.framework.base DEBUG 2025-07-23 15:16:14,999 [pN:main,p:2070463,tN:MainThread] Enabling 'admin' controller, class: AdminGalaxy +galaxy.web.framework.base DEBUG 2025-07-23 15:16:15,830 [pN:main,p:2070463,tN:MainThread] Enabling 'library_datasets' API controller, class: LibraryDatasetsController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:16,122 [pN:main,p:2070463,tN:MainThread] Enabling 'jobs' API controller, class: JobController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:16,339 [pN:main,p:2070463,tN:MainThread] Enabling 'job_files' API controller, class: JobFilesAPIController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:16,462 [pN:main,p:2070463,tN:MainThread] Enabling 'toolshed' API controller, class: ToolShedController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:16,894 [pN:main,p:2070463,tN:MainThread] Enabling 'tools' API controller, class: ToolsController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:17,192 [pN:main,p:2070463,tN:MainThread] Enabling 'trs_consumer' API controller, class: TrsConsumeAPIController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:17,194 [pN:main,p:2070463,tN:MainThread] Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:17,194 [pN:main,p:2070463,tN:MainThread] Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:17,195 [pN:main,p:2070463,tN:MainThread] Enabling 'container_resolution' API controller, class: ContainerResolutionAPIController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:17,197 [pN:main,p:2070463,tN:MainThread] Enabling 'job_ports' API controller, class: JobPortsAPIController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:17,200 [pN:main,p:2070463,tN:MainThread] Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:17,400 [pN:main,p:2070463,tN:MainThread] Enabling 'history_content_provenance' API controller, class: HDAProvenanceController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:17,400 [pN:main,p:2070463,tN:MainThread] Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:17,448 [pN:main,p:2070463,tN:MainThread] Enabling 'tool_entry_points' API controller, class: ToolEntryPointsAPIController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:17,794 [pN:main,p:2070463,tN:MainThread] Enabling 'authenticate' API controller, class: AuthenticationController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:18,086 [pN:main,p:2070463,tN:MainThread] Enabling 'trs_search' API controller, class: TrsSearchAPIController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:18,181 [pN:main,p:2070463,tN:MainThread] Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:18,482 [pN:main,p:2070463,tN:MainThread] Enabling 'forms' API controller, class: FormDefinitionAPIController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:19,390 [pN:main,p:2070463,tN:MainThread] Enabling 'workflows' API controller, class: WorkflowsAPIController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:19,415 [pN:main,p:2070463,tN:MainThread] Enabling 'uploads' API controller, class: UploadsAPIController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:19,934 [pN:main,p:2070463,tN:MainThread] Enabling 'history_annotations' API controller, class: HistoryAnnotationsController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:19,934 [pN:main,p:2070463,tN:MainThread] Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:19,934 [pN:main,p:2070463,tN:MainThread] Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:20,037 [pN:main,p:2070463,tN:MainThread] Enabling 'sanitize_allow' API controller, class: SanitizeAllowController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:20,038 [pN:main,p:2070463,tN:MainThread] Enabling 'page_revisions' API controller, class: PageRevisionsController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:20,848 [pN:main,p:2070463,tN:MainThread] Enabling 'users' API controller, class: UserAPIController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:20,849 [pN:main,p:2070463,tN:MainThread] Enabling 'webhooks' API controller, class: WebhooksController +galaxy.web.framework.base DEBUG 2025-07-23 15:16:20,999 [pN:main,p:2070463,tN:MainThread] Enabling 'plugins' API controller, class: PluginsController +galaxy.webapps.util DEBUG 2025-07-23 15:16:21,256 [pN:main,p:2070463,tN:MainThread] Enabling 'paste.httpexceptions' middleware +galaxy.webapps.util DEBUG 2025-07-23 15:16:21,257 [pN:main,p:2070463,tN:MainThread] Enabling 'RemoteUser' middleware +galaxy.webapps.util DEBUG 2025-07-23 15:16:21,257 [pN:main,p:2070463,tN:MainThread] Enabling 'ErrorMiddleware' middleware +galaxy.webapps.util DEBUG 2025-07-23 15:16:21,257 [pN:main,p:2070463,tN:MainThread] Enabling 'TusMiddleware' middleware +galaxy.webapps.util DEBUG 2025-07-23 15:16:21,257 [pN:main,p:2070463,tN:MainThread] Enabling 'TusMiddleware' middleware +galaxy.webapps.util DEBUG 2025-07-23 15:16:21,257 [pN:main,p:2070463,tN:MainThread] Enabling 'XForwardedHostMiddleware' middleware +galaxy.webapps.util DEBUG 2025-07-23 15:16:21,257 [pN:main,p:2070463,tN:MainThread] Enabling 'RequestIDMiddleware' middleware +galaxy.webapps.util DEBUG 2025-07-23 15:16:21,257 [pN:main,p:2070463,tN:MainThread] Enabling 'build_url_map' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2025-07-23 15:16:21,257 [pN:main,p:2070463,tN:MainThread] Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 140376766005888)> is alive. +galaxy.web_stack DEBUG 2025-07-23 15:16:24,912 [pN:main.1,p:2070704,tN:Thread-2] server_name set to: main.1 +galaxy.jobs.handler INFO 2025-07-23 15:16:24,918 [pN:main.1,p:2070704,tN:WorkflowRequestMonitor.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method for handler 'main.1', tag(s): None, _default_ +galaxy.jobs.manager DEBUG 2025-07-23 15:16:24,919 [pN:main.1,p:2070704,tN:Thread-2] Initializing job handler +galaxy.jobs INFO 2025-07-23 15:16:24,919 [pN:main.1,p:2070704,tN:Thread-2] Handler 'main.1' will load all configured runner plugins +galaxy.jobs.runners.state_handler_factory DEBUG 2025-07-23 15:16:24,964 [pN:main.1,p:2070704,tN:Thread-2] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs DEBUG 2025-07-23 15:16:24,964 [pN:main.1,p:2070704,tN:Thread-2] Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'planemo_runner' +galaxy.jobs.handler DEBUG 2025-07-23 15:16:24,964 [pN:main.1,p:2070704,tN:Thread-2] Loaded job runners plugins: planemo_runner +galaxy.jobs.runners DEBUG 2025-07-23 15:16:24,965 [pN:main.1,p:2070704,tN:Thread-2] Starting 4 LocalRunner workers +galaxy.jobs.handler DEBUG 2025-07-23 15:16:24,990 [pN:main.1,p:2070704,tN:Thread-2] Handler queue starting for jobs assigned to handler: main.1 +galaxy.jobs.handler INFO 2025-07-23 15:16:25,012 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method for handler 'main.1', tag(s): +galaxy.jobs.handler INFO 2025-07-23 15:16:25,013 [pN:main.1,p:2070704,tN:Thread-2] job handler queue started +galaxy.jobs.handler INFO 2025-07-23 15:16:25,016 [pN:main.1,p:2070704,tN:Thread-2] job handler stop queue started +galaxy.queue_worker INFO 2025-07-23 15:16:25,021 [pN:main.1,p:2070704,tN:Thread-2] Binding and starting galaxy control worker for main.1 +galaxy.queue_worker DEBUG 2025-07-23 15:16:25,031 [pN:main.1,p:2070704,tN:Thread-2] Executing toolbox reload on 'main.1' +galaxy.util WARNING 2025-07-23 15:16:25,056 [pN:main.1,p:2070704,tN:Thread-2] directory not found: /scratch/rico/galaxy/config/plugins/activities +galaxy.tools WARNING 2025-07-23 15:16:25,067 [pN:main.1,p:2070704,tN:Thread-2] The default shed tool config file (/scratch/rico/tmp/tmp9ssqcs9d/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2025-07-23 15:16:25,067 [pN:main.1,p:2070704,tN:Thread-2] Parsing the tool configuration /scratch/rico/tmp/tmp9ssqcs9d/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:25,083 [pN:main.1,p:2070704,tN:Thread-2] Tool path for tool configuration /scratch/rico/tmp/tmp9ssqcs9d/tool_conf.xml is None +galaxy.tools WARNING 2025-07-23 15:16:25,084 [pN:main.1,p:2070704,tN:Thread-2] The default shed tool config file (/scratch/rico/tmp/tmp9ssqcs9d/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2025-07-23 15:16:25,085 [pN:main.1,p:2070704,tN:Thread-2] Parsing the tool configuration /scratch/rico/tmp/tmp9ssqcs9d/shed_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:25,094 [pN:main.1,p:2070704,tN:Thread-2] Tool path for shed tool configuration /scratch/rico/tmp/tmp9ssqcs9d/shed_tools_conf.xml is /scratch/rico/tmp/tmp9ssqcs9d/shed_tools +galaxy.tools WARNING 2025-07-23 15:16:25,103 [pN:main.1,p:2070704,tN:Thread-2] The default shed tool config file (/scratch/rico/tmp/tmp9ssqcs9d/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2025-07-23 15:16:25,103 [pN:main.1,p:2070704,tN:Thread-2] Parsing the tool configuration /scratch/rico/tmp/tmp9ssqcs9d/empty_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:25,104 [pN:main.1,p:2070704,tN:Thread-2] Tool path for tool configuration /scratch/rico/tmp/tmp9ssqcs9d/empty_tool_conf.xml is None +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:25,104 [pN:main.1,p:2070704,tN:Thread-2] Reading tools from config files finished (37.751 ms) +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:25,108 [pN:main.1,p:2070704,tN:Thread-2] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:25,109 [pN:main.1,p:2070704,tN:Thread-2] Loading tool panel finished (2.095 ms) +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:25,119 [pN:main.1,p:2070704,tN:Thread-2] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2025-07-23 15:16:25,119 [pN:main.1,p:2070704,tN:Thread-2] Loading EDAM tool panel finished (8.710 ms) +galaxy.tool_util.toolbox.base DEBUG 2025-07-23 15:16:25,122 [pN:main.1,p:2070704,tN:Thread-2] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2025-07-23 15:16:25,128 [pN:main.1,p:2070704,tN:Thread-2] Loading EDAM tool panel finished (8.852 ms) +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,131 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,133 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,139 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,140 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,140 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,140 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,140 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,141 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,147 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,147 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,147 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,147 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,148 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,150 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,151 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,151 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,160 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.model.database_heartbeat DEBUG 2025-07-23 15:16:25,162 [pN:main.1,p:2070704,tN:database_heartbeart_main.1.thread] main.1 is config watcher +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,163 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,186 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,187 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,187 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,188 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: ucsc_bigbedtobed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,188 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,190 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,190 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,191 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,194 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,195 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,195 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,196 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,196 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,196 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,197 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,197 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,197 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,197 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,198 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,198 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,199 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,199 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,199 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,200 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,200 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,200 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,200 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,201 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,201 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,202 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,202 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,202 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,202 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,203 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,203 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,203 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,203 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,204 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,204 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,204 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,204 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,204 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,205 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,205 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,205 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,205 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,205 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,206 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,206 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,206 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,207 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,207 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,207 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,207 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,207 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,208 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,208 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,208 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,208 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,208 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_archive_to_directory +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,209 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_archive_to_directory +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,209 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_archive_to_directory +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,209 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_archive_to_directory +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,210 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,210 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,210 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,211 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,211 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,211 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,211 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,212 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,212 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,212 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,212 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,213 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,213 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,213 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,213 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,213 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,214 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,214 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,214 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,215 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,215 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,215 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,215 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,215 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,216 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,216 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,216 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,216 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,217 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,217 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,217 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,217 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,218 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,218 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,218 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,218 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,219 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,219 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,219 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,219 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,219 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,220 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,220 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,220 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,220 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,220 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,221 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,221 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,221 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,221 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,221 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,222 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,222 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,222 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,222 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,223 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,223 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,223 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,223 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,224 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,224 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,224 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,224 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,224 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,225 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,225 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,225 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,225 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,226 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,226 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,226 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,226 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,227 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,227 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,227 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,227 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,227 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,228 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,228 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,228 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,228 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,228 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,229 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,229 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,229 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,229 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,230 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,230 [pN:main.1,p:2070704,tN:Thread-2] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2025-07-23 15:16:25,236 [pN:main.1,p:2070704,tN:Thread-2] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2025-07-23 15:16:25,241 [pN:main.1,p:2070704,tN:Thread-2] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2025-07-23 15:16:25,244 [pN:main.1,p:2070704,tN:Thread-2] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2025-07-23 15:16:25,247 [pN:main.1,p:2070704,tN:Thread-2] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2025-07-23 15:16:25,250 [pN:main.1,p:2070704,tN:Thread-2] Loaded data fetch tool: __DATA_FETCH__ +galaxy.queue_worker INFO 2025-07-23 15:16:25,251 [pN:main.1,p:2070704,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. +galaxy.queue_worker DEBUG 2025-07-23 15:16:25,267 [pN:main.1,p:2070704,tN:Thread-2] Toolbox reload (235.703 ms) +galaxy.queue_worker INFO 2025-07-23 15:16:25,267 [pN:main.1,p:2070704,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. +galaxy.web_stack INFO 2025-07-23 15:16:25,274 [pN:main.1,p:2070704,tN:Thread-2] Galaxy server instance 'main.1' is running + +Serving on http://127.0.0.1:40809 + +python_multipart.multipart DEBUG 2025-07-23 15:16:26,065 [pN:main.1,p:2070704,tN:MainThread] Calling on_field_start with no data +python_multipart.multipart DEBUG 2025-07-23 15:16:26,065 [pN:main.1,p:2070704,tN:MainThread] Calling on_field_name with data[0:4] +python_multipart.multipart DEBUG 2025-07-23 15:16:26,065 [pN:main.1,p:2070704,tN:MainThread] Calling on_field_data with data[5:57] +python_multipart.multipart DEBUG 2025-07-23 15:16:26,065 [pN:main.1,p:2070704,tN:MainThread] Calling on_field_end with no data +python_multipart.multipart DEBUG 2025-07-23 15:16:26,066 [pN:main.1,p:2070704,tN:MainThread] Calling on_end with no data +galaxy.queue_worker INFO 2025-07-23 15:16:26,205 [pN:main.1,p:2070704,tN:Thread-1] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.tools.search DEBUG 2025-07-23 15:16:26,206 [pN:main.1,p:2070704,tN:Thread-1] Starting to build toolbox index of panel default. +galaxy.tools INFO 2025-07-23 15:16:26,387 [pN:main.1,p:2070704,tN:WSGI_0] Validated and populated state for tool request (31.160 ms) +galaxy.security.object_wrapper WARNING 2025-07-23 15:16:26,414 [pN:main.1,p:2070704,tN:WSGI_0] Unable to create dynamic subclass SafeStringWrapper__galaxy.model.none_like.None__NoneType__NotImplementedType__Number__SafeStringWrapper__ToolParameterValueWrapper__bool__bytearray__ellipsis for <class 'galaxy.model.none_like.NoneDataset'>, None: type() doesn't support MRO entry resolution; use types.new_class() +galaxy.managers.collections DEBUG 2025-07-23 15:16:26,503 [pN:main.1,p:2070704,tN:WSGI_0] Created collection with 18 elements +galaxy.tools.actions INFO 2025-07-23 15:16:26,504 [pN:main.1,p:2070704,tN:WSGI_0] Handled collection output named output_files for tool ncbi_egapx (89.070 ms) +galaxy.managers.collections DEBUG 2025-07-23 15:16:26,522 [pN:main.1,p:2070704,tN:WSGI_0] Created collection with 5 elements +galaxy.tools.actions INFO 2025-07-23 15:16:26,522 [pN:main.1,p:2070704,tN:WSGI_0] Handled collection output named nextflow_stats for tool ncbi_egapx (17.955 ms) +galaxy.managers.collections DEBUG 2025-07-23 15:16:26,525 [pN:main.1,p:2070704,tN:WSGI_0] Created collection with 0 elements +galaxy.tools.actions INFO 2025-07-23 15:16:26,526 [pN:main.1,p:2070704,tN:WSGI_0] Handled collection output named star_alignments for tool ncbi_egapx (3.255 ms) +galaxy.tools.actions INFO 2025-07-23 15:16:26,530 [pN:main.1,p:2070704,tN:WSGI_0] Handled output named complete_genomic_gff for tool ncbi_egapx (3.239 ms) +galaxy.tools.actions INFO 2025-07-23 15:16:26,536 [pN:main.1,p:2070704,tN:WSGI_0] Added output datasets to history (6.176 ms) +galaxy.tools.actions INFO 2025-07-23 15:16:26,547 [pN:main.1,p:2070704,tN:WSGI_0] Setup for job Job[unflushed,tool_id=ncbi_egapx] complete, ready to be enqueued (10.297 ms) +galaxy.tools.execute DEBUG 2025-07-23 15:16:26,548 [pN:main.1,p:2070704,tN:WSGI_0] Tool ncbi_egapx created job None (144.634 ms) +galaxy.web_stack.handlers INFO 2025-07-23 15:16:26,639 [pN:main.1,p:2070704,tN:WSGI_0] (Job[id=1,tool_id=ncbi_egapx]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +galaxy.tools.execute DEBUG 2025-07-23 15:16:26,645 [pN:main.1,p:2070704,tN:WSGI_0] Created 1 job(s) for tool ncbi_egapx request (257.451 ms) +galaxy.tools.search DEBUG 2025-07-23 15:16:27,158 [pN:main.1,p:2070704,tN:Thread-1] Toolbox index of panel default finished (952.537 ms) +galaxy.tools.search DEBUG 2025-07-23 15:16:27,159 [pN:main.1,p:2070704,tN:Thread-1] Starting to build toolbox index of panel ontology:edam_operations. +galaxy.tools.search DEBUG 2025-07-23 15:16:27,253 [pN:main.1,p:2070704,tN:Thread-1] Toolbox index of panel ontology:edam_operations finished (94.158 ms) +galaxy.tools.search DEBUG 2025-07-23 15:16:27,254 [pN:main.1,p:2070704,tN:Thread-1] Starting to build toolbox index of panel ontology:edam_topics. +galaxy.tools.search DEBUG 2025-07-23 15:16:27,344 [pN:main.1,p:2070704,tN:Thread-1] Toolbox index of panel ontology:edam_topics finished (90.555 ms) +galaxy.queue_worker INFO 2025-07-23 15:16:27,350 [pN:main.1,p:2070704,tN:Thread-1] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.tools.search DEBUG 2025-07-23 15:16:27,350 [pN:main.1,p:2070704,tN:Thread-1] Starting to build toolbox index of panel default. +galaxy.tools.search DEBUG 2025-07-23 15:16:27,354 [pN:main.1,p:2070704,tN:Thread-1] Toolbox index of panel default finished (4.340 ms) +galaxy.tools.search DEBUG 2025-07-23 15:16:27,354 [pN:main.1,p:2070704,tN:Thread-1] Starting to build toolbox index of panel ontology:edam_operations. +galaxy.tools.search DEBUG 2025-07-23 15:16:27,357 [pN:main.1,p:2070704,tN:Thread-1] Toolbox index of panel ontology:edam_operations finished (2.981 ms) +galaxy.tools.search DEBUG 2025-07-23 15:16:27,358 [pN:main.1,p:2070704,tN:Thread-1] Starting to build toolbox index of panel ontology:edam_topics. +galaxy.tools.search DEBUG 2025-07-23 15:16:27,360 [pN:main.1,p:2070704,tN:Thread-1] Toolbox index of panel ontology:edam_topics finished (2.455 ms) +galaxy.jobs.mapper DEBUG 2025-07-23 15:16:27,404 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] (1) Mapped job to destination id: planemo_dest +galaxy.jobs.handler DEBUG 2025-07-23 15:16:27,416 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] (1) Dispatching to planemo_runner runner +galaxy.jobs DEBUG 2025-07-23 15:16:27,475 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] (1) Working directory for job is: /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1 +galaxy.jobs.runners DEBUG 2025-07-23 15:16:27,486 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] Job [1] queued (70.283 ms) +galaxy.jobs.handler INFO 2025-07-23 15:16:27,501 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] (1) Job dispatched +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,693 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for annotated_genome with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_5de46d50-0f66-44bb-8852-9f2dd2dfa684.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,694 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for complete_genomic_gtf with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_0f8de3c4-24b6-4e15-a3fe-cb88dce7a638.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,696 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for complete_genomic_fna with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_86b1b0d7-edc0-494c-b475-6a00fdaa8ecc.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,696 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for complete_cds with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_4005a9fb-3e55-4283-a0ba-77fe8d82e5de.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,696 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for complete_transcripts with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_564cb214-d05e-40da-aa72-65c50bbeced4.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,696 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for complete_proteins with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_1d257eea-a324-46cd-83a8-494c0324c541.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,697 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for annotation_data with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_87b2cce4-30bd-4c8e-8a30-6be2ebd20ae3.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,697 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for sra_metadata with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_843b8b4f-1ac1-45aa-8ca4-9670e5d9845b.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,697 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for gnomon_accept_ftable_annot with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_b84745a3-0ebf-45be-87b2-d99560922fc4.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,697 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for gnomon_contam_rpt with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_81cb1317-08b4-48f9-9dc7-ad4f9f9456e0.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,698 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for gnomon_report with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_8e4f9bc0-bab6-4c3f-af25-a6c9e6f3a91e.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,698 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for gnomon_quality_report with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_2d22879e-6fe2-483f-9373-80d6be054347.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,698 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for busco_report with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_283e64f8-1a0d-405a-a967-0da98f110146.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,698 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for busco_report_json with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_768444e3-6fbf-432b-8722-931960626e7d.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,701 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for stats_feature_counts with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_2e650590-d0d5-4760-a010-36e201e94dfa.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,703 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for stats_feature_stats with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_b6853bf2-98f3-4573-a484-e49b1dc11906.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,705 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for validated_all_unannotated with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_904262d0-13c6-448d-bce8-1aaa9fbc8d36.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,705 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for validated_genome with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_3aff342c-7c8d-468b-a1d2-0a6c74b728a7.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,709 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for nextflow_log with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_78db6609-c17e-4889-ab79-28c01e9cacfd.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,710 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for run_report with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_60cc9fc6-513e-40af-ae64-b958743fee8d.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,710 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for run_timeline with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_cea0b32c-175d-48e8-b754-4aefb0090998.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,710 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for run_trace with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_abd6cb6c-2406-4fb6-8103-01a2e8568555.dat +galaxy.tools.evaluation INFO 2025-07-23 15:16:27,713 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Updating param_dict for run_params with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_503fe38c-0618-4a15-b891-a87e3eca8d64.dat +galaxy.jobs DEBUG 2025-07-23 15:16:27,854 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Job wrapper for Job [1] prepared (332.092 ms) +galaxy.tool_util.deps.containers INFO 2025-07-23 15:16:27,855 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [ContainerDescription[identifier=quay.io/galaxy/egapx:0.4.1-alpha,type=docker]] +galaxy.jobs.command_factory INFO 2025-07-23 15:16:27,896 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Built script [/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/tool_script.sh] for tool command [mkdir -p reads && source /galaxy/env.bash && python3 /galaxy/scripts/galaxy-resource-config.py && python3 /galaxy/egapx/ui/egapx.py '/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/configs/tmpqb3w902i' -e galaxy -o 'egapx_out' && if [ -e egapx_out/accept.gff ]; then ln -s accept.gff egapx_out/complete.genomic.gff; fi && bash '/scratch/rico/galaxytools/tools/ncbi_egapx/get-bams.bash'] +galaxy.jobs.runners DEBUG 2025-07-23 15:16:28,175 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] (1) command is: cd working; +_on_exit() { + docker kill 29ad7c8238cb4b59ade0eadec1aedcf0 &> /dev/null +} +trap _on_exit EXIT +docker inspect quay.io/galaxy/egapx:0.4.1-alpha > /dev/null 2>&1 +[ $? -ne 0 ] && docker pull quay.io/galaxy/egapx:0.4.1-alpha > /dev/null 2>&1 + +docker run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -e "GALAXY_MEMORY_MB=$GALAXY_MEMORY_MB" -e "GALAXY_MEMORY_MB_PER_SLOT=$GALAXY_MEMORY_MB_PER_SLOT" -e "HOME=$HOME" -e "_GALAXY_JOB_HOME_DIR=$_GALAXY_JOB_HOME_DIR" -e "_GALAXY_JOB_TMP_DIR=$_GALAXY_JOB_TMP_DIR" -e "TMPDIR=$TMPDIR" -e "TMP=$TMP" -e "TEMP=$TEMP" -e "NXF_DEBUG=$NXF_DEBUG" -e "EGAPX_RNASEQ_QUERY_LIMIT=$EGAPX_RNASEQ_QUERY_LIMIT" --name 29ad7c8238cb4b59ade0eadec1aedcf0 -v "$_GALAXY_JOB_TMP_DIR:$_GALAXY_JOB_TMP_DIR:rw" -v "$TMPDIR:$TMPDIR:rw" -v "$TMP:$TMP:rw" -v "$TEMP:$TEMP:rw" -v /scratch/rico/galaxy:/scratch/rico/galaxy:ro -v /scratch/rico/galaxytools/tools/ncbi_egapx:/scratch/rico/galaxytools/tools/ncbi_egapx:ro -v /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1:/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1:ro -v /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs:/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs:rw -v "$_GALAXY_JOB_HOME_DIR:$_GALAXY_JOB_HOME_DIR:rw" -v /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working:/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working:rw -v /scratch/rico/tmp/tmp9ssqcs9d/files:/scratch/rico/tmp/tmp9ssqcs9d/files:ro -v /scratch/rico/galaxy/tool-data:/scratch/rico/galaxy/tool-data:ro -v /scratch/rico/galaxytools/tools/ncbi_egapx/test-data:/scratch/rico/galaxytools/tools/ncbi_egapx/test-data:ro --cpus ${GALAXY_SLOTS:-1} -w /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working --rm --user 1028:1028 quay.io/galaxy/egapx:0.4.1-alpha /bin/sh /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/tool_script.sh > '../outputs/tool_stdout' 2> '../outputs/tool_stderr'; return_code=$?; echo $return_code > /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/galaxy_1.ec; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/annotated_genome.asn" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_5de46d50-0f66-44bb-8852-9f2dd2dfa684.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/annotated_genome.asn" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_5de46d50-0f66-44bb-8852-9f2dd2dfa684.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/complete.genomic.gtf" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_0f8de3c4-24b6-4e15-a3fe-cb88dce7a638.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/complete.genomic.gtf" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_0f8de3c4-24b6-4e15-a3fe-cb88dce7a638.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/complete.genomic.fna" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_86b1b0d7-edc0-494c-b475-6a00fdaa8ecc.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/complete.genomic.fna" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_86b1b0d7-edc0-494c-b475-6a00fdaa8ecc.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/complete.cds.fna" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_4005a9fb-3e55-4283-a0ba-77fe8d82e5de.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/complete.cds.fna" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_4005a9fb-3e55-4283-a0ba-77fe8d82e5de.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/complete.transcripts.fna" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_564cb214-d05e-40da-aa72-65c50bbeced4.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/complete.transcripts.fna" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_564cb214-d05e-40da-aa72-65c50bbeced4.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/complete.proteins.faa" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_1d257eea-a324-46cd-83a8-494c0324c541.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/complete.proteins.faa" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_1d257eea-a324-46cd-83a8-494c0324c541.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/annotation_data.cmt" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_87b2cce4-30bd-4c8e-8a30-6be2ebd20ae3.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/annotation_data.cmt" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_87b2cce4-30bd-4c8e-8a30-6be2ebd20ae3.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/sra_metadata.dat" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_843b8b4f-1ac1-45aa-8ca4-9670e5d9845b.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/sra_metadata.dat" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_843b8b4f-1ac1-45aa-8ca4-9670e5d9845b.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/annot_builder_output/accept.ftable_annot" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_b84745a3-0ebf-45be-87b2-d99560922fc4.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/annot_builder_output/accept.ftable_annot" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_b84745a3-0ebf-45be-87b2-d99560922fc4.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/GNOMON/contam_rpt.tsv" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_81cb1317-08b4-48f9-9dc7-ad4f9f9456e0.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/GNOMON/contam_rpt.tsv" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_81cb1317-08b4-48f9-9dc7-ad4f9f9456e0.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/GNOMON/new.gnomon_report.txt" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_8e4f9bc0-bab6-4c3f-af25-a6c9e6f3a91e.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/GNOMON/new.gnomon_report.txt" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_8e4f9bc0-bab6-4c3f-af25-a6c9e6f3a91e.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/GNOMON/new.gnomon_quality_report.txt" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_2d22879e-6fe2-483f-9373-80d6be054347.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/GNOMON/new.gnomon_quality_report.txt" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_2d22879e-6fe2-483f-9373-80d6be054347.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/busco/short_summary"*".txt" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_283e64f8-1a0d-405a-a967-0da98f110146.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/busco/short_summary"*".txt" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_283e64f8-1a0d-405a-a967-0da98f110146.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/busco/short_summary"*".json" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_768444e3-6fbf-432b-8722-931960626e7d.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/busco/short_summary"*".json" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_768444e3-6fbf-432b-8722-931960626e7d.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/stats/feature_counts.xml" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_2e650590-d0d5-4760-a010-36e201e94dfa.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/stats/feature_counts.xml" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_2e650590-d0d5-4760-a010-36e201e94dfa.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/stats/feature_stats.xml" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_b6853bf2-98f3-4573-a484-e49b1dc11906.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/stats/feature_stats.xml" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_b6853bf2-98f3-4573-a484-e49b1dc11906.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/validated/all_unannotated.val" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_904262d0-13c6-448d-bce8-1aaa9fbc8d36.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/validated/all_unannotated.val" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_904262d0-13c6-448d-bce8-1aaa9fbc8d36.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/validated/genome.val" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_3aff342c-7c8d-468b-a1d2-0a6c74b728a7.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/validated/genome.val" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_3aff342c-7c8d-468b-a1d2-0a6c74b728a7.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/nextflow/nextflow.log" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_78db6609-c17e-4889-ab79-28c01e9cacfd.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/nextflow/nextflow.log" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_78db6609-c17e-4889-ab79-28c01e9cacfd.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/nextflow/run.report.html" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_60cc9fc6-513e-40af-ae64-b958743fee8d.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/nextflow/run.report.html" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_60cc9fc6-513e-40af-ae64-b958743fee8d.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/nextflow/run.timeline.html" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_cea0b32c-175d-48e8-b754-4aefb0090998.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/nextflow/run.timeline.html" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_cea0b32c-175d-48e8-b754-4aefb0090998.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/nextflow/run.trace.txt" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_abd6cb6c-2406-4fb6-8103-01a2e8568555.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/nextflow/run.trace.txt" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_abd6cb6c-2406-4fb6-8103-01a2e8568555.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/nextflow/run_params.yaml" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_503fe38c-0618-4a15-b891-a87e3eca8d64.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/nextflow/run_params.yaml" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_503fe38c-0618-4a15-b891-a87e3eca8d64.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/complete.genomic.gff" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_f2dcc77c-3dff-4aba-b5aa-a586e0daf1f9.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/complete.genomic.gff" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_f2dcc77c-3dff-4aba-b5aa-a586e0daf1f9.dat" ; fi; cd '/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1'; +[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code" +galaxy.jobs.runners.local DEBUG 2025-07-23 15:16:28,210 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] (1) executing job script: /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/galaxy_1.sh +galaxy.jobs.runners.util.process_groups DEBUG 2025-07-23 15:50:19,950 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 2070725 +galaxy.jobs.runners.local DEBUG 2025-07-23 15:50:19,951 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] execution finished: /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/galaxy_1.sh +galaxy.jobs DEBUG 2025-07-23 15:50:19,979 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_5de46d50-0f66-44bb-8852-9f2dd2dfa684.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/5/d/e/dataset_5de46d50-0f66-44bb-8852-9f2dd2dfa684.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,979 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_0f8de3c4-24b6-4e15-a3fe-cb88dce7a638.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/0/f/8/dataset_0f8de3c4-24b6-4e15-a3fe-cb88dce7a638.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,980 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_86b1b0d7-edc0-494c-b475-6a00fdaa8ecc.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/8/6/b/dataset_86b1b0d7-edc0-494c-b475-6a00fdaa8ecc.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,980 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_4005a9fb-3e55-4283-a0ba-77fe8d82e5de.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/4/0/0/dataset_4005a9fb-3e55-4283-a0ba-77fe8d82e5de.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,980 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_564cb214-d05e-40da-aa72-65c50bbeced4.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/5/6/4/dataset_564cb214-d05e-40da-aa72-65c50bbeced4.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,980 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_1d257eea-a324-46cd-83a8-494c0324c541.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/1/d/2/dataset_1d257eea-a324-46cd-83a8-494c0324c541.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,980 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_87b2cce4-30bd-4c8e-8a30-6be2ebd20ae3.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/8/7/b/dataset_87b2cce4-30bd-4c8e-8a30-6be2ebd20ae3.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,980 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_843b8b4f-1ac1-45aa-8ca4-9670e5d9845b.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/8/4/3/dataset_843b8b4f-1ac1-45aa-8ca4-9670e5d9845b.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,980 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_b84745a3-0ebf-45be-87b2-d99560922fc4.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/b/8/4/dataset_b84745a3-0ebf-45be-87b2-d99560922fc4.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,980 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_81cb1317-08b4-48f9-9dc7-ad4f9f9456e0.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/8/1/c/dataset_81cb1317-08b4-48f9-9dc7-ad4f9f9456e0.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,980 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_8e4f9bc0-bab6-4c3f-af25-a6c9e6f3a91e.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/8/e/4/dataset_8e4f9bc0-bab6-4c3f-af25-a6c9e6f3a91e.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,981 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_2d22879e-6fe2-483f-9373-80d6be054347.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/2/d/2/dataset_2d22879e-6fe2-483f-9373-80d6be054347.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,981 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_283e64f8-1a0d-405a-a967-0da98f110146.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/2/8/3/dataset_283e64f8-1a0d-405a-a967-0da98f110146.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,981 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_768444e3-6fbf-432b-8722-931960626e7d.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/7/6/8/dataset_768444e3-6fbf-432b-8722-931960626e7d.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,981 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_2e650590-d0d5-4760-a010-36e201e94dfa.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/2/e/6/dataset_2e650590-d0d5-4760-a010-36e201e94dfa.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,981 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_b6853bf2-98f3-4573-a484-e49b1dc11906.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/b/6/8/dataset_b6853bf2-98f3-4573-a484-e49b1dc11906.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,981 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_904262d0-13c6-448d-bce8-1aaa9fbc8d36.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/9/0/4/dataset_904262d0-13c6-448d-bce8-1aaa9fbc8d36.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,981 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_3aff342c-7c8d-468b-a1d2-0a6c74b728a7.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/3/a/f/dataset_3aff342c-7c8d-468b-a1d2-0a6c74b728a7.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,981 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_78db6609-c17e-4889-ab79-28c01e9cacfd.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/7/8/d/dataset_78db6609-c17e-4889-ab79-28c01e9cacfd.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,982 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_60cc9fc6-513e-40af-ae64-b958743fee8d.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/6/0/c/dataset_60cc9fc6-513e-40af-ae64-b958743fee8d.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,982 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_cea0b32c-175d-48e8-b754-4aefb0090998.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/c/e/a/dataset_cea0b32c-175d-48e8-b754-4aefb0090998.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,982 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_abd6cb6c-2406-4fb6-8103-01a2e8568555.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/a/b/d/dataset_abd6cb6c-2406-4fb6-8103-01a2e8568555.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,982 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_503fe38c-0618-4a15-b891-a87e3eca8d64.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/5/0/3/dataset_503fe38c-0618-4a15-b891-a87e3eca8d64.dat +galaxy.jobs DEBUG 2025-07-23 15:50:19,982 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/outputs/dataset_f2dcc77c-3dff-4aba-b5aa-a586e0daf1f9.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/f/2/d/dataset_f2dcc77c-3dff-4aba-b5aa-a586e0daf1f9.dat +galaxy.model.store.discover DEBUG 2025-07-23 15:50:20,089 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] (1) Created dynamic collection dataset for path [/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/bam.DCtVIkLXcz/GCF_020809275.1_ASM2080927v1_genomic-SRR8506572-Aligned.out.Sorted.bam] with element identifier [GCF_020809275.1_ASM2080927v1_genomic-SRR8506572-Aligned.out.Sorted] for output [star_alignments] (1.433 ms) +galaxy.model.store.discover DEBUG 2025-07-23 15:50:20,092 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] (1) Created dynamic collection dataset for path [/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/1/working/egapx_out/bam.DCtVIkLXcz/GCF_020809275.1_ASM2080927v1_genomic-SRR9005248-Aligned.out.Sorted.bam] with element identifier [GCF_020809275.1_ASM2080927v1_genomic-SRR9005248-Aligned.out.Sorted] for output [star_alignments] (0.959 ms) +galaxy.model.store.discover DEBUG 2025-07-23 15:50:20,192 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] (1) Add dynamic collection datasets to history for output [star_alignments] (99.499 ms) +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,433 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 1 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,444 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 2 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,450 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 3 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,453 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 4 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,460 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 5 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,466 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 6 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,477 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 7 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,482 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 8 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,507 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 9 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,531 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 10 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,534 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 11 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,537 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 12 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,541 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 13 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,544 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 14 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,546 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 15 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,549 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 16 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,573 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 17 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,578 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 18 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,582 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 19 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,586 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 20 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,589 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 21 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,593 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 22 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,597 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 23 +galaxy.model.metadata DEBUG 2025-07-23 15:50:20,601 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 24 +galaxy.jobs DEBUG 2025-07-23 15:50:20,687 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 1 executed (715.972 ms) +python_multipart.multipart DEBUG 2025-07-23 15:50:28,041 [pN:main.1,p:2070704,tN:MainThread] Calling on_field_start with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,042 [pN:main.1,p:2070704,tN:MainThread] Calling on_field_name with data[0:4] +python_multipart.multipart DEBUG 2025-07-23 15:50:28,042 [pN:main.1,p:2070704,tN:MainThread] Calling on_field_data with data[5:57] +python_multipart.multipart DEBUG 2025-07-23 15:50:28,042 [pN:main.1,p:2070704,tN:MainThread] Calling on_field_end with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,042 [pN:main.1,p:2070704,tN:MainThread] Calling on_end with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,219 [pN:main.1,p:2070704,tN:MainThread] Calling on_part_begin with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,219 [pN:main.1,p:2070704,tN:MainThread] Calling on_header_field with data[36:55] +python_multipart.multipart DEBUG 2025-07-23 15:50:28,220 [pN:main.1,p:2070704,tN:MainThread] Calling on_header_value with data[57:85] +python_multipart.multipart DEBUG 2025-07-23 15:50:28,220 [pN:main.1,p:2070704,tN:MainThread] Calling on_header_end with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,220 [pN:main.1,p:2070704,tN:MainThread] Calling on_headers_finished with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,220 [pN:main.1,p:2070704,tN:MainThread] Calling on_part_data with data[89:105] +python_multipart.multipart DEBUG 2025-07-23 15:50:28,221 [pN:main.1,p:2070704,tN:MainThread] Calling on_part_end with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,222 [pN:main.1,p:2070704,tN:MainThread] Calling on_part_begin with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,223 [pN:main.1,p:2070704,tN:MainThread] Calling on_header_field with data[143:162] +python_multipart.multipart DEBUG 2025-07-23 15:50:28,223 [pN:main.1,p:2070704,tN:MainThread] Calling on_header_value with data[164:189] +python_multipart.multipart DEBUG 2025-07-23 15:50:28,223 [pN:main.1,p:2070704,tN:MainThread] Calling on_header_end with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,223 [pN:main.1,p:2070704,tN:MainThread] Calling on_headers_finished with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,223 [pN:main.1,p:2070704,tN:MainThread] Calling on_part_data with data[193:386] +python_multipart.multipart DEBUG 2025-07-23 15:50:28,223 [pN:main.1,p:2070704,tN:MainThread] Calling on_part_end with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,224 [pN:main.1,p:2070704,tN:MainThread] Calling on_part_begin with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,224 [pN:main.1,p:2070704,tN:MainThread] Calling on_header_field with data[424:443] +python_multipart.multipart DEBUG 2025-07-23 15:50:28,224 [pN:main.1,p:2070704,tN:MainThread] Calling on_header_value with data[445:503] +python_multipart.multipart DEBUG 2025-07-23 15:50:28,224 [pN:main.1,p:2070704,tN:MainThread] Calling on_header_end with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,224 [pN:main.1,p:2070704,tN:MainThread] Calling on_headers_finished with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,225 [pN:main.1,p:2070704,tN:MainThread] Calling on_part_data with data[507:1114] +python_multipart.multipart DEBUG 2025-07-23 15:50:28,225 [pN:main.1,p:2070704,tN:MainThread] Calling on_part_end with no data +python_multipart.multipart DEBUG 2025-07-23 15:50:28,225 [pN:main.1,p:2070704,tN:MainThread] Calling on_end with no data +galaxy.tools INFO 2025-07-23 15:50:28,254 [pN:main.1,p:2070704,tN:AnyIO worker thread] Validated and populated state for tool request (0.553 ms) +galaxy.tools.actions.upload DEBUG 2025-07-23 15:50:28,260 [pN:main.1,p:2070704,tN:AnyIO worker thread] Persisted uploads (0.028 ms) +galaxy.tools.actions.upload DEBUG 2025-07-23 15:50:28,322 [pN:main.1,p:2070704,tN:AnyIO worker thread] Created upload job (5.266 ms) +galaxy.tools.execute DEBUG 2025-07-23 15:50:28,323 [pN:main.1,p:2070704,tN:AnyIO worker thread] Tool __DATA_FETCH__ created job None (62.906 ms) +galaxy.web_stack.handlers INFO 2025-07-23 15:50:28,348 [pN:main.1,p:2070704,tN:AnyIO worker thread] (Job[id=2,tool_id=__DATA_FETCH__]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +galaxy.tools.execute DEBUG 2025-07-23 15:50:28,355 [pN:main.1,p:2070704,tN:AnyIO worker thread] Created 1 job(s) for tool __DATA_FETCH__ request (100.073 ms) +galaxy.jobs.mapper DEBUG 2025-07-23 15:50:29,254 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: planemo_dest +galaxy.jobs.handler DEBUG 2025-07-23 15:50:29,258 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to planemo_runner runner +galaxy.jobs DEBUG 2025-07-23 15:50:29,292 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/2 +galaxy.jobs.runners DEBUG 2025-07-23 15:50:29,346 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] Job [2] queued (87.759 ms) +galaxy.jobs.handler INFO 2025-07-23 15:50:29,369 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched +galaxy.jobs DEBUG 2025-07-23 15:50:29,462 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Job wrapper for Job [2] prepared (74.804 ms) +galaxy.tool_util.deps.containers INFO 2025-07-23 15:50:29,462 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.containers INFO 2025-07-23 15:50:29,463 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Checking with container resolver [CachedMulledDockerContainerResolver[namespace=biocontainers]] found description [None] +galaxy.tool_util.deps.containers INFO 2025-07-23 15:50:29,463 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Checking with container resolver [CachedMulledDockerContainerResolver[namespace=local]] found description [None] +galaxy.tool_util.deps.containers INFO 2025-07-23 15:50:29,463 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [None] +galaxy.tool_util.deps.containers INFO 2025-07-23 15:50:29,463 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Checking with container resolver [BuildDockerContainerResolver[namespace=local]] found description [None] +galaxy.jobs.command_factory INFO 2025-07-23 15:50:29,498 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] Built script [/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/2/tool_script.sh] for tool command [python '/scratch/rico/galaxy/lib/galaxy/tools/data_fetch.py' --galaxy-root '/scratch/rico/galaxy' --datatypes-registry '/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/2/registry.xml' --request-version '1' --request '/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/2/configs/tmpq6gekxm3'] +galaxy.jobs.runners DEBUG 2025-07-23 15:50:29,539 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] (2) command is: cd working; /bin/bash /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/2/tool_script.sh > '../outputs/tool_stdout' 2> '../outputs/tool_stderr'; return_code=$?; echo $return_code > /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/2/galaxy_2.ec; cd '/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/2'; +[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code" +galaxy.jobs.runners.local DEBUG 2025-07-23 15:50:29,576 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] (2) executing job script: /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/2/galaxy_2.sh +galaxy.jobs.runners.util.process_groups DEBUG 2025-07-23 15:50:38,941 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 2186507 +galaxy.jobs.runners.local DEBUG 2025-07-23 15:50:38,942 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] execution finished: /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/2/galaxy_2.sh +galaxy.jobs DEBUG 2025-07-23 15:50:38,966 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/2/outputs/dataset_20e7659e-07fb-45ba-aaf6-3119db1dd838.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/2/0/e/dataset_20e7659e-07fb-45ba-aaf6-3119db1dd838.dat +galaxy.tool_util.provided_metadata DEBUG 2025-07-23 15:50:38,981 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'input.yaml', 'dbkey': '?', 'ext': 'yaml', 'link_data_only': False, 'sources': [], 'hashes': [], 'info': 'uploaded yaml file', 'state': 'ok', 'filename': '/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/2/working/data_fetch_upload_cab618sj', 'object_id': 27}]}]}] +galaxy.jobs DEBUG 2025-07-23 15:50:39,086 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 2 executed (128.788 ms) +galaxy.tools INFO 2025-07-23 15:50:39,437 [pN:main.1,p:2070704,tN:WSGI_0] Validated and populated state for tool request (13.039 ms) +galaxy.managers.collections DEBUG 2025-07-23 15:50:39,475 [pN:main.1,p:2070704,tN:WSGI_0] Created collection with 18 elements +galaxy.tools.actions INFO 2025-07-23 15:50:39,477 [pN:main.1,p:2070704,tN:WSGI_0] Handled collection output named output_files for tool ncbi_egapx (32.018 ms) +galaxy.managers.collections DEBUG 2025-07-23 15:50:39,484 [pN:main.1,p:2070704,tN:WSGI_0] Created collection with 5 elements +galaxy.tools.actions INFO 2025-07-23 15:50:39,485 [pN:main.1,p:2070704,tN:WSGI_0] Handled collection output named nextflow_stats for tool ncbi_egapx (8.250 ms) +galaxy.managers.collections DEBUG 2025-07-23 15:50:39,486 [pN:main.1,p:2070704,tN:WSGI_0] Created collection with 0 elements +galaxy.tools.actions INFO 2025-07-23 15:50:39,486 [pN:main.1,p:2070704,tN:WSGI_0] Handled collection output named star_alignments for tool ncbi_egapx (0.858 ms) +galaxy.tools.actions INFO 2025-07-23 15:50:39,487 [pN:main.1,p:2070704,tN:WSGI_0] Handled output named complete_genomic_gff for tool ncbi_egapx (1.047 ms) +galaxy.tools.actions INFO 2025-07-23 15:50:39,492 [pN:main.1,p:2070704,tN:WSGI_0] Added output datasets to history (4.853 ms) +galaxy.tools.actions INFO 2025-07-23 15:50:39,504 [pN:main.1,p:2070704,tN:WSGI_0] Setup for job Job[unflushed,tool_id=ncbi_egapx] complete, ready to be enqueued (11.307 ms) +galaxy.tools.execute DEBUG 2025-07-23 15:50:39,504 [pN:main.1,p:2070704,tN:WSGI_0] Tool ncbi_egapx created job None (63.269 ms) +galaxy.web_stack.handlers INFO 2025-07-23 15:50:39,564 [pN:main.1,p:2070704,tN:WSGI_0] (Job[id=3,tool_id=ncbi_egapx]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +galaxy.tools.execute DEBUG 2025-07-23 15:50:39,569 [pN:main.1,p:2070704,tN:WSGI_0] Created 1 job(s) for tool ncbi_egapx request (132.176 ms) +galaxy.jobs.mapper DEBUG 2025-07-23 15:50:39,679 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] (3) Mapped job to destination id: planemo_dest +galaxy.jobs.handler DEBUG 2025-07-23 15:50:39,700 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] (3) Dispatching to planemo_runner runner +galaxy.jobs DEBUG 2025-07-23 15:50:39,783 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] (3) Working directory for job is: /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3 +galaxy.jobs.runners DEBUG 2025-07-23 15:50:39,798 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] Job [3] queued (97.543 ms) +galaxy.jobs.handler INFO 2025-07-23 15:50:39,823 [pN:main.1,p:2070704,tN:JobHandlerQueue.monitor_thread] (3) Job dispatched +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,944 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for annotated_genome with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_b70aff95-9600-4805-b43e-bcf34b178e36.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,944 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for complete_genomic_gtf with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_844310c4-ca03-421a-b205-795e3cd81570.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,945 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for complete_genomic_fna with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_703dd77c-3f29-45ea-974d-ebdd8960ca21.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,945 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for complete_cds with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_2a439892-cedb-476f-a238-9ab07f8159c0.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,945 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for complete_transcripts with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_6da64e33-c511-4c04-8617-218fd1be83da.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,945 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for complete_proteins with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_4d0cdaaf-54c4-4710-8425-26e50a70fc18.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,945 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for annotation_data with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_96f21bb7-3c75-4584-a5ea-a187165c66c7.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,945 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for sra_metadata with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_73c96b52-307a-4627-990a-89ab07204aa7.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,945 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for gnomon_accept_ftable_annot with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_7be665e5-6390-4a25-8620-f6842d895a19.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,945 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for gnomon_contam_rpt with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_3c0bc95d-f543-4e09-bb39-8bd5e3349afd.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,945 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for gnomon_report with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_173c8997-d878-41cd-b600-4c6af5ca9601.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,945 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for gnomon_quality_report with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_2d944478-d56d-481a-a1fc-536326f20e6b.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,945 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for busco_report with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_f11d3722-9ba7-40bd-9f91-4329add8dd8d.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,945 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for busco_report_json with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_fd1c8116-690f-4bff-96ed-68c87e66cdc4.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,946 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for stats_feature_counts with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_f846430a-de2c-4053-b5fb-a58bf781f705.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,946 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for stats_feature_stats with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_4d3ddf53-22b7-493a-b9c4-49d7df7c8f14.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,946 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for validated_all_unannotated with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_df65ecec-0563-4f05-9d76-7ea286135e4c.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,946 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for validated_genome with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_4bfb8d84-9ca5-4f5d-a466-2cce5dc5bb3d.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,948 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for nextflow_log with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_eb6379e4-1031-41e7-af93-0e4e96b45324.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,949 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for run_report with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_bdf4bb3f-e41b-4bae-95fb-c9437f7c7ba1.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,949 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for run_timeline with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_3f358eae-3b80-4061-b794-e77148355711.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,949 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for run_trace with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_fe495e49-a2cf-45d2-b46a-89bbc6a89593.dat +galaxy.tools.evaluation INFO 2025-07-23 15:50:39,949 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Updating param_dict for run_params with /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_b31991c8-a963-4057-a862-7d410b3417f3.dat +galaxy.jobs DEBUG 2025-07-23 15:50:39,980 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Job wrapper for Job [3] prepared (142.504 ms) +galaxy.tool_util.deps.containers INFO 2025-07-23 15:50:39,981 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [ContainerDescription[identifier=quay.io/galaxy/egapx:0.4.1-alpha,type=docker]] +galaxy.jobs.command_factory INFO 2025-07-23 15:50:40,026 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] Built script [/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/tool_script.sh] for tool command [source /galaxy/env.bash && python3 /galaxy/scripts/galaxy-resource-config.py && python3 /galaxy/egapx/ui/egapx.py '/scratch/rico/tmp/tmp9ssqcs9d/files/2/0/e/dataset_20e7659e-07fb-45ba-aaf6-3119db1dd838.dat' -e galaxy -o 'egapx_out' && if [ -e egapx_out/accept.gff ]; then ln -s accept.gff egapx_out/complete.genomic.gff; fi && bash '/scratch/rico/galaxytools/tools/ncbi_egapx/get-bams.bash'] +galaxy.jobs.runners DEBUG 2025-07-23 15:50:40,260 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] (3) command is: cd working; +_on_exit() { + docker kill 1ac64cab5b9540d48127a246f45f3084 &> /dev/null +} +trap _on_exit EXIT +docker inspect quay.io/galaxy/egapx:0.4.1-alpha > /dev/null 2>&1 +[ $? -ne 0 ] && docker pull quay.io/galaxy/egapx:0.4.1-alpha > /dev/null 2>&1 + +docker run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -e "GALAXY_MEMORY_MB=$GALAXY_MEMORY_MB" -e "GALAXY_MEMORY_MB_PER_SLOT=$GALAXY_MEMORY_MB_PER_SLOT" -e "HOME=$HOME" -e "_GALAXY_JOB_HOME_DIR=$_GALAXY_JOB_HOME_DIR" -e "_GALAXY_JOB_TMP_DIR=$_GALAXY_JOB_TMP_DIR" -e "TMPDIR=$TMPDIR" -e "TMP=$TMP" -e "TEMP=$TEMP" -e "NXF_DEBUG=$NXF_DEBUG" -e "EGAPX_RNASEQ_QUERY_LIMIT=$EGAPX_RNASEQ_QUERY_LIMIT" --name 1ac64cab5b9540d48127a246f45f3084 -v "$_GALAXY_JOB_TMP_DIR:$_GALAXY_JOB_TMP_DIR:rw" -v "$TMPDIR:$TMPDIR:rw" -v "$TMP:$TMP:rw" -v "$TEMP:$TEMP:rw" -v /scratch/rico/galaxy:/scratch/rico/galaxy:ro -v /scratch/rico/galaxytools/tools/ncbi_egapx:/scratch/rico/galaxytools/tools/ncbi_egapx:ro -v /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3:/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3:ro -v /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs:/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs:rw -v "$_GALAXY_JOB_HOME_DIR:$_GALAXY_JOB_HOME_DIR:rw" -v /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working:/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working:rw -v /scratch/rico/tmp/tmp9ssqcs9d/files:/scratch/rico/tmp/tmp9ssqcs9d/files:ro -v /scratch/rico/galaxy/tool-data:/scratch/rico/galaxy/tool-data:ro -v /scratch/rico/galaxytools/tools/ncbi_egapx/test-data:/scratch/rico/galaxytools/tools/ncbi_egapx/test-data:ro --cpus ${GALAXY_SLOTS:-1} -w /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working --rm --user 1028:1028 quay.io/galaxy/egapx:0.4.1-alpha /bin/sh /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/tool_script.sh > '../outputs/tool_stdout' 2> '../outputs/tool_stderr'; return_code=$?; echo $return_code > /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/galaxy_3.ec; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/annotated_genome.asn" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_b70aff95-9600-4805-b43e-bcf34b178e36.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/annotated_genome.asn" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_b70aff95-9600-4805-b43e-bcf34b178e36.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/complete.genomic.gtf" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_844310c4-ca03-421a-b205-795e3cd81570.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/complete.genomic.gtf" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_844310c4-ca03-421a-b205-795e3cd81570.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/complete.genomic.fna" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_703dd77c-3f29-45ea-974d-ebdd8960ca21.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/complete.genomic.fna" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_703dd77c-3f29-45ea-974d-ebdd8960ca21.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/complete.cds.fna" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_2a439892-cedb-476f-a238-9ab07f8159c0.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/complete.cds.fna" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_2a439892-cedb-476f-a238-9ab07f8159c0.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/complete.transcripts.fna" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_6da64e33-c511-4c04-8617-218fd1be83da.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/complete.transcripts.fna" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_6da64e33-c511-4c04-8617-218fd1be83da.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/complete.proteins.faa" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_4d0cdaaf-54c4-4710-8425-26e50a70fc18.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/complete.proteins.faa" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_4d0cdaaf-54c4-4710-8425-26e50a70fc18.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/annotation_data.cmt" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_96f21bb7-3c75-4584-a5ea-a187165c66c7.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/annotation_data.cmt" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_96f21bb7-3c75-4584-a5ea-a187165c66c7.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/sra_metadata.dat" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_73c96b52-307a-4627-990a-89ab07204aa7.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/sra_metadata.dat" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_73c96b52-307a-4627-990a-89ab07204aa7.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/annot_builder_output/accept.ftable_annot" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_7be665e5-6390-4a25-8620-f6842d895a19.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/annot_builder_output/accept.ftable_annot" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_7be665e5-6390-4a25-8620-f6842d895a19.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/GNOMON/contam_rpt.tsv" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_3c0bc95d-f543-4e09-bb39-8bd5e3349afd.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/GNOMON/contam_rpt.tsv" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_3c0bc95d-f543-4e09-bb39-8bd5e3349afd.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/GNOMON/new.gnomon_report.txt" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_173c8997-d878-41cd-b600-4c6af5ca9601.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/GNOMON/new.gnomon_report.txt" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_173c8997-d878-41cd-b600-4c6af5ca9601.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/GNOMON/new.gnomon_quality_report.txt" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_2d944478-d56d-481a-a1fc-536326f20e6b.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/GNOMON/new.gnomon_quality_report.txt" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_2d944478-d56d-481a-a1fc-536326f20e6b.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/busco/short_summary"*".txt" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_f11d3722-9ba7-40bd-9f91-4329add8dd8d.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/busco/short_summary"*".txt" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_f11d3722-9ba7-40bd-9f91-4329add8dd8d.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/busco/short_summary"*".json" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_fd1c8116-690f-4bff-96ed-68c87e66cdc4.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/busco/short_summary"*".json" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_fd1c8116-690f-4bff-96ed-68c87e66cdc4.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/stats/feature_counts.xml" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_f846430a-de2c-4053-b5fb-a58bf781f705.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/stats/feature_counts.xml" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_f846430a-de2c-4053-b5fb-a58bf781f705.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/stats/feature_stats.xml" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_4d3ddf53-22b7-493a-b9c4-49d7df7c8f14.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/stats/feature_stats.xml" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_4d3ddf53-22b7-493a-b9c4-49d7df7c8f14.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/validated/all_unannotated.val" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_df65ecec-0563-4f05-9d76-7ea286135e4c.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/validated/all_unannotated.val" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_df65ecec-0563-4f05-9d76-7ea286135e4c.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/validated/genome.val" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_4bfb8d84-9ca5-4f5d-a466-2cce5dc5bb3d.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/validated/genome.val" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_4bfb8d84-9ca5-4f5d-a466-2cce5dc5bb3d.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/nextflow/nextflow.log" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_eb6379e4-1031-41e7-af93-0e4e96b45324.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/nextflow/nextflow.log" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_eb6379e4-1031-41e7-af93-0e4e96b45324.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/nextflow/run.report.html" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_bdf4bb3f-e41b-4bae-95fb-c9437f7c7ba1.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/nextflow/run.report.html" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_bdf4bb3f-e41b-4bae-95fb-c9437f7c7ba1.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/nextflow/run.timeline.html" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_3f358eae-3b80-4061-b794-e77148355711.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/nextflow/run.timeline.html" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_3f358eae-3b80-4061-b794-e77148355711.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/nextflow/run.trace.txt" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_fe495e49-a2cf-45d2-b46a-89bbc6a89593.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/nextflow/run.trace.txt" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_fe495e49-a2cf-45d2-b46a-89bbc6a89593.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/nextflow/run_params.yaml" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_b31991c8-a963-4057-a862-7d410b3417f3.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/nextflow/run_params.yaml" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_b31991c8-a963-4057-a862-7d410b3417f3.dat" ; fi; +if [ -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/complete.genomic.gff" -a -f "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_bc8b8eac-989c-40a5-bcae-efc33f8ee403.dat" ] ; then cp "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/complete.genomic.gff" "/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_bc8b8eac-989c-40a5-bcae-efc33f8ee403.dat" ; fi; cd '/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3'; +[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code" +galaxy.jobs.runners.local DEBUG 2025-07-23 15:50:40,290 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] (3) executing job script: /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/galaxy_3.sh +galaxy.util.task DEBUG 2025-07-23 16:16:24,928 [pN:main.1,p:2070704,tN:HistoryAuditTablePruneTask] Executed periodic task HistoryAuditTablePruneTask (14.088 ms) +galaxy.jobs.runners.util.process_groups DEBUG 2025-07-23 16:26:08,929 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 2186669 +galaxy.jobs.runners.local DEBUG 2025-07-23 16:26:08,930 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] execution finished: /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/galaxy_3.sh +galaxy.jobs DEBUG 2025-07-23 16:26:08,959 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_b70aff95-9600-4805-b43e-bcf34b178e36.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/b/7/0/dataset_b70aff95-9600-4805-b43e-bcf34b178e36.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,960 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_844310c4-ca03-421a-b205-795e3cd81570.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/8/4/4/dataset_844310c4-ca03-421a-b205-795e3cd81570.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,960 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_703dd77c-3f29-45ea-974d-ebdd8960ca21.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/7/0/3/dataset_703dd77c-3f29-45ea-974d-ebdd8960ca21.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,960 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_2a439892-cedb-476f-a238-9ab07f8159c0.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/2/a/4/dataset_2a439892-cedb-476f-a238-9ab07f8159c0.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,960 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_6da64e33-c511-4c04-8617-218fd1be83da.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/6/d/a/dataset_6da64e33-c511-4c04-8617-218fd1be83da.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,960 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_4d0cdaaf-54c4-4710-8425-26e50a70fc18.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/4/d/0/dataset_4d0cdaaf-54c4-4710-8425-26e50a70fc18.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,960 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_96f21bb7-3c75-4584-a5ea-a187165c66c7.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/9/6/f/dataset_96f21bb7-3c75-4584-a5ea-a187165c66c7.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,961 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_73c96b52-307a-4627-990a-89ab07204aa7.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/7/3/c/dataset_73c96b52-307a-4627-990a-89ab07204aa7.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,961 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_7be665e5-6390-4a25-8620-f6842d895a19.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/7/b/e/dataset_7be665e5-6390-4a25-8620-f6842d895a19.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,961 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_3c0bc95d-f543-4e09-bb39-8bd5e3349afd.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/3/c/0/dataset_3c0bc95d-f543-4e09-bb39-8bd5e3349afd.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,961 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_173c8997-d878-41cd-b600-4c6af5ca9601.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/1/7/3/dataset_173c8997-d878-41cd-b600-4c6af5ca9601.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,961 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_2d944478-d56d-481a-a1fc-536326f20e6b.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/2/d/9/dataset_2d944478-d56d-481a-a1fc-536326f20e6b.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,961 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_f11d3722-9ba7-40bd-9f91-4329add8dd8d.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/f/1/1/dataset_f11d3722-9ba7-40bd-9f91-4329add8dd8d.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,961 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_fd1c8116-690f-4bff-96ed-68c87e66cdc4.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/f/d/1/dataset_fd1c8116-690f-4bff-96ed-68c87e66cdc4.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,962 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_f846430a-de2c-4053-b5fb-a58bf781f705.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/f/8/4/dataset_f846430a-de2c-4053-b5fb-a58bf781f705.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,962 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_4d3ddf53-22b7-493a-b9c4-49d7df7c8f14.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/4/d/3/dataset_4d3ddf53-22b7-493a-b9c4-49d7df7c8f14.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,962 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_df65ecec-0563-4f05-9d76-7ea286135e4c.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/d/f/6/dataset_df65ecec-0563-4f05-9d76-7ea286135e4c.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,962 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_4bfb8d84-9ca5-4f5d-a466-2cce5dc5bb3d.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/4/b/f/dataset_4bfb8d84-9ca5-4f5d-a466-2cce5dc5bb3d.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,962 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_eb6379e4-1031-41e7-af93-0e4e96b45324.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/e/b/6/dataset_eb6379e4-1031-41e7-af93-0e4e96b45324.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,962 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_bdf4bb3f-e41b-4bae-95fb-c9437f7c7ba1.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/b/d/f/dataset_bdf4bb3f-e41b-4bae-95fb-c9437f7c7ba1.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,962 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_3f358eae-3b80-4061-b794-e77148355711.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/3/f/3/dataset_3f358eae-3b80-4061-b794-e77148355711.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,963 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_fe495e49-a2cf-45d2-b46a-89bbc6a89593.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/f/e/4/dataset_fe495e49-a2cf-45d2-b46a-89bbc6a89593.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,963 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_b31991c8-a963-4057-a862-7d410b3417f3.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/b/3/1/dataset_b31991c8-a963-4057-a862-7d410b3417f3.dat +galaxy.jobs DEBUG 2025-07-23 16:26:08,963 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] finish(): Moved /scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/outputs/dataset_bc8b8eac-989c-40a5-bcae-efc33f8ee403.dat to /scratch/rico/tmp/tmp9ssqcs9d/files/b/c/8/dataset_bc8b8eac-989c-40a5-bcae-efc33f8ee403.dat +galaxy.model.store.discover DEBUG 2025-07-23 16:26:09,047 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] (3) Created dynamic collection dataset for path [/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/bam.6CAY7ywo0x/GCF_020809275.1_ASM2080927v1_genomic-SRR8506572-Aligned.out.Sorted.bam] with element identifier [GCF_020809275.1_ASM2080927v1_genomic-SRR8506572-Aligned.out.Sorted] for output [star_alignments] (1.368 ms) +galaxy.model.store.discover DEBUG 2025-07-23 16:26:09,047 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] (3) Created dynamic collection dataset for path [/scratch/rico/tmp/tmp9ssqcs9d/job_working_directory/000/3/working/egapx_out/bam.6CAY7ywo0x/GCF_020809275.1_ASM2080927v1_genomic-SRR9005248-Aligned.out.Sorted.bam] with element identifier [GCF_020809275.1_ASM2080927v1_genomic-SRR9005248-Aligned.out.Sorted] for output [star_alignments] (0.660 ms) +galaxy.model.store.discover DEBUG 2025-07-23 16:26:09,131 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] (3) Add dynamic collection datasets to history for output [star_alignments] (82.752 ms) +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,412 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 28 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,420 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 29 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,432 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 30 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,435 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 31 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,441 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 32 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,445 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 33 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,448 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 34 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,459 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 35 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,487 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 36 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,511 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 37 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,514 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 38 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,517 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 39 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,520 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 40 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,523 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 41 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,526 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 42 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,529 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 43 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,553 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 44 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,556 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 45 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,559 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 46 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,562 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 47 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,564 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 48 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,567 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 49 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,570 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 50 +galaxy.model.metadata DEBUG 2025-07-23 16:26:09,573 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 51 +galaxy.jobs DEBUG 2025-07-23 16:26:09,652 [pN:main.1,p:2070704,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 3 executed (703.883 ms) +Shut down +supervisord has terminated +All 2 test(s) executed passed. +ncbi_egapx (Test #1): passed +ncbi_egapx (Test #2): passed