Mercurial > repos > richard-burhans > ncbi_egapx
diff serve.out @ 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 | |
| children |
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--- /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) 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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 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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 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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 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