=== START 2026-09-18T16:38:56Z === === docker: Docker version 24.0.6, build ed223bc === git --git-dir /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_repo config remote.origin.fetch '+refs/*:refs/*' git --git-dir /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_repo config remote.origin.mirror true git --git-dir /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_repo remote update >/dev/null 2>&1 galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input git clone --branch release_26.1 --depth 1 file:///Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_repo /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev Cloning into '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev'... if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /Users/mvandenb/.local/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /opt/homebrew/bin/python3.12; echo "Created virtualenv"; fi && if [ -e "$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 ${COMMON_STARTUP_ARGS} galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input Activated a virtualenv for Galaxy /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1 Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample Activating virtualenv at /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1 Using Python 3.12.13 environment at: /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1 Checked 313 packages in 155ms Trying to resolve path for the 'email_ban_file' option but it's empty/None Using Python 3.12.13 environment at: /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1 Using Python 3.12.13 environment at: /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1 Resolved 7 packages in 1.15s Prepared 1 package in 23ms Installed 1 package in 4ms + pykube-ng==23.6.0 The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable. Starting Galaxy with command [cd /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev && if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /Users/mvandenb/.local/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /opt/homebrew/bin/python3.12; echo "Created virtualenv"; fi && if [ -e "$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 && /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/run.sh $COMMON_STARTUP_ARGS --server-name main] Activating virtualenv at /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1 Using Python 3.12.13 environment at: /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1 Checked 313 packages in 23ms 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 Using Python 3.12.13 environment at: /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1 Using Python 3.12.13 environment at: /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1 Checked 2 packages in 5ms The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable. Activating virtualenv at /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1 Executing: galaxy Working directory: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev Executing: PYTHONPATH=lib GALAXY_CONFIG_FILE=/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy.yml celery --app galaxy.celery worker --concurrency 2 --loglevel DEBUG --pool threads --queues celery,galaxy.internal,galaxy.external Working directory: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev Working directory: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev Executing: npm_config_yes=true npx @galaxyproject/gx-it-proxy@>=0.0.6 --ip localhost --port 57895 --sessions /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/database/interactivetools_map.sqlite --verbose --proxyPathPrefix /interactivetool/ep Executing: PYTHONPATH=lib GALAXY_CONFIG_FILE=/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy.yml OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES gunicorn 'galaxy.webapps.galaxy.fast_factory:factory()' --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b localhost:57880 --workers=1 --config python:galaxy.web_stack.gunicorn_config --no-control-socket Working directory: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev Executing: PYTHONPATH=lib GALAXY_CONFIG_FILE=/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy.yml celery --app galaxy.celery beat --loglevel DEBUG --schedule /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/gravity/celerybeat-schedule [2026-09-18 18:39:17 +0200] [72527] [INFO] Starting gunicorn 26.0.0 [2026-09-18 18:39:17 +0200] [72527] [INFO] Listening at: http://127.0.0.1:57880 (72527) [2026-09-18 18:39:17 +0200] [72527] [INFO] Using worker: galaxy.webapps.galaxy.workers.Worker [2026-09-18 18:39:17 +0200] [72534] [INFO] Booting worker with pid: 72534 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 Watching path /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/database/interactivetools_map.sqlite Listening on localhost:57895 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 [2026-09-18 18:39:20,717: DEBUG/MainProcess] | Worker: Preparing bootsteps. [2026-09-18 18:39:20,718: DEBUG/MainProcess] | Worker: Building graph... [2026-09-18 18:39:20,718: DEBUG/MainProcess] | Worker: New boot order: {Beat, StateDB, Timer, Hub, Pool, Autoscaler, Consumer} [2026-09-18 18:39:20,721: DEBUG/MainProcess] | Consumer: Preparing bootsteps. [2026-09-18 18:39:20,721: DEBUG/MainProcess] Setting default socket timeout to 30 [2026-09-18 18:39:20,722: INFO/MainProcess] beat: Starting... [2026-09-18 18:39:20,722: DEBUG/MainProcess] | Consumer: Building graph... [2026-09-18 18:39:20,732: DEBUG/MainProcess] | Consumer: New boot order: {Connection, Events, Mingle, Tasks, DelayedDelivery, Agent, Control, Heart, Gossip, event loop} [2026-09-18 18:39:20,746: DEBUG/MainProcess] Current schedule: [2026-09-18 18:39:20,746: DEBUG/MainProcess] beat: Ticking with max interval->5.00 minutes [2026-09-18 18:39:20,747: DEBUG/MainProcess] beat: Waking up in 5.00 minutes. -------------- celery@Mac v5.6.3 (recovery) --- ***** ----- -- ******* ---- macOS-26.5.2-arm64-arm-64bit 2026-09-18 18:39:20 - *** --- * --- - ** ---------- [config] - ** ---------- .> app: galaxy:0x10ede7b90 - ** ---------- .> transport: sqlalchemy+sqlite:////private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/celery_broker.sqlite - ** ---------- .> results: sqlite:////private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/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.bulk_move_storage . galaxy.change_datatype . galaxy.clean_object_store_caches . galaxy.cleanup_expired_notifications . galaxy.cleanup_jwds . galaxy.cleanup_short_term_storage . galaxy.cleanup_stale_concurrency_slots . galaxy.compute_dataset_hash . galaxy.dispatch_pending_notifications . galaxy.emit_queue_metrics_task . galaxy.execute_workflow_completion_hook . 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_expired_bulk_storage_operations . galaxy.prune_history_audit_table . galaxy.prune_kombu_sqla_transport . galaxy.purge_datasets . galaxy.purge_hda . galaxy.purge_history_datasets . galaxy.queue_jobs . galaxy.recalculate_user_disk_usage . galaxy.recover_stale_bulk_storage_operation_runs . galaxy.refresh_gtn_database . galaxy.refresh_iwc_manifest . galaxy.renew_vault_token . 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 [2026-09-18 18:39:20,771: DEBUG/MainProcess] | Worker: Starting Pool [2026-09-18 18:39:20,771: DEBUG/MainProcess] ^-- substep ok [2026-09-18 18:39:20,771: DEBUG/MainProcess] | Worker: Starting Consumer [2026-09-18 18:39:20,771: DEBUG/MainProcess] | Consumer: Starting Connection [2026-09-18 18:39:20,774: INFO/MainProcess] Connected to sqlalchemy+sqlite:////private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/celery_broker.sqlite [2026-09-18 18:39:20,774: DEBUG/MainProcess] ^-- substep ok [2026-09-18 18:39:20,774: DEBUG/MainProcess] | Consumer: Starting Events [2026-09-18 18:39:20,774: DEBUG/MainProcess] ^-- substep ok [2026-09-18 18:39:20,774: DEBUG/MainProcess] | Consumer: Starting Tasks [2026-09-18 18:39:20,788: DEBUG/MainProcess] ^-- substep ok [2026-09-18 18:39:20,788: DEBUG/MainProcess] | Consumer: Starting Heart [2026-09-18 18:39:20,788: DEBUG/MainProcess] ^-- substep ok [2026-09-18 18:39:20,788: DEBUG/MainProcess] | Consumer: Starting event loop [2026-09-18 18:39:20,788: INFO/MainProcess] celery@Mac ready. DEBUG:yacman.yacman:Using yacman version 1.0.0 /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1/lib/python3.12/site-packages/paste/urlparser.py:15: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. import pkg_resources DEBUG:galaxy.app:python path is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev, /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1/bin, /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/lib, /opt/homebrew/Cellar/python@3.12/3.12.13/Frameworks/Python.framework/Versions/3.12/lib/python312.zip, /opt/homebrew/Cellar/python@3.12/3.12.13/Frameworks/Python.framework/Versions/3.12/lib/python3.12, /opt/homebrew/Cellar/python@3.12/3.12.13/Frameworks/Python.framework/Versions/3.12/lib/python3.12/lib-dynload, /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1/lib/python3.12/site-packages, /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1/lib/python3.12/site-packages/setuptools/_vendor DEBUG:galaxy.config:Configuration directory is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve DEBUG:galaxy.config:Data directory is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/database DEBUG:galaxy.config:Managed config directory is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve 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 /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/version.json INFO:galaxy.model.migrations:Creating database for URI [sqlite:////private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy.sqlite?isolation_level=IMMEDIATE] INFO:alembic.runtime.migration:Context impl SQLiteImpl. INFO:alembic.runtime.migration:Will assume non-transactional DDL. INFO:alembic.runtime.migration:Running stamp_revision -> fac9c76612f9 DEBUG:alembic.runtime.migration:new branch insert fac9c76612f9 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. DEBUG:galaxy.web_stack:GunicornApplicationStack initialized galaxy.web_stack.handlers INFO 2026-09-18 18:39:21,581 [pN:main,p:72534,tN:MainThread] JobConfiguration: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION', set the `assign_with` attribute on to override the default galaxy.jobs INFO 2026-09-18 18:39:21,581 [pN:main,p:72534,tN:MainThread] Job handler assignment methods set to: db-transaction-isolation galaxy.config.url_headers WARNING 2026-09-18 18:39:21,582 [pN:main,p:72534,tN:MainThread] URL headers configuration file not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/url_headers_conf.yml. Using null configuration. galaxy.queue_worker INFO 2026-09-18 18:39:21,583 [pN:main,p:72534,tN:MainThread] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/celery_broker.sqlite galaxy.datatypes.registry ERROR 2026-09-18 18:39:22,073 [pN:main,p:72534,tN:MainThread] Error importing datatype module galaxy.datatypes.html Traceback (most recent call last): File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/lib/galaxy/datatypes/registry.py", line 235, in load_datatypes module = __import__(datatype_module) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ ModuleNotFoundError: No module named 'galaxy.datatypes.html' galaxy.visualization.genomes ERROR 2026-09-18 18:39:22,262 [pN:main.1,p:72534,tN:MainThread] Error reading twobit.loc Traceback (most recent call last): File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/lib/galaxy/visualization/genomes.py", line 225, in reload_genomes with open(twobit_path) as f: ^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/tool-data/twobit.loc' galaxy.util WARNING 2026-09-18 18:39:22,287 [pN:main.1,p:72534,tN:MainThread] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/config/plugins/activities galaxy.tools WARNING 2026-09-18 18:39:22,288 [pN:main.1,p:72534,tN:MainThread] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:39:22,288 [pN:main.1,p:72534,tN:MainThread] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/tool_conf.xml galaxy.tools WARNING 2026-09-18 18:39:22,315 [pN:main.1,p:72534,tN:MainThread] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:39:22,315 [pN:main.1,p:72534,tN:MainThread] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/shed_tools_conf.xml galaxy.tools WARNING 2026-09-18 18:39:22,315 [pN:main.1,p:72534,tN:MainThread] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:39:22,315 [pN:main.1,p:72534,tN:MainThread] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/empty_tool_conf.xml galaxy.tools.search WARNING 2026-09-18 18:39:22,322 [pN:main.1,p:72534,tN:MainThread] Index at '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/database/tool_search_index/default' uses outdated schema, creating a new index galaxy.tools.search WARNING 2026-09-18 18:39:22,323 [pN:main.1,p:72534,tN:MainThread] Index at '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/database/tool_search_index/my_panel' uses outdated schema, creating a new index galaxy.tools.search WARNING 2026-09-18 18:39:22,324 [pN:main.1,p:72534,tN:MainThread] Index at '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/database/tool_search_index/ontology:edam_operations' uses outdated schema, creating a new index galaxy.tools.search WARNING 2026-09-18 18:39:22,325 [pN:main.1,p:72534,tN:MainThread] Index at '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/database/tool_search_index/ontology:edam_topics' uses outdated schema, creating a new index galaxy.datatypes.display_applications.application ERROR 2026-09-18 18:39:22,328 [pN:main.1,p:72534,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 2026-09-18 18:39:22,328 [pN:main.1,p:72534,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 2026-09-18 18:39:22,331 [pN:main.1,p:72534,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 2026-09-18 18:39:22,331 [pN:main.1,p:72534,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 2026-09-18 18:39:22,332 [pN:main.1,p:72534,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 2026-09-18 18:39:22,334 [pN:main.1,p:72534,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 2026-09-18 18:39:22,335 [pN:main.1,p:72534,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 2026-09-18 18:39:22,335 [pN:main.1,p:72534,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 2026-09-18 18:39:22,337 [pN:main.1,p:72534,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 2026-09-18 18:39:22,337 [pN:main.1,p:72534,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 2026-09-18 18:39:22,338 [pN:main.1,p:72534,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 2026-09-18 18:39:22,338 [pN:main.1,p:72534,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 2026-09-18 18:39:22,339 [pN:main.1,p:72534,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 2026-09-18 18:39:22,339 [pN:main.1,p:72534,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 2026-09-18 18:39:22,339 [pN:main.1,p:72534,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 2026-09-18 18:39:22,340 [pN:main.1,p:72534,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 2026-09-18 18:39:22,511 [pN:main.1,p:72534,tN:MainThread] VisualizationsRegistry, loaded plugin: example galaxy.tours._impl INFO 2026-09-18 18:39:22,517 [pN:main.1,p:72534,tN:MainThread] Loaded tour 'core.galaxy_ui' galaxy.tours._impl INFO 2026-09-18 18:39:22,521 [pN:main.1,p:72534,tN:MainThread] Loaded tour 'core.deferred' galaxy.tours._impl INFO 2026-09-18 18:39:22,524 [pN:main.1,p:72534,tN:MainThread] Loaded tour 'core.windows' galaxy.tours._impl INFO 2026-09-18 18:39:22,526 [pN:main.1,p:72534,tN:MainThread] Loaded tour 'core.visualizations' galaxy.tours._impl INFO 2026-09-18 18:39:22,530 [pN:main.1,p:72534,tN:MainThread] Loaded tour 'core.history' galaxy.workflow.scheduling_manager INFO 2026-09-18 18:39:22,542 [pN:main.1,p:72534,tN:MainThread] No workflow schedulers plugin config file defined, using default scheduler. galaxy.web_stack.handlers INFO 2026-09-18 18:39:22,542 [pN:main.1,p:72534,tN:MainThread] WorkflowSchedulingManager: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION', set the `assign_with` attribute on to override the default galaxy.jobs.handler INFO 2026-09-18 18:39:22,545 [pN:main.1,p:72534,tN:WorkflowRequestMonitor.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION' assignment method for handler 'main.1', tag(s): None, _default_ galaxy.workflow.completion_hooks INFO 2026-09-18 18:39:22,548 [pN:main.1,p:72534,tN:MainThread] Enabling workflow completion hook: send_notification galaxy.workflow.completion_hooks INFO 2026-09-18 18:39:22,548 [pN:main.1,p:72534,tN:MainThread] Enabling workflow completion hook: export_to_file_source galaxy.workflow.completion_monitor INFO 2026-09-18 18:39:22,548 [pN:main.1,p:72534,tN:MainThread] Starting workflow completion monitor galaxy.jobs INFO 2026-09-18 18:39:22,549 [pN:main.1,p:72534,tN:MainThread] Handler 'main.1' will load all configured runner plugins galaxy.jobs.handler INFO 2026-09-18 18:39:22,563 [pN:main.1,p:72534,tN:JobHandlerQueue.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION' assignment method for handler 'main.1', tag(s): galaxy.jobs.handler INFO 2026-09-18 18:39:22,563 [pN:main.1,p:72534,tN:MainThread] job handler queue started galaxy.jobs.handler INFO 2026-09-18 18:39:22,564 [pN:main.1,p:72534,tN:MainThread] job handler stop queue started galaxy.queue_worker INFO 2026-09-18 18:39:22,565 [pN:main.1,p:72534,tN:MainThread] Binding and starting galaxy control worker for main.1 galaxy.queue_worker INFO 2026-09-18 18:39:22,567 [pN:main.1,p:72534,tN:MainThread] Queuing async task rebuild_toolbox_search_index for main.1. galaxy.app INFO 2026-09-18 18:39:22,586 [pN:main.1,p:72534,tN:MainThread] Galaxy app startup finished (1384.813 ms) galaxy.queue_worker INFO 2026-09-18 18:39:23,714 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. galaxy.web_stack INFO 2026-09-18 18:39:26,964 [pN:main.1,p:72534,tN:MainThread] Galaxy server instance 'main.1' is running Serving on http://127.0.0.1:57880 ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing ephemeris.shed_tools WARNING: 'tool_shed' not a valid key. Will be skipped during parsing [2026-09-18 18:39:30 +0200] [72534] [INFO] Started server process [72534] [2026-09-18 18:39:30 +0200] [72534] [INFO] Waiting for application startup. [2026-09-18 18:39:30 +0200] [72534] [INFO] Application startup complete. uvicorn.access INFO 2026-09-18 18:39:30,915 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:57932 - "GET /api/version HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:39:30,949 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:57934 - "GET /api/tools?in_panel=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:39:30,954 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:57936 - "GET /api/tools?in_panel=False HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:39:30,960 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:57938 - "GET /api/tool_shed_repositories HTTP/1.1" 200 galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-18 18:39:33,749 [pN:main.1,p:72534,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/devteam/fastqc' at 24:2c64fded1286 galaxy.queue_worker INFO 2026-09-18 18:39:38,214 [pN:main.1,p:72534,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1. galaxy.queue_worker INFO 2026-09-18 18:39:38,566 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now. galaxy.util WARNING 2026-09-18 18:39:38,568 [pN:main.1,p:72534,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/config/plugins/activities galaxy.tools WARNING 2026-09-18 18:39:38,569 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:39:38,570 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/tool_conf.xml galaxy.tools WARNING 2026-09-18 18:39:38,571 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:39:38,571 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/shed_tools_conf.xml galaxy.tools WARNING 2026-09-18 18:39:38,572 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:39:38,572 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/empty_tool_conf.xml galaxy.queue_worker INFO 2026-09-18 18:39:38,588 [pN:main.1,p:72534,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. galaxy.queue_worker INFO 2026-09-18 18:39:38,595 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. uvicorn.access INFO 2026-09-18 18:39:38,649 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:57940 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.queue_worker INFO 2026-09-18 18:39:39,226 [pN:main.1,p:72534,tN:Thread-4 (check)] Sending reload_toolbox control task. galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-18 18:39:40,847 [pN:main.1,p:72534,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt' at 46:f6168dd17f82 galaxy.tool_util.data WARNING 2026-09-18 18:39:46,152 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:39:46,153 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:39:46,153 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:39:46,154 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:39:46,154 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:39:46,154 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:39:46,155 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:39:46,155 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:39:46,155 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:39:46,156 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:39:46,156 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:39:46,157 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:39:46,157 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:39:46,157 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:39:46,158 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['TGTAGGCC', 'Dummy-Adapter (do not use me)']) to data table 'adapters', but this entry already exists and allow_duplicates is False. galaxy.queue_worker INFO 2026-09-18 18:39:54,756 [pN:main.1,p:72534,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1. galaxy.queue_worker INFO 2026-09-18 18:39:55,446 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now. galaxy.util WARNING 2026-09-18 18:39:55,447 [pN:main.1,p:72534,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/config/plugins/activities galaxy.tools WARNING 2026-09-18 18:39:55,448 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:39:55,448 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/tool_conf.xml galaxy.tools WARNING 2026-09-18 18:39:55,449 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:39:55,450 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/shed_tools_conf.xml galaxy.tools WARNING 2026-09-18 18:39:55,450 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:39:55,450 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/empty_tool_conf.xml galaxy.queue_worker INFO 2026-09-18 18:39:55,462 [pN:main.1,p:72534,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. galaxy.queue_worker INFO 2026-09-18 18:39:55,466 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. uvicorn.access INFO 2026-09-18 18:39:55,569 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:57950 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.queue_worker INFO 2026-09-18 18:39:55,777 [pN:main.1,p:72534,tN:Thread-4 (check)] Sending reload_toolbox control task. galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-18 18:39:57,726 [pN:main.1,p:72534,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar' at 34:d8d32326fbfb galaxy.queue_worker INFO 2026-09-18 18:40:01,842 [pN:main.1,p:72534,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1. galaxy.queue_worker INFO 2026-09-18 18:40:02,684 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now. galaxy.util WARNING 2026-09-18 18:40:02,686 [pN:main.1,p:72534,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/config/plugins/activities galaxy.tools WARNING 2026-09-18 18:40:02,687 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:02,688 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/tool_conf.xml galaxy.tools WARNING 2026-09-18 18:40:02,689 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:02,689 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/shed_tools_conf.xml galaxy.tools WARNING 2026-09-18 18:40:02,690 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:02,690 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/empty_tool_conf.xml galaxy.queue_worker INFO 2026-09-18 18:40:02,705 [pN:main.1,p:72534,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. galaxy.queue_worker INFO 2026-09-18 18:40:02,712 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. uvicorn.access INFO 2026-09-18 18:40:02,802 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:57967 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.queue_worker INFO 2026-09-18 18:40:02,858 [pN:main.1,p:72534,tN:Thread-4 (check)] Sending reload_toolbox control task. galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-18 18:40:04,975 [pN:main.1,p:72534,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/map_param_value' at 3:022a635f2283 galaxy.queue_worker INFO 2026-09-18 18:40:06,892 [pN:main.1,p:72534,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1. galaxy.queue_worker INFO 2026-09-18 18:40:06,909 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now. galaxy.util WARNING 2026-09-18 18:40:06,911 [pN:main.1,p:72534,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/config/plugins/activities galaxy.tools WARNING 2026-09-18 18:40:06,913 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:06,913 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/tool_conf.xml galaxy.tools WARNING 2026-09-18 18:40:06,914 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:06,914 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/shed_tools_conf.xml galaxy.tools WARNING 2026-09-18 18:40:06,915 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:06,916 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/empty_tool_conf.xml galaxy.queue_worker INFO 2026-09-18 18:40:06,931 [pN:main.1,p:72534,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. galaxy.queue_worker INFO 2026-09-18 18:40:06,936 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. uvicorn.access INFO 2026-09-18 18:40:06,994 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:57980 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.queue_worker INFO 2026-09-18 18:40:07,925 [pN:main.1,p:72534,tN:Thread-4 (check)] Sending reload_toolbox control task. galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-18 18:40:09,109 [pN:main.1,p:72534,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/featurecounts' at 36:37d067694d40 galaxy.tool_util.data WARNING 2026-09-18 18:40:11,654 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['hg38', 'hg38']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:40:11,655 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['hg19', 'hg19']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:40:11,655 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['mm10', 'mm10']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:40:11,655 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['mm9', 'mm9']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:40:11,655 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['hg38', 'hg38']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:40:11,655 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['hg19', 'hg19']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:40:11,656 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['mm10', 'mm10']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False. galaxy.tool_util.data WARNING 2026-09-18 18:40:11,656 [pN:main.1,p:72534,tN:WSGI_0] Attempted to add fields (['mm9', 'mm9']) to data table 'featurecounts_anno', but this entry already exists and allow_duplicates is False. galaxy.queue_worker INFO 2026-09-18 18:40:12,987 [pN:main.1,p:72534,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1. galaxy.queue_worker INFO 2026-09-18 18:40:13,082 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now. galaxy.util WARNING 2026-09-18 18:40:13,083 [pN:main.1,p:72534,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/config/plugins/activities galaxy.tools WARNING 2026-09-18 18:40:13,084 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:13,084 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/tool_conf.xml galaxy.tools WARNING 2026-09-18 18:40:13,085 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:13,085 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/shed_tools_conf.xml galaxy.tools WARNING 2026-09-18 18:40:13,086 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:13,086 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/empty_tool_conf.xml galaxy.queue_worker INFO 2026-09-18 18:40:13,095 [pN:main.1,p:72534,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. galaxy.queue_worker INFO 2026-09-18 18:40:13,100 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. uvicorn.access INFO 2026-09-18 18:40:13,153 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:57990 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.queue_worker INFO 2026-09-18 18:40:13,996 [pN:main.1,p:72534,tN:Thread-4 (check)] Sending reload_toolbox control task. galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-18 18:40:15,257 [pN:main.1,p:72534,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param' at 1:e188c9826e0f galaxy.queue_worker INFO 2026-09-18 18:40:17,033 [pN:main.1,p:72534,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1. galaxy.queue_worker INFO 2026-09-18 18:40:17,399 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now. galaxy.util WARNING 2026-09-18 18:40:17,401 [pN:main.1,p:72534,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/config/plugins/activities galaxy.tools WARNING 2026-09-18 18:40:17,402 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:17,403 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/tool_conf.xml galaxy.tools WARNING 2026-09-18 18:40:17,404 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:17,404 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/shed_tools_conf.xml galaxy.tools WARNING 2026-09-18 18:40:17,405 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:17,405 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/empty_tool_conf.xml galaxy.queue_worker INFO 2026-09-18 18:40:17,421 [pN:main.1,p:72534,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. galaxy.queue_worker INFO 2026-09-18 18:40:17,427 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. uvicorn.access INFO 2026-09-18 18:40:17,465 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58000 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.queue_worker INFO 2026-09-18 18:40:18,050 [pN:main.1,p:72534,tN:Thread-4 (check)] Sending reload_toolbox control task. galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager INFO 2026-09-18 18:40:19,183 [pN:main.1,p:72534,tN:WSGI_0] Skipping installation of revision e188c9826e0f of repository 'compose_text_param' because it was installed with the (possibly updated) revision e188c9826e0f and its current installation status is 'Installed'. uvicorn.access INFO 2026-09-18 18:40:19,185 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58009 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager INFO 2026-09-18 18:40:20,925 [pN:main.1,p:72534,tN:WSGI_0] Skipping installation of revision e188c9826e0f of repository 'compose_text_param' because it was installed with the (possibly updated) revision e188c9826e0f and its current installation status is 'Installed'. uvicorn.access INFO 2026-09-18 18:40:20,927 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58014 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-18 18:40:23,212 [pN:main.1,p:72534,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/deseq2' at 35:05f9e54d7e81 galaxy.queue_worker INFO 2026-09-18 18:40:26,118 [pN:main.1,p:72534,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1. galaxy.queue_worker INFO 2026-09-18 18:40:26,609 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now. galaxy.util WARNING 2026-09-18 18:40:26,611 [pN:main.1,p:72534,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/config/plugins/activities galaxy.tools WARNING 2026-09-18 18:40:26,612 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:26,612 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/tool_conf.xml galaxy.tools WARNING 2026-09-18 18:40:26,613 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:26,614 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/shed_tools_conf.xml galaxy.tools WARNING 2026-09-18 18:40:26,615 [pN:main.1,p:72534,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/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 2026-09-18 18:40:26,615 [pN:main.1,p:72534,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/empty_tool_conf.xml galaxy.queue_worker INFO 2026-09-18 18:40:26,629 [pN:main.1,p:72534,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. galaxy.queue_worker INFO 2026-09-18 18:40:26,635 [pN:main.1,p:72534,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. uvicorn.access INFO 2026-09-18 18:40:26,725 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58019 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.queue_worker INFO 2026-09-18 18:40:27,129 [pN:main.1,p:72534,tN:Thread-4 (check)] Sending reload_toolbox control task. galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager INFO 2026-09-18 18:40:28,477 [pN:main.1,p:72534,tN:WSGI_0] Skipping installation of revision 05f9e54d7e81 of repository 'deseq2' because it was installed with the (possibly updated) revision 05f9e54d7e81 and its current installation status is 'Installed'. uvicorn.access INFO 2026-09-18 18:40:28,479 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58031 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager INFO 2026-09-18 18:40:30,230 [pN:main.1,p:72534,tN:WSGI_0] Skipping installation of revision e188c9826e0f of repository 'compose_text_param' because it was installed with the (possibly updated) revision e188c9826e0f and its current installation status is 'Installed'. uvicorn.access INFO 2026-09-18 18:40:30,230 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58036 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager INFO 2026-09-18 18:40:31,935 [pN:main.1,p:72534,tN:WSGI_0] Skipping installation of revision e188c9826e0f of repository 'compose_text_param' because it was installed with the (possibly updated) revision e188c9826e0f and its current installation status is 'Installed'. uvicorn.access INFO 2026-09-18 18:40:31,935 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58042 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:31,945 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58048 - "GET /api/users HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:31,948 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58050 - "GET /api/configuration HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:31,982 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58052 - "POST /api/users HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:31,992 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58054 - "POST /api/users/ebe71a73e20b643c/api_key HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:32,109 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58056 - "POST /api/workflows/upload HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:32,137 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58059 - "POST /api/histories HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:32,140 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58061 - "GET /api/version HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:32,145 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58063 - "GET /api/configuration HTTP/1.1" 200 galaxy.tools INFO 2026-09-18 18:40:32,157 [pN:main.1,p:72534,tN:AnyIO worker thread] Validated and populated state for tool request (0.053 ms) uvicorn.access INFO 2026-09-18 18:40:32,214 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58065 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:32,235 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58067 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:32,518 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58070 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 [2026-09-18 18:40:32,671: INFO/MainProcess] Task galaxy.setup_fetch_data[10c5fb43-a795-4933-99ea-5dcaf3535adf] received [2026-09-18 18:40:32,672: DEBUG/MainProcess] TaskPool: Apply (args:('galaxy.setup_fetch_data', '10c5fb43-a795-4933-99ea-5dcaf3535adf', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': '10c5fb43-a795-4933-99ea-5dcaf3535adf', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '10c5fb43-a795-4933-99ea-5dcaf3535adf', 'parent_id': None, 'argsrepr': '(1,)', 'kwargsrepr': '{\'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request \\\'$request_path\\\'\n ... kwargs:{}) uvicorn.access INFO 2026-09-18 18:40:32,788 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58073 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 [2026-09-18 18:40:32,909: INFO/MainProcess] setup plugin alembic.autogenerate.schemas [2026-09-18 18:40:32,909: INFO/MainProcess] setup plugin alembic.autogenerate.tables [2026-09-18 18:40:32,909: INFO/MainProcess] setup plugin alembic.autogenerate.types [2026-09-18 18:40:32,909: INFO/MainProcess] setup plugin alembic.autogenerate.constraints [2026-09-18 18:40:32,909: INFO/MainProcess] setup plugin alembic.autogenerate.defaults [2026-09-18 18:40:32,909: INFO/MainProcess] setup plugin alembic.autogenerate.comments [2026-09-18 18:40:33,029: DEBUG/MainProcess] python path is: /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1/bin, /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/lib, /opt/homebrew/Cellar/python@3.12/3.12.13/Frameworks/Python.framework/Versions/3.12/lib/python312.zip, /opt/homebrew/Cellar/python@3.12/3.12.13/Frameworks/Python.framework/Versions/3.12/lib/python3.12, /opt/homebrew/Cellar/python@3.12/3.12.13/Frameworks/Python.framework/Versions/3.12/lib/python3.12/lib-dynload, /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1/lib/python3.12/site-packages [2026-09-18 18:40:33,030: DEBUG/MainProcess] Configuration directory is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve [2026-09-18 18:40:33,030: DEBUG/MainProcess] Data directory is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/database [2026-09-18 18:40:33,030: DEBUG/MainProcess] Managed config directory is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve uvicorn.access INFO 2026-09-18 18:40:33,058 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58076 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 [2026-09-18 18:40:33,217: WARNING/MainProcess] Option master_api_key has been deprecated in favor of bootstrap_admin_api_key [2026-09-18 18:40:33,217: WARNING/MainProcess] Trying to resolve path for the 'email_ban_file' option but it's empty/None [2026-09-18 18:40:33,217: WARNING/MainProcess] Trying to resolve path for the 'data_manager_config_file' option but it's empty/None [2026-09-18 18:40:33,217: DEBUG/MainProcess] No extra version JSON file detected at /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/version.json [2026-09-18 18:40:33,219: INFO/MainProcess] Install database targeting Galaxy's database configuration. [2026-09-18 18:40:33,225: DEBUG/main] WeblessApplicationStack initialized [2026-09-18 18:40:33,229: DEBUG/main] Read job configuration from file: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_conf.yml [2026-09-18 18:40:33,231: DEBUG/main] Database does not support WITH FOR UPDATE statement, cannot use DB-SKIP-LOCKED handler assignment [2026-09-18 18:40:33,231: INFO/main] JobConfiguration: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION', set the `assign_with` attribute on to override the default [2026-09-18 18:40:33,231: INFO/main] Job handler assignment methods set to: db-transaction-isolation [2026-09-18 18:40:33,231: DEBUG/main] default set to child with id or tag 'local' [2026-09-18 18:40:33,231: DEBUG/main] Done loading job configuration [2026-09-18 18:40:33,233: WARNING/main] URL headers configuration file not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/url_headers_conf.yml. Using null configuration. [2026-09-18 18:40:33,234: INFO/main] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/celery_broker.sqlite [2026-09-18 18:40:33,263: WARNING/main] /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1/lib/python3.12/site-packages/fs/__init__.py:4: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. __import__("pkg_resources").declare_namespace(__name__) # type: ignore uvicorn.access INFO 2026-09-18 18:40:33,327 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58079 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 [2026-09-18 18:40:33,523: DEBUG/main] Loading datatypes from /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/lib/galaxy/config/sample/datatypes_conf.xml.sample [2026-09-18 18:40:33,523: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.h. [2026-09-18 18:40:33,523: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.c. [2026-09-18 18:40:33,523: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cpp. [2026-09-18 18:40:33,523: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.py. [2026-09-18 18:40:33,523: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.go. [2026-09-18 18:40:33,523: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.rs. [2026-09-18 18:40:33,523: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cs. [2026-09-18 18:40:33,523: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markdown. [2026-09-18 18:40:33,523: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension rmd. [2026-09-18 18:40:33,523: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hep.root. [2026-09-18 18:40:33,523: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:JP2 from the datatype registry for extension jp2. [2026-09-18 18:40:33,523: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry for extension ab1. [2026-09-18 18:40:33,523: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension a2m. [2026-09-18 18:40:33,524: DEBUG/main] Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry for extension afg. [2026-09-18 18:40:33,524: DEBUG/main] Retrieved datatype module galaxy.datatypes.goldenpath:GoldenPath from the datatype registry for extension agp. [2026-09-18 18:40:33,524: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension alto. [2026-09-18 18:40:33,524: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension page.xml. [2026-09-18 18:40:33,524: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension abbyy.xml. [2026-09-18 18:40:33,525: ERROR/main] Error importing datatype module galaxy.datatypes.html Traceback (most recent call last): File "/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/lib/galaxy/datatypes/registry.py", line 235, in load_datatypes module = __import__(datatype_module) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ ModuleNotFoundError: No module named 'galaxy.datatypes.html' [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_cog_profile. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_composite. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension anvio_classifier. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioContigsDB from the datatype registry for extension anvio_contigs_db. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioDB from the datatype registry for extension anvio_db. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioGenomesDB from the datatype registry for extension anvio_genomes_db. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioPanDB from the datatype registry for extension anvio_pan_db. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_pfam_profile. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioProfileDB from the datatype registry for extension anvio_profile_db. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioSamplesDB from the datatype registry for extension anvio_samples_db. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension anvio_state. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioStructureDB from the datatype registry for extension anvio_structure_db. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension anvio_variability. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry for extension arff. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Paf from the datatype registry for extension paf. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Taf from the datatype registry for extension taf. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Gfa1 from the datatype registry for extension gfa1. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Gfa2 from the datatype registry for extension gfa2. [2026-09-18 18:40:33,526: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension asn1. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension asn1-binary. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry for extension axt. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry for extension fli. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry for extension bam. [2026-09-18 18:40:33,527: DEBUG/main] Loaded preferred visualization definition: bam -> igv [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bai. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BamInputSorted from the datatype registry for extension qname_input_sorted.bam. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BamQuerynameSorted from the datatype registry for extension qname_sorted.bam. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BamNative from the datatype registry for extension unsorted.bam. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ProBam from the datatype registry for extension probam. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry for extension cram. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry for extension bed. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry for extension bedgraph. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry for extension bedstrict. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry for extension bed6. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry for extension bed12. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:ProBed from the datatype registry for extension probed. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry for extension len. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:DAA from the datatype registry for extension daa. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RMA6 from the datatype registry for extension rma6. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:DMND from the datatype registry for extension dmnd. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Parquet from the datatype registry for extension parquet. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension arrow. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Idat from the datatype registry for extension idat. [2026-09-18 18:40:33,527: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry for extension bigbed. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry for extension bigwig. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cxb. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry for extension chrint. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension csv. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:GeoCSV from the datatype registry for extension geocsv. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension tsv. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension intermine_tabular. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry for extension customtrack. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry for extension bowtie_color_index. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry for extension bowtie_base_index. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry for extension csfasta. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension data. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gz. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension binary. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension las. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension laz. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension pnts. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension d3_hierarchy. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:CytoscapeJson from the datatype registry for extension cytoscapejson. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension freq.json. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:ImgtJson from the datatype registry for extension imgt.json. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:GeoJson from the datatype registry for extension geojson. [2026-09-18 18:40:33,528: DEBUG/main] Loaded preferred visualization definition: geojson -> openlayers [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:VitessceJson from the datatype registry for extension vitessce.json. [2026-09-18 18:40:33,528: DEBUG/main] Loaded preferred visualization definition: vitessce.json -> vitessce [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:AuspiceJson from the datatype registry for extension auspice.json. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:DataManagerJson from the datatype registry for extension data_manager_json. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry for extension dbn. [2026-09-18 18:40:33,528: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension fai. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension fasta. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fastg from the datatype registry for extension fastg. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry for extension fastq. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry for extension fastqsanger. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry for extension fastqsolexa. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry for extension fastqcssanger. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry for extension fastqillumina. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry for extension fqtoc. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry for extension eland. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry for extension elandmulti. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry for extension genetrack. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension a3m. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry for extension gff. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry for extension gff3. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry for extension gif. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry for extension gmaj.zip. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension graph_dot. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry for extension gtf. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension toolshed.gz. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hdf4. [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension h5. [2026-09-18 18:40:33,529: DEBUG/main] Loaded preferred visualization definition: h5 -> h5web [2026-09-18 18:40:33,529: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension scool. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Grib from the datatype registry for extension grib. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Loom from the datatype registry for extension loom. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Anndata from the datatype registry for extension h5ad. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension h5mu. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Visium from the datatype registry for extension visium.tar.gz. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mz5. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mzmlb. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mbi. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hyphy_results.json. [2026-09-18 18:40:33,530: DEBUG/main] Loaded preferred visualization definition: hyphy_results.json -> hyphyvision [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hivtrace. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Hic from the datatype registry for extension hic. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Cool from the datatype registry for extension cool. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MCool from the datatype registry for extension mcool. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5MLM from the datatype registry for extension h5mlm. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:LudwigModel from the datatype registry for extension ludwig_model. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension html. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension ludwig_report.html. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry for extension interval. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension jellyfish. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_ktab. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_hist. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_prof. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension fastk_ktab_tar. [2026-09-18 18:40:33,530: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Numpy from the datatype registry for extension npy. uvicorn.access INFO 2026-09-18 18:40:33,597 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58081 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 [2026-09-18 18:40:33,609: DEBUG/main] Retrieved datatype module galaxy.datatypes.isa:IsaTab from the datatype registry for extension isa-tab. [2026-09-18 18:40:33,609: DEBUG/main] Retrieved datatype module galaxy.datatypes.isa:IsaJson from the datatype registry for extension isa-json. [2026-09-18 18:40:33,609: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension picard_interval_list. [2026-09-18 18:40:33,609: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_interval. [2026-09-18 18:40:33,609: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_report. [2026-09-18 18:40:33,609: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_dbsnp. [2026-09-18 18:40:33,609: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_tranche. [2026-09-18 18:40:33,609: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_recal. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cnn. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cns. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cnr. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hhr. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry for extension jpg. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tiff. [2026-09-18 18:40:33,610: DEBUG/main] Loaded preferred visualization definition: tiff -> tiffviewer [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf2. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf8. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension btf. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tif. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension svs. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension scn. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension bif. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:OMETiff from the datatype registry for extension ome.tiff. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Dicom from the datatype registry for extension dcm. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vms. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vmu. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension ndpi. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry for extension mrxs. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry for extension svslide. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry for extension bmp. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry for extension im. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry for extension pcd. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry for extension pcx. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry for extension ppm. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry for extension psd. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry for extension xbm. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry for extension xpm. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry for extension rgb. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry for extension pbm. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry for extension pgm. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nrrd. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nhdr. [2026-09-18 18:40:33,610: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry for extension rna_eps. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Artifact from the datatype registry for extension qza. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Visualization from the datatype registry for extension qzv. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Metadata from the datatype registry for extension qiime2.tabular. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension zip. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension ncbi_genome_dataset.zip. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedZarrZipArchive from the datatype registry for extension zarr.zip. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedOMEZarrZipArchive from the datatype registry for extension ome_zarr.zip. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:SpatialData from the datatype registry for extension spatialdata.zip. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension tar. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension directory. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension bwa_index. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension bwa_mem2_index. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension egapx_local_cache. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension lexicmap_index. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension kmindex. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:ZarrDirectory from the datatype registry for extension zarr. [2026-09-18 18:40:33,611: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:OMEZarr from the datatype registry for extension ome_zarr. [2026-09-18 18:40:33,612: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension yaml. [2026-09-18 18:40:33,612: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mrm. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Dta from the datatype registry for extension dta. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Dta2d from the datatype registry for extension dta2d. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Edta from the datatype registry for extension edta. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension pepxml. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension raw_pepxml. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension peptideprophet_pepxml. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension interprophet_pepxml. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry for extension protxml. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ParamXml from the datatype registry for extension paramxml. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Kroenik from the datatype registry for extension kroenik. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepList from the datatype registry for extension peplist. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PSMS from the datatype registry for extension psms. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry for extension pepxml.tsv. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry for extension protxml.tsv. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry for extension mascotdat. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry for extension mzid. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry for extension idxml. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry for extension tandem. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sirius.ms. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry for extension thermo.raw. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BafTar from the datatype registry for extension brukerbaf.d.tar. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:YepTar from the datatype registry for extension agilentbrukeryep.d.tar. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:TdfTar from the datatype registry for extension brukertdf.d.tar. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MassHunterTar from the datatype registry for extension agilentmasshunter.d.tar. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MassLynxTar from the datatype registry for extension watersmasslynx.raw.tar. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:WiffTar from the datatype registry for extension wiff.tar. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Wiff2Tar from the datatype registry for extension wiff2.tar. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MascotXML from the datatype registry for extension mascotxml. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzTab from the datatype registry for extension mztab. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzTab2 from the datatype registry for extension mztab2. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry for extension mzml. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:NmrML from the datatype registry for extension nmrml. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Meryldb from the datatype registry for extension meryldb. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Bref3 from the datatype registry for extension bref3. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry for extension mgf. [2026-09-18 18:40:33,613: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry for extension wiff. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Wiff2 from the datatype registry for extension wiff2. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry for extension mzxml. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry for extension mzdata. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry for extension ms2. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry for extension mzq. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry for extension sqlite. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry for extension mz.sqlite. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OSW from the datatype registry for extension osw. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:PQP from the datatype registry for extension pqp. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry for extension traml. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:TrafoXML from the datatype registry for extension trafoxml. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry for extension featurexml. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry for extension consensusxml. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry for extension uniprotxml. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:XquestXML from the datatype registry for extension xquest.xml. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:XquestSpecXML from the datatype registry for extension spec.xml. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:QCML from the datatype registry for extension qcml. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension mzqc. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry for extension msp. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry for extension splib_noindex. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry for extension splib. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BlibSQlite from the datatype registry for extension blib. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:DlibSQlite from the datatype registry for extension dlib. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ElibSQlite from the datatype registry for extension elib. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry for extension hlf. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry for extension idpdb. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry for extension sf3. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cps. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry for extension ct. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:PostgresqlArchive from the datatype registry for extension postgresql. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MongoDBArchive from the datatype registry for extension mongodb. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GeneNoteBook from the datatype registry for extension genenotebook. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry for extension searchgui_archive. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry for extension fast5.tar. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry for extension fast5.tar.gz. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry for extension fast5.tar.bz2. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveXz from the datatype registry for extension fast5.tar.xz. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Pod5 from the datatype registry for extension pod5. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension peptideshaker_archive. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension percin. [2026-09-18 18:40:33,614: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension percout. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hardklor. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension kronik. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry for extension imzml. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Analyze75 from the datatype registry for extension analyze75. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Nifti1 from the datatype registry for extension nii1. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Nifti2 from the datatype registry for extension nii2. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Gifti from the datatype registry for extension gii. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tck from the datatype registry for extension tck. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Trk from the datatype registry for extension trk. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Mrc2014 from the datatype registry for extension mrc. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Star from the datatype registry for extension star. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PEFF from the datatype registry for extension peff. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension toml. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension colab.tar. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.flow:FCS from the datatype registry for extension fcs. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowtext. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowclr. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowmfi. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat1. [2026-09-18 18:40:33,615: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat2. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat3. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowscore. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowframe. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension fsom. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowset. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension amnisflow.cif. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension metacyto_clr.txt. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.metacyto:mSummary from the datatype registry for extension metacyto_summary.txt. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.metacyto:mStats from the datatype registry for extension metacyto_stats.txt. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_compute_matrix_archive. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_coverage_matrix. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry for extension netcdf. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry for extension eps. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry for extension rast. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry for extension laj. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry for extension lav. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry for extension maf. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry for extension mafcustomtrack. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:MatrixMarket from the datatype registry for extension mtx. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CMAP from the datatype registry for extension cmap. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry for extension encodepeak. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:FourDNPairs from the datatype registry for extension 4dn_pairs. [2026-09-18 18:40:33,616: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:FourDNPairsam from the datatype registry for extension 4dn_pairsam. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry for extension pdf. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry for extension pileup. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Psl from the datatype registry for extension psl. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry for extension obo. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry for extension owl. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry for extension png. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry for extension qual. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry for extension qualsolexa. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry for extension qualillumina. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry for extension qualsolid. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry for extension qual454. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry for extension roadmaps. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry for extension sam. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry for extension scf. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry for extension sequences. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry for extension snpeffdb. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry for extension snpsiftdbnsfp. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dbnsfp.tabular. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry for extension sff. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry for extension sra. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:SraManifest from the datatype registry for extension sra_manifest.tabular. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension svg. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry for extension taxonomy. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension tabular. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry for extension twobit. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:SQmass from the datatype registry for extension sqmass. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry for extension gemini.sqlite. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ChiraSQLite from the datatype registry for extension chira.sqlite. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CuffDiffSQlite from the datatype registry for extension cuffdiff.sqlite. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GAFASQLite from the datatype registry for extension gafa.sqlite. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:NcbiTaxonomySQlite from the datatype registry for extension ncbitaxonomy.sqlite. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension txt. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry for extension linecount. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry for extension memepsp. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry for extension memexml. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry for extension cisml. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Tei from the datatype registry for extension tei. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xml. [2026-09-18 18:40:33,617: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xsd. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Dzi from the datatype registry for extension dzi. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry for extension vcf. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf_bgzip. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry for extension bcf_uncompressed. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry for extension velvet. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry for extension wig. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension interval_index. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension odgi. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension vg. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.loci. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.dist. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.snarls. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.gamp. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.min. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.zipcodes. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.gg. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gbz. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gbwt. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hal. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hal.pg. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hal.hg. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension xg. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gam. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf2. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf3. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension onnx. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tabix. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:IntervalTabix from the datatype registry for extension interval_tabix.gz. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:JuicerMediumTabix from the datatype registry for extension juicer_medium_tabix.gz. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:BedTabix from the datatype registry for extension bed_tabix.gz. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:GffTabix from the datatype registry for extension gff_tabix.gz. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension bgzip. [2026-09-18 18:40:33,618: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension gwas_bgzip. [2026-09-18 18:40:33,619: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension gwas_tabix.gz. [2026-09-18 18:40:33,619: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry for extension vcf_bgzip. [2026-09-18 18:40:33,619: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bus. [2026-09-18 18:40:33,619: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension kallisto.idx. [2026-09-18 18:40:33,619: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry for extension phyloxml. [2026-09-18 18:40:33,619: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension newick. [2026-09-18 18:40:33,619: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension nhx. [2026-09-18 18:40:33,619: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry for extension nex. [2026-09-18 18:40:33,619: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:IQTree from the datatype registry for extension iqtree. [2026-09-18 18:40:33,619: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension beast.trees. [2026-09-18 18:40:33,620: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mldist. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry for extension affybatch. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry for extension eigenstratgeno. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry for extension eigenstratpca. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry for extension eset. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry for extension fped. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry for extension fphe. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry for extension gg. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry for extension ldindep. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry for extension malist. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry for extension lped. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry for extension pbed. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry for extension pheno. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry for extension pphe. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry for extension rexpbase. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry for extension rgenetics. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry for extension snptest. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry for extension snpmatrix. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension xls. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry for extension ipynb. [2026-09-18 18:40:33,621: DEBUG/main] Loaded preferred visualization definition: ipynb -> jupyterlite [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension json. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Text from the datatype registry for extension tool_markdown. [2026-09-18 18:40:33,621: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:ExpressionJson from the datatype registry for extension expression.json. [2026-09-18 18:40:33,622: DEBUG/main] Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry for extension xgmml. [2026-09-18 18:40:33,622: DEBUG/main] Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry for extension sif. [2026-09-18 18:40:33,622: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry for extension triples. [2026-09-18 18:40:33,622: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry for extension hdt. [2026-09-18 18:40:33,622: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry for extension nt. [2026-09-18 18:40:33,622: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry for extension n3. [2026-09-18 18:40:33,622: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry for extension ttl. [2026-09-18 18:40:33,622: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry for extension rdf. [2026-09-18 18:40:33,622: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry for extension jsonld. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Sbol from the datatype registry for extension sbol. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension excel.xls. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry for extension xlsx. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Docx from the datatype registry for extension docx. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Pptx from the datatype registry for extension pptx. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension btwisted. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cai. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cat_db. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension charge. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension checktrans. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension chips. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codcmp. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension coderet. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension compseq. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgplot. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgreport. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cusp. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cut. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dan. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension digest. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dreg. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension einverted. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension epestfind. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension equicktandem. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension est2genome. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension etandem. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension freak. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzznuc. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzzpro. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzztran. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gaf. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension garnier. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension geecee. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension helixturnhelix. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hmoment. [2026-09-18 18:40:33,623: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension isochore. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension match. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nametable. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension needle. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgreport. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgseek. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension noreturn. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension palindrome. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepcoil. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepinfo. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepstats. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension polydot. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension preg. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prettyseq. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension primersearch. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showfeat. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showorf. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sixpack. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension strider. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension supermatcher. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension syco. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension textsearch. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension vectorstrip. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wobble. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wordcount. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dbmotif. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension diffseq. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension excel. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feattable. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension motif. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension regions. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension seqtable. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension simple. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension table. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension tagseq. [2026-09-18 18:40:33,624: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension acedb. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension clustal. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codata. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension embl. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fitch. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gcg. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry for extension genbank. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hennig86. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ig. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifer. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifernon. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mega. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension meganon. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ncbi. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexus. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexusnon. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.phylip:Phylip from the datatype registry for extension phylip. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension phylipnon. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pir. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension staden. [2026-09-18 18:40:33,625: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension swiss. [2026-09-18 18:40:33,626: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:Msf from the datatype registry for extension msf. [2026-09-18 18:40:33,626: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx0. [2026-09-18 18:40:33,626: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx1. [2026-09-18 18:40:33,626: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx10. [2026-09-18 18:40:33,626: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx2. [2026-09-18 18:40:33,626: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx3. [2026-09-18 18:40:33,626: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pair. [2026-09-18 18:40:33,626: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension score. [2026-09-18 18:40:33,626: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srs. [2026-09-18 18:40:33,626: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srspair. [2026-09-18 18:40:33,626: DEBUG/main] Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry for extension snaphmm. [2026-09-18 18:40:33,626: DEBUG/main] Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry for extension augustus. [2026-09-18 18:40:33,626: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ICM from the datatype registry for extension icm. [2026-09-18 18:40:33,627: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:InfernalCM from the datatype registry for extension cm. [2026-09-18 18:40:33,627: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry for extension hmm2. [2026-09-18 18:40:33,627: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry for extension hmm3. [2026-09-18 18:40:33,627: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry for extension stockholm. [2026-09-18 18:40:33,627: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry for extension xmfa. [2026-09-18 18:40:33,627: DEBUG/main] Retrieved datatype module galaxy.datatypes.microarrays:Cel from the datatype registry for extension cel. [2026-09-18 18:40:33,627: DEBUG/main] Retrieved datatype module galaxy.datatypes.microarrays:Gpr from the datatype registry for extension gpr. [2026-09-18 18:40:33,627: DEBUG/main] Retrieved datatype module galaxy.datatypes.microarrays:Gal from the datatype registry for extension gal. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension rds. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension phyloseq. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.sce. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.raw. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.msnbase.raw. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.findchrompeaks. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.group. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.retcor. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.fillpeaks. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.positive. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.negative. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.quick. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.hdf5:HDF5SummarizedExperiment from the datatype registry for extension rdata.se. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rdock_as. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rrd. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Prm from the datatype registry for extension prm. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry for extension oxlicg. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry for extension oxling. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry for extension oxlits. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry for extension oxlist. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry for extension oxliss. [2026-09-18 18:40:33,628: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry for extension oxligl. [2026-09-18 18:40:33,629: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry for extension stl. [2026-09-18 18:40:33,629: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry for extension plyascii. [2026-09-18 18:40:33,629: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry for extension plybinary. [2026-09-18 18:40:33,629: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry for extension vtkascii. [2026-09-18 18:40:33,629: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry for extension vtkbinary. [2026-09-18 18:40:33,629: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtpAscii from the datatype registry for extension vtpascii. [2026-09-18 18:40:33,629: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtpBinary from the datatype registry for extension vtpbinary. [2026-09-18 18:40:33,630: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry for extension biom1. [2026-09-18 18:40:33,630: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry for extension biom2. [2026-09-18 18:40:33,630: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MashSketch from the datatype registry for extension msh. [2026-09-18 18:40:33,630: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:SourmashSignature from the datatype registry for extension sourmash.sig. [2026-09-18 18:40:33,630: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry for extension scidx. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry for extension smi. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry for extension sdf. [2026-09-18 18:40:33,631: DEBUG/main] Loaded preferred visualization definition: sdf -> molstar [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry for extension inchi. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry for extension mol. [2026-09-18 18:40:33,631: DEBUG/main] Loaded preferred visualization definition: mol -> molstar [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry for extension mol2. [2026-09-18 18:40:33,631: DEBUG/main] Loaded preferred visualization definition: mol2 -> molstar [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry for extension cml. [2026-09-18 18:40:33,631: DEBUG/main] Loaded preferred visualization definition: cml -> molstar [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry for extension fps. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry for extension obfs. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry for extension drf. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry for extension phar. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry for extension pdb. [2026-09-18 18:40:33,631: DEBUG/main] Loaded preferred visualization definition: pdb -> molstar [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry for extension pdbqt. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:PQR from the datatype registry for extension pqr. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:Cell from the datatype registry for extension cell. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:CIF from the datatype registry for extension cif. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:XYZ from the datatype registry for extension xyz. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:ExtendedXYZ from the datatype registry for extension extxyz. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:Magres from the datatype registry for extension magres. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Trr from the datatype registry for extension trr. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Dcd from the datatype registry for extension dcd. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension top. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prmtop. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension itp. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mdp. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ndx. [2026-09-18 18:40:33,631: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension xvg. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Xtc from the datatype registry for extension xtc. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Cpt from the datatype registry for extension cpt. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Edr from the datatype registry for extension edr. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tpr. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:GRO from the datatype registry for extension gro. [2026-09-18 18:40:33,632: DEBUG/main] Loaded preferred visualization definition: gro -> molstar [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension inpcrd. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Vel from the datatype registry for extension vel. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry for extension grd. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry for extension grd.tgz. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.otu. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.list. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.sabund. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.rabund. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.shared. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.relabund. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry for extension mothur.names. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.design. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry for extension mothur.summary. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.groups. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry for extension mothur.oligos. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension mothur.align. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.accnos. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.otulabels. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mothur.otu.corr. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry for extension mothur.map. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry for extension mothur.align.check. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry for extension mothur.align.report. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry for extension mothur.filter. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry for extension mothur.dist. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mothur.tre. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry for extension mothur.pair.dist. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mothur.square.dist. [2026-09-18 18:40:33,632: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry for extension mothur.lower.dist. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.ref.taxonomy. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.seq.taxonomy. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.rdp.taxonomy. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry for extension mothur.cons.taxonomy. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry for extension mothur.tax.summary. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry for extension mothur.freq. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.quan. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.quan. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.masked.quan. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.masked.quan. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry for extension mothur.axes. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry for extension mothur.sff.flow. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry for extension mothur.count_table. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry for extension neostore. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDBzip from the datatype registry for extension neostore.zip. [2026-09-18 18:40:33,633: DEBUG/main] Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry for extension trackhub. [2026-09-18 18:40:33,634: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry for extension blastxml. [2026-09-18 18:40:33,634: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry for extension blastdbn. [2026-09-18 18:40:33,634: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry for extension blastdbp. [2026-09-18 18:40:33,634: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry for extension blastdbd. [2026-09-18 18:40:33,634: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:LastDb from the datatype registry for extension lastdb. [2026-09-18 18:40:33,634: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb5 from the datatype registry for extension blastdbn5. [2026-09-18 18:40:33,634: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb5 from the datatype registry for extension blastdbp5. [2026-09-18 18:40:33,634: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb5 from the datatype registry for extension blastdbd5. [2026-09-18 18:40:33,634: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension maskinfo-asn1. [2026-09-18 18:40:33,634: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension maskinfo-asn1-binary. [2026-09-18 18:40:33,634: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension pssm-asn1. [2026-09-18 18:40:33,634: DEBUG/main] Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry for extension ptkscmp. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry for extension smat. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:GenotypeMatrix from the datatype registry for extension alohomora_gts. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_map. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_maf. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_ped. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension linkage_pedin. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:DataIn from the datatype registry for extension linkage_datain. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:MarkerMap from the datatype registry for extension linkage_map. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_ihaplo. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_descent. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:AllegroLOD from the datatype registry for extension allegro_fparam. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:IdeasPre from the datatype registry for extension ideaspre. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Sbml from the datatype registry for extension sbml. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.spaln:SpalnNuclDb from the datatype registry for extension spalndbnp. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.spaln:SpalnProtDb from the datatype registry for extension spalndba. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_dada. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_errorrates. [2026-09-18 18:40:33,635: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_mergepairs. [2026-09-18 18:40:33,636: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_sequencetable. [2026-09-18 18:40:33,636: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_uniques. [2026-09-18 18:40:33,636: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension ampvis2. [2026-09-18 18:40:33,636: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension ckpt. [2026-09-18 18:40:33,636: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tgz. [2026-09-18 18:40:33,637: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Wav from the datatype registry for extension wav. [2026-09-18 18:40:33,637: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mp3 from the datatype registry for extension mp3. [2026-09-18 18:40:33,637: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Ogg from the datatype registry for extension ogg. [2026-09-18 18:40:33,637: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Wma from the datatype registry for extension wma. [2026-09-18 18:40:33,637: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mkv from the datatype registry for extension mkv. [2026-09-18 18:40:33,637: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mp4 from the datatype registry for extension mp4. [2026-09-18 18:40:33,637: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:M4a from the datatype registry for extension m4a. [2026-09-18 18:40:33,637: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Flv from the datatype registry for extension flv. [2026-09-18 18:40:33,637: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Flac from the datatype registry for extension flac. [2026-09-18 18:40:33,637: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Webm from the datatype registry for extension webm. [2026-09-18 18:40:33,637: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mpg from the datatype registry for extension mpg. [2026-09-18 18:40:33,637: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mov from the datatype registry for extension mov. [2026-09-18 18:40:33,637: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Avi from the datatype registry for extension avi. [2026-09-18 18:40:33,637: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Wmv from the datatype registry for extension wmv. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.speech:TextGrid from the datatype registry for extension textgrid. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.speech:BPF from the datatype registry for extension par. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension ffindex. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension ffdata. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Pretext from the datatype registry for extension pretext. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension immuneml_receptors.html. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:HexrdMaterials from the datatype registry for extension hexrd.materials.h5. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension npz. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:HexrdImagesNpz from the datatype registry for extension hexrd.images.npz. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:HexrdEtaOmeNpz from the datatype registry for extension hexrd.eta_ome.npz. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension hexrd.scored_orientations.npz. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hexrd.accepted_orientations. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension hexrd.yml. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTess from the datatype registry for extension neper.tess. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTesr from the datatype registry for extension neper.tesr. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPoints from the datatype registry for extension neper.points. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPointsTabular from the datatype registry for extension neper.points.tsv. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperMultiScaleCell from the datatype registry for extension neper.mscell. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshMsh from the datatype registry for extension gmsh.msh. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshGeo from the datatype registry for extension gmsh.geo. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:ZsetGeof from the datatype registry for extension zset.geof. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkXml from the datatype registry for extension vtkxml. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GocadSGrid from the datatype registry for extension gocad.sg. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:FeflowFem from the datatype registry for extension feflow.fem. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:AsciiRaster from the datatype registry for extension raster.asc. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension stl. [2026-09-18 18:40:33,638: DEBUG/main] Overriding conflicting datatype with extension 'stl', using datatype from /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/lib/galaxy/config/sample/datatypes_conf.xml.sample. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Text from the datatype registry for extension pov. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:PithyaResult from the datatype registry for extension pithya.result. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:PithyaProperty from the datatype registry for extension pithya.property. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:PithyaModel from the datatype registry for extension pithya.model. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:BCSLts from the datatype registry for extension bcsl.ts. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:BCSLmodel from the datatype registry for extension bcsl.model. [2026-09-18 18:40:33,638: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:StormSample from the datatype registry for extension storm.sample. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:StormCheck from the datatype registry for extension storm.check. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:CTLresult from the datatype registry for extension ctl.result. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Castep from the datatype registry for extension castep. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Param from the datatype registry for extension param. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:FormattedDensity from the datatype registry for extension den_fmt. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.larch:AthenaProject from the datatype registry for extension prj. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.larch:FEFFInput from the datatype registry for extension inp. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension sp. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension gds. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension feff. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feffit. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bil. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hdr. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.gis:Shapefile from the datatype registry for extension shp. [2026-09-18 18:40:33,639: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:FITS from the datatype registry for extension fits. [2026-09-18 18:40:33,639: DEBUG/main] Loaded preferred visualization definition: fits -> aladin [2026-09-18 18:40:33,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.chain:Chain from the datatype registry for extension chain. [2026-09-18 18:40:33,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.chain:Net from the datatype registry for extension ucsc.net. [2026-09-18 18:40:33,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bcsp. [2026-09-18 18:40:33,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rd. [2026-09-18 18:40:33,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Safetensors from the datatype registry for extension safetensors. [2026-09-18 18:40:33,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension mlmodel. [2026-09-18 18:40:33,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension deacon.idx. [2026-09-18 18:40:33,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:TensorBoardEvents from the datatype registry for extension tfevents. [2026-09-18 18:40:33,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension rmsx.json. [2026-09-18 18:40:33,640: DEBUG/main] Loaded preferred visualization definition: rmsx.json -> rmsxflipbook [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtpAscii' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtpBinary' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkXml' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTess' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTesr' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:GmshMsh' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:GocadSGrid' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:FeflowFem' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:AsciiRaster' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.goldenpath:GoldenPath' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:JP2' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQmass' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OSW' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:PQP' [2026-09-18 18:40:33,640: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:ElibSQlite' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:DlibSQlite' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:BlibSQlite' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:ChiraSQLite' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CuffDiffSQlite' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:GAFASQLite' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:NcbiTaxonomySQlite' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5MLM' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Hic' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cool' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:MCool' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Loom' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Anndata' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdMaterials' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Grib' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdImagesNpz' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdEtaOmeNpz' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Npz' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamQuerynameSorted' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamNative' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:DAA' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:RMA6' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Parquet' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:BafTar' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:TdfTar' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassHunterTar' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassLynxTar' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:YepTar' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:WiffTar' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveXz' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pod5' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Meryldb' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bref3' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:PostgresqlArchive' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:ICM' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Idat' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Trr' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Dcd' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xtc' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cpt' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Edr' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Vel' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xlsx' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Docx' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pptx' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Numpy' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Metadata' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Artifact' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Visualization' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:SpatialData' [2026-09-18 18:40:33,641: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedOMEZarrZipArchive' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedZarrZipArchive' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedZipArchive' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pretext' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.chain:Chain' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.chain:Net' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Gifti' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:Dzi' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:Sbml' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Dta2d' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Edta' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ConsensusXML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:IdXML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:FeatureXML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MascotXML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Ms2' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab2' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ParamXml' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:NmrML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Kroenik' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepList' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PSMS' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TrafoXML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestXML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestSpecXML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:QCML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Wiff' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PEFF' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:Sbol' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' [2026-09-18 18:40:33,642: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastg' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Cell' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CIF' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:ExtendedXYZ' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:XYZ' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Magres' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PQR' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:GRO' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.phylip:Phylip' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqCSSanger' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Html' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Psl' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Paf' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Taf' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:FourDNPairs' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:FourDNPairsam' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' [2026-09-18 18:40:33,643: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:IQTree' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:ImgtJson' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:CytoscapeJson' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:GeoJson' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:VitessceJson' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaResult' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLts' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Json' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.genetics:GenotypeMatrix' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.genetics:DataIn' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.genetics:MarkerMap' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.genetics:AllegroLOD' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CMAP' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:GeoCSV' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mSummary' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mStats' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:MatrixMarket' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:InfernalCM' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Cel' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gpr' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gal' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:RDS' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Mrc2014' [2026-09-18 18:40:33,644: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Png' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:OMETiff' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Dicom' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Im' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Tck' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Trk' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti1' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti2' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Star' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Wav' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp3' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp4' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:M4a' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Flv' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Ogg' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mpg' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mov' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Avi' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Wmv' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Wma' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Webm' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mkv' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.speech:TextGrid' [2026-09-18 18:40:33,645: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.speech:BPF' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.larch:FEFFInput' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.larch:AthenaProject' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Castep' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:CTLresult' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:FormattedDensity' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Param' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Yaml' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:FITS' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.neo4j:Neo4jDBzip' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaProperty' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaModel' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLmodel' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:StormSample' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:StormCheck' [2026-09-18 18:40:33,646: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:SourmashSignature' [2026-09-18 18:40:33,647: DEBUG/main] Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. [2026-09-18 18:40:33,648: DEBUG/main] Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] [2026-09-18 18:40:33,648: DEBUG/main] Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] [2026-09-18 18:40:33,648: DEBUG/main] Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt [2026-09-18 18:40:33,648: DEBUG/main] Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt [2026-09-18 18:40:33,648: DEBUG/main] Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. [2026-09-18 18:40:33,648: DEBUG/main] Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample [2026-09-18 18:40:33,648: DEBUG/main] Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. [2026-09-18 18:40:33,648: DEBUG/main] Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample [2026-09-18 18:40:33,652: DEBUG/main] Loaded 1 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/tool-data/shed/adapters.loc' for 'adapters' [2026-09-18 18:40:33,652: DEBUG/main] Loaded tool data table 'adapters' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/shed_tool_data_table_conf.xml' [2026-09-18 18:40:33,652: DEBUG/main] Loaded 0 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/tool-data/shed/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned' [2026-09-18 18:40:33,652: DEBUG/main] Loaded tool data table 'rnastar_index2x_versioned' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/shed_tool_data_table_conf.xml' [2026-09-18 18:40:33,652: DEBUG/main] Loaded 0 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/tool-data/shed/gene_sets.loc' for 'gene_sets' [2026-09-18 18:40:33,652: DEBUG/main] Loaded tool data table 'gene_sets' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/shed_tool_data_table_conf.xml' [2026-09-18 18:40:33,653: DEBUG/main] Loaded 4 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/galaxy-dev/tool-data/shed/featurecounts_anno.loc' for 'featurecounts_anno' [2026-09-18 18:40:33,653: DEBUG/main] Loaded tool data table 'featurecounts_anno' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/shed_tool_data_table_conf.xml' [2026-09-18 18:40:33,653: DEBUG/main] Loading references to tool sheds from /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/tool_sheds_conf.xml [2026-09-18 18:40:33,653: DEBUG/main] Loaded reference to tool shed: toolshed.g2.bx.psu.edu [2026-09-18 18:40:33,752: DEBUG/main] No parameter model for tool '__DATA_FETCH__': Cannot generate a tool parameter model for upload_dataset inputs [2026-09-18 18:40:33,772: DEBUG/main] (1) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/1 [2026-09-18 18:40:33,819: DEBUG/main] Job wrapper for Job [1] prepared (15.765 ms) [2026-09-18 18:40:33,819: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (67.458 ms) [2026-09-18 18:40:33,833: INFO/main] Task galaxy.setup_fetch_data[10c5fb43-a795-4933-99ea-5dcaf3535adf] succeeded in 1.1605284167453647s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/1', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/1/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-18 18:40:33,866 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58084 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:34,133 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58086 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:34,408 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58088 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:34,681 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58091 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 [2026-09-18 18:40:34,686: INFO/main] Task galaxy.fetch_data[30a14d4b-6666-4698-9cb8-e8b83869a9b9] received [2026-09-18 18:40:34,686: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '30a14d4b-6666-4698-9cb8-e8b83869a9b9', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '30a14d4b-6666-4698-9cb8-e8b83869a9b9', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '10c5fb43-a795-4933-99ea-5dcaf3535adf', 'parent_id': '10c5fb43-a795-4933-99ea-5dcaf3535adf', 'argsrepr': "(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/1', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/1/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 1}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '30a14d4b-6666-4698-9cb8-e8b83869a9b9', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{}) uvicorn.access INFO 2026-09-18 18:40:34,947 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58093 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:35,217 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58097 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:35,480 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58100 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:35,748 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58102 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:36,018 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58105 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:36,279 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58107 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:36,541 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58111 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 Option master_api_key has been deprecated in favor of bootstrap_admin_api_key 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 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 uvicorn.access INFO 2026-09-18 18:40:36,806 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58114 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:37,076 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58116 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:37,339 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58119 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:37,606 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58122 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:37,873 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58124 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:38,142 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58127 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:38,410 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58129 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:38,674 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58133 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:38,940 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58136 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:39,207 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58139 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 [2026-09-18 18:40:39,428: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (4741.572 ms) [2026-09-18 18:40:39,433: INFO/main] Task galaxy.fetch_data[30a14d4b-6666-4698-9cb8-e8b83869a9b9] succeeded in 4.746809625066817s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/1' uvicorn.access INFO 2026-09-18 18:40:39,477 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58141 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 [2026-09-18 18:40:39,742: INFO/main] Task galaxy.set_job_metadata[5c8ef36d-4cc2-4ecd-a500-b681a98ee715] received [2026-09-18 18:40:39,742: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '5c8ef36d-4cc2-4ecd-a500-b681a98ee715', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '5c8ef36d-4cc2-4ecd-a500-b681a98ee715', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '10c5fb43-a795-4933-99ea-5dcaf3535adf', 'parent_id': '30a14d4b-6666-4698-9cb8-e8b83869a9b9', 'argsrepr': "('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/1',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 1}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '5c8ef36d-4cc2-4ecd-a500-b681a98ee715', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '00b85cd6-ecd8-4680-8567-74014954fb15'}, 'reply_to':... kwargs:{}) uvicorn.access INFO 2026-09-18 18:40:39,751 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58144 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 [2026-09-18 18:40:39,800: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (56.690 ms) [2026-09-18 18:40:39,804: INFO/main] Task galaxy.set_job_metadata[5c8ef36d-4cc2-4ecd-a500-b681a98ee715] succeeded in 0.06129466649144888s: None uvicorn.access INFO 2026-09-18 18:40:40,014 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58147 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:40,281 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58149 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:40,553 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58152 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 [2026-09-18 18:40:40,753: INFO/main] Task galaxy.finish_job[77d8b3d4-cc22-482c-a422-74f677e7ed15] received [2026-09-18 18:40:40,753: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '77d8b3d4-cc22-482c-a422-74f677e7ed15', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '77d8b3d4-cc22-482c-a422-74f677e7ed15', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '10c5fb43-a795-4933-99ea-5dcaf3535adf', 'parent_id': '5c8ef36d-4cc2-4ecd-a500-b681a98ee715', 'argsrepr': '()', 'kwargsrepr': '{\'job_id\': 1, \'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request... kwargs:{}) [2026-09-18 18:40:40,762: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/1/outputs/dataset_066cb959-8d76-46e1-9c57-5e49516511d5.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/files/0/6/6/dataset_066cb959-8d76-46e1-9c57-5e49516511d5.dat [2026-09-18 18:40:40,765: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'AR0382_A_1.fastq.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [{'hash_function': 'SHA-1', 'hash_value': '7686fa073a0089b0376bbe1d3b819b4ea14e3a67'}], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/1/working/gxupload_0', 'object_id': 1}]}]}] uvicorn.access INFO 2026-09-18 18:40:40,824 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58155 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 [2026-09-18 18:40:40,834: INFO/main] Collecting metrics for Job 1 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/1 [2026-09-18 18:40:40,837: DEBUG/main] job_wrapper.finish for job 1 executed (80.611 ms) [2026-09-18 18:40:40,837: INFO/main] Successfully executed Celery task finish_job finish_job (83.683 ms) [2026-09-18 18:40:40,839: INFO/main] Task galaxy.finish_job[77d8b3d4-cc22-482c-a422-74f677e7ed15] succeeded in 0.08570270892232656s: None uvicorn.access INFO 2026-09-18 18:40:41,093 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58158 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 galaxy.tools INFO 2026-09-18 18:40:41,100 [pN:main.1,p:72534,tN:AnyIO worker thread] Validated and populated state for tool request (0.060 ms) uvicorn.access INFO 2026-09-18 18:40:41,122 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58160 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:41,129 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58162 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:41,405 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58164 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:41,670 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58167 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 [2026-09-18 18:40:41,772: INFO/main] Task galaxy.setup_fetch_data[b8328bfb-8612-4f53-8023-368c1a3ed902] received [2026-09-18 18:40:41,772: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', 'b8328bfb-8612-4f53-8023-368c1a3ed902', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': 'b8328bfb-8612-4f53-8023-368c1a3ed902', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'b8328bfb-8612-4f53-8023-368c1a3ed902', 'parent_id': None, 'argsrepr': '(2,)', 'kwargsrepr': '{\'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request \\\'$request_path\\\'\n ... kwargs:{}) [2026-09-18 18:40:41,790: DEBUG/main] (2) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/2 [2026-09-18 18:40:41,822: DEBUG/main] Job wrapper for Job [2] prepared (13.780 ms) [2026-09-18 18:40:41,822: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (48.875 ms) [2026-09-18 18:40:41,826: INFO/main] Task galaxy.setup_fetch_data[b8328bfb-8612-4f53-8023-368c1a3ed902] succeeded in 0.05337312538176775s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/2', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/2/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-18 18:40:41,939 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58171 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:42,228 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58173 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:42,507 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58176 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:42,774 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58179 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 [2026-09-18 18:40:42,789: INFO/main] Task galaxy.fetch_data[917242d8-4434-4366-ab47-6051b4ea5913] received [2026-09-18 18:40:42,789: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '917242d8-4434-4366-ab47-6051b4ea5913', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '917242d8-4434-4366-ab47-6051b4ea5913', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'b8328bfb-8612-4f53-8023-368c1a3ed902', 'parent_id': 'b8328bfb-8612-4f53-8023-368c1a3ed902', 'argsrepr': "(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/2', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/2/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 2}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '917242d8-4434-4366-ab47-6051b4ea5913', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{}) [2026-09-18 18:40:42,846: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (56.165 ms) [2026-09-18 18:40:42,851: INFO/main] Task galaxy.fetch_data[917242d8-4434-4366-ab47-6051b4ea5913] succeeded in 0.06102833431214094s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/2' uvicorn.access INFO 2026-09-18 18:40:43,045 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58181 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:43,320 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58184 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:43,596 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58187 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 [2026-09-18 18:40:43,813: INFO/main] Task galaxy.set_job_metadata[3f3c4bdc-0f43-4560-8ad2-4ce1cd6aad30] received [2026-09-18 18:40:43,813: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '3f3c4bdc-0f43-4560-8ad2-4ce1cd6aad30', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '3f3c4bdc-0f43-4560-8ad2-4ce1cd6aad30', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'b8328bfb-8612-4f53-8023-368c1a3ed902', 'parent_id': '917242d8-4434-4366-ab47-6051b4ea5913', 'argsrepr': "('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/2',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 2}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '3f3c4bdc-0f43-4560-8ad2-4ce1cd6aad30', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '300e9905-8f6e-4cdf-9b4d-8dd90fa82050'}, 'reply_to':... kwargs:{}) uvicorn.access INFO 2026-09-18 18:40:43,866 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58189 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 [2026-09-18 18:40:44,030: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (215.645 ms) [2026-09-18 18:40:44,034: INFO/main] Task galaxy.set_job_metadata[3f3c4bdc-0f43-4560-8ad2-4ce1cd6aad30] succeeded in 0.21985683403909206s: None uvicorn.access INFO 2026-09-18 18:40:44,139 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58192 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:44,404 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58196 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:44,673 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58198 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 [2026-09-18 18:40:44,830: INFO/main] Task galaxy.finish_job[ac7ae1c4-f9ec-4d70-8ff1-0222fe5c2fb0] received [2026-09-18 18:40:44,830: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', 'ac7ae1c4-f9ec-4d70-8ff1-0222fe5c2fb0', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': 'ac7ae1c4-f9ec-4d70-8ff1-0222fe5c2fb0', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'b8328bfb-8612-4f53-8023-368c1a3ed902', 'parent_id': '3f3c4bdc-0f43-4560-8ad2-4ce1cd6aad30', 'argsrepr': '()', 'kwargsrepr': '{\'job_id\': 2, \'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request... kwargs:{}) [2026-09-18 18:40:44,837: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/2/outputs/dataset_6d7dd0ff-9551-4e23-ad12-1c636fad162e.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/files/6/d/7/dataset_6d7dd0ff-9551-4e23-ad12-1c636fad162e.dat [2026-09-18 18:40:44,838: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'AR0382_A_2.fastq.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [{'hash_function': 'SHA-1', 'hash_value': 'f1749c97d907abffd4f5ee36139c22b15376d2af'}], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/2/working/gxupload_0', 'object_id': 2}]}]}] [2026-09-18 18:40:44,897: INFO/main] Collecting metrics for Job 2 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/2 [2026-09-18 18:40:44,900: DEBUG/main] job_wrapper.finish for job 2 executed (66.676 ms) [2026-09-18 18:40:44,900: INFO/main] Successfully executed Celery task finish_job finish_job (70.170 ms) [2026-09-18 18:40:44,902: INFO/main] Task galaxy.finish_job[ac7ae1c4-f9ec-4d70-8ff1-0222fe5c2fb0] succeeded in 0.07220837567001581s: None uvicorn.access INFO 2026-09-18 18:40:44,936 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58201 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 galaxy.tools INFO 2026-09-18 18:40:44,943 [pN:main.1,p:72534,tN:AnyIO worker thread] Validated and populated state for tool request (0.040 ms) uvicorn.access INFO 2026-09-18 18:40:44,964 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58203 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:44,971 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58205 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:45,241 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58208 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:45,513 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58210 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:45,794 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58213 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 [2026-09-18 18:40:45,840: INFO/main] Task galaxy.setup_fetch_data[849ba075-b2b7-4f88-8003-ef898455af07] received [2026-09-18 18:40:45,840: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', '849ba075-b2b7-4f88-8003-ef898455af07', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': '849ba075-b2b7-4f88-8003-ef898455af07', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '849ba075-b2b7-4f88-8003-ef898455af07', 'parent_id': None, 'argsrepr': '(3,)', 'kwargsrepr': '{\'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request \\\'$request_path\\\'\n ... kwargs:{}) [2026-09-18 18:40:45,853: DEBUG/main] (3) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/3 [2026-09-18 18:40:45,878: DEBUG/main] Job wrapper for Job [3] prepared (9.575 ms) [2026-09-18 18:40:45,878: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (36.829 ms) [2026-09-18 18:40:45,881: INFO/main] Task galaxy.setup_fetch_data[849ba075-b2b7-4f88-8003-ef898455af07] succeeded in 0.040900290943682194s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/3', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/3/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-18 18:40:46,062 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58217 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:46,325 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58219 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:46,604 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58221 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 [2026-09-18 18:40:46,849: INFO/main] Task galaxy.fetch_data[cdc22038-cf58-4077-a629-00bac97df77d] received [2026-09-18 18:40:46,849: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', 'cdc22038-cf58-4077-a629-00bac97df77d', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': 'cdc22038-cf58-4077-a629-00bac97df77d', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '849ba075-b2b7-4f88-8003-ef898455af07', 'parent_id': '849ba075-b2b7-4f88-8003-ef898455af07', 'argsrepr': "(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/3', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/3/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 3}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'cdc22038-cf58-4077-a629-00bac97df77d', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{}) uvicorn.access INFO 2026-09-18 18:40:46,865 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58223 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 [2026-09-18 18:40:46,904: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (53.935 ms) [2026-09-18 18:40:46,908: INFO/main] Task galaxy.fetch_data[cdc22038-cf58-4077-a629-00bac97df77d] succeeded in 0.0586123326793313s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/3' uvicorn.access INFO 2026-09-18 18:40:47,140 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58225 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:47,409 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58228 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:47,699 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58230 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 [2026-09-18 18:40:47,869: INFO/main] Task galaxy.set_job_metadata[c63bb2ba-725d-4f34-a1ab-1eafc5607678] received [2026-09-18 18:40:47,869: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', 'c63bb2ba-725d-4f34-a1ab-1eafc5607678', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': 'c63bb2ba-725d-4f34-a1ab-1eafc5607678', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '849ba075-b2b7-4f88-8003-ef898455af07', 'parent_id': 'cdc22038-cf58-4077-a629-00bac97df77d', 'argsrepr': "('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/3',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 3}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'c63bb2ba-725d-4f34-a1ab-1eafc5607678', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '2d1b4feb-dd07-4c9f-ae5d-6ecffb22aad8'}, 'reply_to':... kwargs:{}) [2026-09-18 18:40:47,934: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (63.751 ms) [2026-09-18 18:40:47,938: INFO/main] Task galaxy.set_job_metadata[c63bb2ba-725d-4f34-a1ab-1eafc5607678] succeeded in 0.06835225038230419s: None uvicorn.access INFO 2026-09-18 18:40:47,973 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58232 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:48,242 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58234 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:48,516 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58236 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:48,816 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58238 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 [2026-09-18 18:40:48,889: INFO/main] Task galaxy.finish_job[89535312-5237-4614-bf9c-8deef4d4fa6e] received [2026-09-18 18:40:48,890: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '89535312-5237-4614-bf9c-8deef4d4fa6e', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '89535312-5237-4614-bf9c-8deef4d4fa6e', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '849ba075-b2b7-4f88-8003-ef898455af07', 'parent_id': 'c63bb2ba-725d-4f34-a1ab-1eafc5607678', 'argsrepr': '()', 'kwargsrepr': '{\'job_id\': 3, \'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request... kwargs:{}) [2026-09-18 18:40:48,900: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/3/outputs/dataset_6c7a97bc-0d26-4cdf-81ac-92a497b4d9a8.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/files/6/c/7/dataset_6c7a97bc-0d26-4cdf-81ac-92a497b4d9a8.dat [2026-09-18 18:40:48,901: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'AR0382_B_1.fastq.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [{'hash_function': 'SHA-1', 'hash_value': 'a120941043541873bd674fc8e5cab4bf7d8dcc37'}], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/3/working/gxupload_0', 'object_id': 3}]}]}] [2026-09-18 18:40:48,966: INFO/main] Collecting metrics for Job 3 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/3 [2026-09-18 18:40:48,969: DEBUG/main] job_wrapper.finish for job 3 executed (74.716 ms) [2026-09-18 18:40:48,969: INFO/main] Successfully executed Celery task finish_job finish_job (79.005 ms) [2026-09-18 18:40:48,971: INFO/main] Task galaxy.finish_job[89535312-5237-4614-bf9c-8deef4d4fa6e] succeeded in 0.08104841597378254s: None uvicorn.access INFO 2026-09-18 18:40:49,086 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58240 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 galaxy.tools INFO 2026-09-18 18:40:49,094 [pN:main.1,p:72534,tN:AnyIO worker thread] Validated and populated state for tool request (0.040 ms) uvicorn.access INFO 2026-09-18 18:40:49,117 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58242 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:49,125 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58244 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:49,403 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58246 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:49,695 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58248 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 [2026-09-18 18:40:49,914: INFO/main] Task galaxy.setup_fetch_data[1033bb56-c89e-4fd3-b601-9a4c59374f3a] received [2026-09-18 18:40:49,915: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', '1033bb56-c89e-4fd3-b601-9a4c59374f3a', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': '1033bb56-c89e-4fd3-b601-9a4c59374f3a', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '1033bb56-c89e-4fd3-b601-9a4c59374f3a', 'parent_id': None, 'argsrepr': '(4,)', 'kwargsrepr': '{\'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request \\\'$request_path\\\'\n ... kwargs:{}) [2026-09-18 18:40:49,936: DEBUG/main] (4) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/4 [2026-09-18 18:40:49,966: DEBUG/main] Job wrapper for Job [4] prepared (11.440 ms) [2026-09-18 18:40:49,966: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (50.098 ms) uvicorn.access INFO 2026-09-18 18:40:49,969 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58250 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 [2026-09-18 18:40:49,971: INFO/main] Task galaxy.setup_fetch_data[1033bb56-c89e-4fd3-b601-9a4c59374f3a] succeeded in 0.05475183296948671s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/4', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/4/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-18 18:40:50,263 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58252 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:50,551 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58254 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:50,848 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58256 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 [2026-09-18 18:40:50,936: INFO/main] Task galaxy.fetch_data[49b5360b-987c-4758-96ba-f4f6c2e221fb] received [2026-09-18 18:40:50,936: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '49b5360b-987c-4758-96ba-f4f6c2e221fb', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '49b5360b-987c-4758-96ba-f4f6c2e221fb', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '1033bb56-c89e-4fd3-b601-9a4c59374f3a', 'parent_id': '1033bb56-c89e-4fd3-b601-9a4c59374f3a', 'argsrepr': "(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/4', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/4/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 4}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '49b5360b-987c-4758-96ba-f4f6c2e221fb', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{}) uvicorn.access INFO 2026-09-18 18:40:51,119 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58258 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:51,386 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58260 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:51,649 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58262 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:51,910 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58264 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:52,175 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58266 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:52,445 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58268 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 [2026-09-18 18:40:52,448: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (1511.236 ms) [2026-09-18 18:40:52,452: INFO/main] Task galaxy.fetch_data[49b5360b-987c-4758-96ba-f4f6c2e221fb] succeeded in 1.5155106242746115s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/4' uvicorn.access INFO 2026-09-18 18:40:52,717 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58270 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 [2026-09-18 18:40:52,963: INFO/main] Task galaxy.set_job_metadata[1d11c7bf-5fe7-444d-8c70-9a2297426786] received [2026-09-18 18:40:52,964: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '1d11c7bf-5fe7-444d-8c70-9a2297426786', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '1d11c7bf-5fe7-444d-8c70-9a2297426786', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '1033bb56-c89e-4fd3-b601-9a4c59374f3a', 'parent_id': '49b5360b-987c-4758-96ba-f4f6c2e221fb', 'argsrepr': "('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/4',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 4}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '1d11c7bf-5fe7-444d-8c70-9a2297426786', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '04903843-35fd-4d0f-bd93-bb797da582d3'}, 'reply_to':... kwargs:{}) uvicorn.access INFO 2026-09-18 18:40:52,987 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58273 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 [2026-09-18 18:40:53,174: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (209.408 ms) [2026-09-18 18:40:53,179: INFO/main] Task galaxy.set_job_metadata[1d11c7bf-5fe7-444d-8c70-9a2297426786] succeeded in 0.21393470838665962s: None uvicorn.access INFO 2026-09-18 18:40:53,254 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58275 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:53,530 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58277 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:53,830 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58280 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 [2026-09-18 18:40:53,980: INFO/main] Task galaxy.finish_job[f0ba12ef-8ba7-4201-866a-fe2d79a2ba4d] received [2026-09-18 18:40:53,980: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', 'f0ba12ef-8ba7-4201-866a-fe2d79a2ba4d', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': 'f0ba12ef-8ba7-4201-866a-fe2d79a2ba4d', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '1033bb56-c89e-4fd3-b601-9a4c59374f3a', 'parent_id': '1d11c7bf-5fe7-444d-8c70-9a2297426786', 'argsrepr': '()', 'kwargsrepr': '{\'job_id\': 4, \'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request... kwargs:{}) [2026-09-18 18:40:53,995: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/4/outputs/dataset_6115da6e-fe7b-4621-96a1-6d9502eccc12.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/files/6/1/1/dataset_6115da6e-fe7b-4621-96a1-6d9502eccc12.dat [2026-09-18 18:40:53,997: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'AR0382_B_2.fastq.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [{'hash_function': 'SHA-1', 'hash_value': '8f315372a23e305fc5dc5ee04d31d8a771ccb8f3'}], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/4/working/gxupload_0', 'object_id': 4}]}]}] [2026-09-18 18:40:54,070: INFO/main] Collecting metrics for Job 4 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/4 [2026-09-18 18:40:54,073: DEBUG/main] job_wrapper.finish for job 4 executed (85.426 ms) [2026-09-18 18:40:54,073: INFO/main] Successfully executed Celery task finish_job finish_job (91.899 ms) [2026-09-18 18:40:54,075: INFO/main] Task galaxy.finish_job[f0ba12ef-8ba7-4201-866a-fe2d79a2ba4d] succeeded in 0.09414124954491854s: None uvicorn.access INFO 2026-09-18 18:40:54,100 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58282 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 galaxy.tools INFO 2026-09-18 18:40:54,106 [pN:main.1,p:72534,tN:AnyIO worker thread] Validated and populated state for tool request (0.034 ms) uvicorn.access INFO 2026-09-18 18:40:54,124 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58284 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:54,131 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58286 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:54,415 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58288 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:54,704 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58290 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:54,984 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58292 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 [2026-09-18 18:40:55,002: INFO/main] Task galaxy.setup_fetch_data[055e0797-19cc-425f-a25e-55fb1f67957a] received [2026-09-18 18:40:55,002: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', '055e0797-19cc-425f-a25e-55fb1f67957a', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': '055e0797-19cc-425f-a25e-55fb1f67957a', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '055e0797-19cc-425f-a25e-55fb1f67957a', 'parent_id': None, 'argsrepr': '(5,)', 'kwargsrepr': '{\'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request \\\'$request_path\\\'\n ... kwargs:{}) [2026-09-18 18:40:55,015: DEBUG/main] (5) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/5 [2026-09-18 18:40:55,040: DEBUG/main] Job wrapper for Job [5] prepared (9.120 ms) [2026-09-18 18:40:55,040: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (37.117 ms) [2026-09-18 18:40:55,043: INFO/main] Task galaxy.setup_fetch_data[055e0797-19cc-425f-a25e-55fb1f67957a] succeeded in 0.04101066570729017s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/5', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/5/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-18 18:40:55,261 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58294 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:55,534 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58297 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:55,828 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58299 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 [2026-09-18 18:40:56,024: INFO/main] Task galaxy.fetch_data[2cdcfe9e-291b-4cdc-8430-2b1f01ad9ae8] received [2026-09-18 18:40:56,024: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '2cdcfe9e-291b-4cdc-8430-2b1f01ad9ae8', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '2cdcfe9e-291b-4cdc-8430-2b1f01ad9ae8', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '055e0797-19cc-425f-a25e-55fb1f67957a', 'parent_id': '055e0797-19cc-425f-a25e-55fb1f67957a', 'argsrepr': "(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/5', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/5/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 5}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '2cdcfe9e-291b-4cdc-8430-2b1f01ad9ae8', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{}) uvicorn.access INFO 2026-09-18 18:40:56,091 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58301 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 [2026-09-18 18:40:56,100: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (75.024 ms) [2026-09-18 18:40:56,105: INFO/main] Task galaxy.fetch_data[2cdcfe9e-291b-4cdc-8430-2b1f01ad9ae8] succeeded in 0.08019270841032267s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/5' uvicorn.access INFO 2026-09-18 18:40:56,381 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58303 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:56,659 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58305 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:56,933 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58307 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 [2026-09-18 18:40:57,042: INFO/main] Task galaxy.set_job_metadata[d5ac6362-fa82-4b61-a78d-a904dea3eeb0] received [2026-09-18 18:40:57,042: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', 'd5ac6362-fa82-4b61-a78d-a904dea3eeb0', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': 'd5ac6362-fa82-4b61-a78d-a904dea3eeb0', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '055e0797-19cc-425f-a25e-55fb1f67957a', 'parent_id': '2cdcfe9e-291b-4cdc-8430-2b1f01ad9ae8', 'argsrepr': "('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/5',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 5}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'd5ac6362-fa82-4b61-a78d-a904dea3eeb0', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': 'dbbc2b32-bbe3-4846-9b20-1e3d4b03614d'}, 'reply_to':... kwargs:{}) [2026-09-18 18:40:57,080: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (36.864 ms) [2026-09-18 18:40:57,083: INFO/main] Task galaxy.set_job_metadata[d5ac6362-fa82-4b61-a78d-a904dea3eeb0] succeeded in 0.040526083670556545s: None uvicorn.access INFO 2026-09-18 18:40:57,204 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58309 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:57,480 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58311 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:57,746 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58314 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:58,020 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58316 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 [2026-09-18 18:40:58,057: INFO/main] Task galaxy.finish_job[4c92d98e-1249-4374-b0a2-6ae3193f1681] received [2026-09-18 18:40:58,057: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '4c92d98e-1249-4374-b0a2-6ae3193f1681', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '4c92d98e-1249-4374-b0a2-6ae3193f1681', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '055e0797-19cc-425f-a25e-55fb1f67957a', 'parent_id': 'd5ac6362-fa82-4b61-a78d-a904dea3eeb0', 'argsrepr': '()', 'kwargsrepr': '{\'job_id\': 5, \'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request... kwargs:{}) [2026-09-18 18:40:58,063: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/5/outputs/dataset_906c0f9a-1757-429c-bf18-f89eb20ad4f0.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/files/9/0/6/dataset_906c0f9a-1757-429c-bf18-f89eb20ad4f0.dat [2026-09-18 18:40:58,064: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'AR0387_A_1.fastq.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [{'hash_function': 'SHA-1', 'hash_value': 'd8e170332a2ae20242b8f79c66f287b79fa2c56a'}], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/5/working/gxupload_0', 'object_id': 5}]}]}] [2026-09-18 18:40:58,124: INFO/main] Collecting metrics for Job 5 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/5 [2026-09-18 18:40:58,127: DEBUG/main] job_wrapper.finish for job 5 executed (66.896 ms) [2026-09-18 18:40:58,127: INFO/main] Successfully executed Celery task finish_job finish_job (69.897 ms) [2026-09-18 18:40:58,129: INFO/main] Task galaxy.finish_job[4c92d98e-1249-4374-b0a2-6ae3193f1681] succeeded in 0.07217079028487206s: None uvicorn.access INFO 2026-09-18 18:40:58,291 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58318 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 galaxy.tools INFO 2026-09-18 18:40:58,297 [pN:main.1,p:72534,tN:AnyIO worker thread] Validated and populated state for tool request (0.047 ms) uvicorn.access INFO 2026-09-18 18:40:58,318 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58320 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:58,326 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58322 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:58,599 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58324 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:58,877 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58326 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 [2026-09-18 18:40:59,064: INFO/main] Task galaxy.setup_fetch_data[2bb65d21-d48f-4890-a4f7-f1de1c5365d7] received [2026-09-18 18:40:59,065: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', '2bb65d21-d48f-4890-a4f7-f1de1c5365d7', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': '2bb65d21-d48f-4890-a4f7-f1de1c5365d7', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '2bb65d21-d48f-4890-a4f7-f1de1c5365d7', 'parent_id': None, 'argsrepr': '(6,)', 'kwargsrepr': '{\'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request \\\'$request_path\\\'\n ... kwargs:{}) [2026-09-18 18:40:59,078: DEBUG/main] (6) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/6 [2026-09-18 18:40:59,103: DEBUG/main] Job wrapper for Job [6] prepared (9.663 ms) [2026-09-18 18:40:59,103: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (38.012 ms) [2026-09-18 18:40:59,107: INFO/main] Task galaxy.setup_fetch_data[2bb65d21-d48f-4890-a4f7-f1de1c5365d7] succeeded in 0.042242166586220264s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/6', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/6/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-18 18:40:59,148 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58329 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:59,433 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58331 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:40:59,715 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58334 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:00,012 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58336 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 [2026-09-18 18:41:00,081: INFO/main] Task galaxy.fetch_data[7de07793-ebee-4b56-a2c4-bad3232135e9] received [2026-09-18 18:41:00,081: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '7de07793-ebee-4b56-a2c4-bad3232135e9', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '7de07793-ebee-4b56-a2c4-bad3232135e9', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '2bb65d21-d48f-4890-a4f7-f1de1c5365d7', 'parent_id': '2bb65d21-d48f-4890-a4f7-f1de1c5365d7', 'argsrepr': "(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/6', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/6/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 6}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '7de07793-ebee-4b56-a2c4-bad3232135e9', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{}) [2026-09-18 18:41:00,143: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (61.856 ms) [2026-09-18 18:41:00,149: INFO/main] Task galaxy.fetch_data[7de07793-ebee-4b56-a2c4-bad3232135e9] succeeded in 0.06741916667670012s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/6' uvicorn.access INFO 2026-09-18 18:41:00,275 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58338 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:00,546 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58341 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:00,837 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58343 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 [2026-09-18 18:41:01,099: INFO/main] Task galaxy.set_job_metadata[04e0c45b-9623-423f-a7b4-9d032fff25f1] received [2026-09-18 18:41:01,099: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '04e0c45b-9623-423f-a7b4-9d032fff25f1', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '04e0c45b-9623-423f-a7b4-9d032fff25f1', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '2bb65d21-d48f-4890-a4f7-f1de1c5365d7', 'parent_id': '7de07793-ebee-4b56-a2c4-bad3232135e9', 'argsrepr': "('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/6',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 6}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '04e0c45b-9623-423f-a7b4-9d032fff25f1', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '11b5790c-69fa-4666-9e2b-3d6af06d7a56'}, 'reply_to':... kwargs:{}) uvicorn.access INFO 2026-09-18 18:41:01,115 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58345 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 [2026-09-18 18:41:01,158: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (57.285 ms) [2026-09-18 18:41:01,162: INFO/main] Task galaxy.set_job_metadata[04e0c45b-9623-423f-a7b4-9d032fff25f1] succeeded in 0.06220170855522156s: None uvicorn.access INFO 2026-09-18 18:41:01,385 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58348 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:01,656 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58350 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:01,919 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58352 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 [2026-09-18 18:41:02,108: INFO/main] Task galaxy.finish_job[436bee0a-ffff-414e-a61b-5f7cc8307897] received [2026-09-18 18:41:02,108: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '436bee0a-ffff-414e-a61b-5f7cc8307897', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '436bee0a-ffff-414e-a61b-5f7cc8307897', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '2bb65d21-d48f-4890-a4f7-f1de1c5365d7', 'parent_id': '04e0c45b-9623-423f-a7b4-9d032fff25f1', 'argsrepr': '()', 'kwargsrepr': '{\'job_id\': 6, \'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request... kwargs:{}) [2026-09-18 18:41:02,116: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/6/outputs/dataset_a3ddaff3-e3a5-42df-ba22-5d8ac9955832.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/files/a/3/d/dataset_a3ddaff3-e3a5-42df-ba22-5d8ac9955832.dat [2026-09-18 18:41:02,118: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'AR0387_A_2.fastq.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [{'hash_function': 'SHA-1', 'hash_value': '89a32f456f670a00719362b8d72a1a90110c7e94'}], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/6/working/gxupload_0', 'object_id': 6}]}]}] [2026-09-18 18:41:02,180: INFO/main] Collecting metrics for Job 6 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/6 [2026-09-18 18:41:02,183: DEBUG/main] job_wrapper.finish for job 6 executed (71.181 ms) [2026-09-18 18:41:02,183: INFO/main] Successfully executed Celery task finish_job finish_job (73.820 ms) [2026-09-18 18:41:02,185: INFO/main] Task galaxy.finish_job[436bee0a-ffff-414e-a61b-5f7cc8307897] succeeded in 0.07671383395791054s: None uvicorn.access INFO 2026-09-18 18:41:02,187 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58354 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 galaxy.tools INFO 2026-09-18 18:41:02,194 [pN:main.1,p:72534,tN:AnyIO worker thread] Validated and populated state for tool request (0.067 ms) uvicorn.access INFO 2026-09-18 18:41:02,216 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58356 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:02,224 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58358 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:02,494 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58360 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:02,758 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58362 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:03,028 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58364 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 [2026-09-18 18:41:03,122: INFO/main] Task galaxy.setup_fetch_data[6c41c752-eb83-4f2d-a8df-8bffa2793d3b] received [2026-09-18 18:41:03,122: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', '6c41c752-eb83-4f2d-a8df-8bffa2793d3b', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': '6c41c752-eb83-4f2d-a8df-8bffa2793d3b', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '6c41c752-eb83-4f2d-a8df-8bffa2793d3b', 'parent_id': None, 'argsrepr': '(7,)', 'kwargsrepr': '{\'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request \\\'$request_path\\\'\n ... kwargs:{}) [2026-09-18 18:41:03,130: DEBUG/main] (7) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/7 [2026-09-18 18:41:03,151: DEBUG/main] Job wrapper for Job [7] prepared (7.940 ms) [2026-09-18 18:41:03,151: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (28.211 ms) [2026-09-18 18:41:03,154: INFO/main] Task galaxy.setup_fetch_data[6c41c752-eb83-4f2d-a8df-8bffa2793d3b] succeeded in 0.03201508428901434s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/7', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/7/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-18 18:41:03,294 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58367 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:03,561 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58369 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:03,838 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58371 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:04,118 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58374 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 [2026-09-18 18:41:04,128: INFO/main] Task galaxy.fetch_data[a7de3835-9980-43ec-9b52-cdc975c7bbb2] received [2026-09-18 18:41:04,128: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', 'a7de3835-9980-43ec-9b52-cdc975c7bbb2', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': 'a7de3835-9980-43ec-9b52-cdc975c7bbb2', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '6c41c752-eb83-4f2d-a8df-8bffa2793d3b', 'parent_id': '6c41c752-eb83-4f2d-a8df-8bffa2793d3b', 'argsrepr': "(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/7', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/7/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 7}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'a7de3835-9980-43ec-9b52-cdc975c7bbb2', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{}) [2026-09-18 18:41:04,194: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (65.974 ms) [2026-09-18 18:41:04,198: INFO/main] Task galaxy.fetch_data[a7de3835-9980-43ec-9b52-cdc975c7bbb2] succeeded in 0.06998979207128286s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/7' uvicorn.access INFO 2026-09-18 18:41:04,387 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58376 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:04,648 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58378 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:04,913 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58380 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 [2026-09-18 18:41:05,142: INFO/main] Task galaxy.set_job_metadata[a1529395-c68d-4534-be28-4e5f08d5558d] received [2026-09-18 18:41:05,142: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', 'a1529395-c68d-4534-be28-4e5f08d5558d', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': 'a1529395-c68d-4534-be28-4e5f08d5558d', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '6c41c752-eb83-4f2d-a8df-8bffa2793d3b', 'parent_id': 'a7de3835-9980-43ec-9b52-cdc975c7bbb2', 'argsrepr': "('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/7',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 7}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'a1529395-c68d-4534-be28-4e5f08d5558d', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '6e2b01f6-764d-4fb1-a6ee-387930ebc7f2'}, 'reply_to':... kwargs:{}) uvicorn.access INFO 2026-09-18 18:41:05,180 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58382 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 [2026-09-18 18:41:05,326: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (183.768 ms) [2026-09-18 18:41:05,330: INFO/main] Task galaxy.set_job_metadata[a1529395-c68d-4534-be28-4e5f08d5558d] succeeded in 0.18765395786613226s: None uvicorn.access INFO 2026-09-18 18:41:05,452 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58384 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:05,726 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58386 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:06,014 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58388 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 [2026-09-18 18:41:06,150: INFO/main] Task galaxy.finish_job[07c61d0b-f4d3-4f03-8f77-6f04e56fb496] received [2026-09-18 18:41:06,150: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '07c61d0b-f4d3-4f03-8f77-6f04e56fb496', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '07c61d0b-f4d3-4f03-8f77-6f04e56fb496', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '6c41c752-eb83-4f2d-a8df-8bffa2793d3b', 'parent_id': 'a1529395-c68d-4534-be28-4e5f08d5558d', 'argsrepr': '()', 'kwargsrepr': '{\'job_id\': 7, \'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request... kwargs:{}) [2026-09-18 18:41:06,160: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/7/outputs/dataset_7fcac025-764a-4c5e-aa9c-2c3a0201dccd.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/files/7/f/c/dataset_7fcac025-764a-4c5e-aa9c-2c3a0201dccd.dat [2026-09-18 18:41:06,162: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'AR0387_B_1.fastq.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [{'hash_function': 'SHA-1', 'hash_value': '022d0851c4b94b919c62d6c1af64e3713bb8e138'}], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/7/working/gxupload_0', 'object_id': 7}]}]}] [2026-09-18 18:41:06,229: INFO/main] Collecting metrics for Job 7 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/7 [2026-09-18 18:41:06,232: DEBUG/main] job_wrapper.finish for job 7 executed (76.240 ms) [2026-09-18 18:41:06,232: INFO/main] Successfully executed Celery task finish_job finish_job (81.118 ms) [2026-09-18 18:41:06,234: INFO/main] Task galaxy.finish_job[07c61d0b-f4d3-4f03-8f77-6f04e56fb496] succeeded in 0.08338237553834915s: None uvicorn.access INFO 2026-09-18 18:41:06,284 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58390 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 galaxy.tools INFO 2026-09-18 18:41:06,290 [pN:main.1,p:72534,tN:AnyIO worker thread] Validated and populated state for tool request (0.038 ms) uvicorn.access INFO 2026-09-18 18:41:06,310 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58392 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:06,318 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58394 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:06,587 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58396 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:06,868 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58398 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:07,139 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58401 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 [2026-09-18 18:41:07,164: INFO/main] Task galaxy.setup_fetch_data[51201c1e-5471-443e-8d77-5de39f88907a] received [2026-09-18 18:41:07,164: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', '51201c1e-5471-443e-8d77-5de39f88907a', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': '51201c1e-5471-443e-8d77-5de39f88907a', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '51201c1e-5471-443e-8d77-5de39f88907a', 'parent_id': None, 'argsrepr': '(8,)', 'kwargsrepr': '{\'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request \\\'$request_path\\\'\n ... kwargs:{}) [2026-09-18 18:41:07,175: DEBUG/main] (8) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/8 [2026-09-18 18:41:07,198: DEBUG/main] Job wrapper for Job [8] prepared (8.880 ms) [2026-09-18 18:41:07,198: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (33.593 ms) [2026-09-18 18:41:07,202: INFO/main] Task galaxy.setup_fetch_data[51201c1e-5471-443e-8d77-5de39f88907a] succeeded in 0.037536999210715294s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/8', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/8/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-18 18:41:07,418 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58403 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:07,685 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58405 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:07,969 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58409 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 [2026-09-18 18:41:08,182: INFO/main] Task galaxy.fetch_data[bd5d3acb-1101-4572-9aec-e9d1f96ebd53] received [2026-09-18 18:41:08,182: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', 'bd5d3acb-1101-4572-9aec-e9d1f96ebd53', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': 'bd5d3acb-1101-4572-9aec-e9d1f96ebd53', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '51201c1e-5471-443e-8d77-5de39f88907a', 'parent_id': '51201c1e-5471-443e-8d77-5de39f88907a', 'argsrepr': "(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/8', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/8/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 8}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'bd5d3acb-1101-4572-9aec-e9d1f96ebd53', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{}) uvicorn.access INFO 2026-09-18 18:41:08,236 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58411 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 [2026-09-18 18:41:08,239: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (55.699 ms) [2026-09-18 18:41:08,243: INFO/main] Task galaxy.fetch_data[bd5d3acb-1101-4572-9aec-e9d1f96ebd53] succeeded in 0.060708667151629925s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/8' uvicorn.access INFO 2026-09-18 18:41:08,508 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58413 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:08,785 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58415 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:09,073 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58417 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 [2026-09-18 18:41:09,198: INFO/main] Task galaxy.set_job_metadata[9ff6f6a3-4e65-4356-a6d4-3d2653f760e2] received [2026-09-18 18:41:09,198: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '9ff6f6a3-4e65-4356-a6d4-3d2653f760e2', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '9ff6f6a3-4e65-4356-a6d4-3d2653f760e2', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '51201c1e-5471-443e-8d77-5de39f88907a', 'parent_id': 'bd5d3acb-1101-4572-9aec-e9d1f96ebd53', 'argsrepr': "('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/8',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 8}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '9ff6f6a3-4e65-4356-a6d4-3d2653f760e2', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': 'e9ed9fb2-3c9f-4d7e-b9f6-8827b4eab08e'}, 'reply_to':... kwargs:{}) [2026-09-18 18:41:09,239: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (40.669 ms) [2026-09-18 18:41:09,243: INFO/main] Task galaxy.set_job_metadata[9ff6f6a3-4e65-4356-a6d4-3d2653f760e2] succeeded in 0.044548832811415195s: None uvicorn.access INFO 2026-09-18 18:41:09,341 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58419 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:09,626 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58422 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:09,907 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58424 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:10,192 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58427 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 [2026-09-18 18:41:10,212: INFO/main] Task galaxy.finish_job[5a506c62-a832-42c4-8ec3-117c36fc6fa2] received [2026-09-18 18:41:10,213: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '5a506c62-a832-42c4-8ec3-117c36fc6fa2', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '5a506c62-a832-42c4-8ec3-117c36fc6fa2', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '51201c1e-5471-443e-8d77-5de39f88907a', 'parent_id': '9ff6f6a3-4e65-4356-a6d4-3d2653f760e2', 'argsrepr': '()', 'kwargsrepr': '{\'job_id\': 8, \'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request... kwargs:{}) [2026-09-18 18:41:10,222: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/8/outputs/dataset_2dd04745-a3dc-412f-9047-2fe71daac3c9.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/files/2/d/d/dataset_2dd04745-a3dc-412f-9047-2fe71daac3c9.dat [2026-09-18 18:41:10,224: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'AR0387_B_2.fastq.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [{'hash_function': 'SHA-1', 'hash_value': '28d347eddac1455d3df000846cffb4dc0a472c4d'}], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/8/working/gxupload_0', 'object_id': 8}]}]}] [2026-09-18 18:41:10,289: INFO/main] Collecting metrics for Job 8 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/8 [2026-09-18 18:41:10,292: DEBUG/main] job_wrapper.finish for job 8 executed (73.342 ms) [2026-09-18 18:41:10,292: INFO/main] Successfully executed Celery task finish_job finish_job (78.360 ms) [2026-09-18 18:41:10,294: INFO/main] Task galaxy.finish_job[5a506c62-a832-42c4-8ec3-117c36fc6fa2] succeeded in 0.08045241702347994s: None uvicorn.access INFO 2026-09-18 18:41:10,461 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58429 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 galaxy.tools INFO 2026-09-18 18:41:10,468 [pN:main.1,p:72534,tN:AnyIO worker thread] Validated and populated state for tool request (0.038 ms) uvicorn.access INFO 2026-09-18 18:41:10,489 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58431 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:10,496 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58433 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:10,770 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58435 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:11,046 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58437 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 [2026-09-18 18:41:11,226: INFO/main] Task galaxy.setup_fetch_data[497af4f9-5dd0-454b-b18f-f7089ce5104c] received [2026-09-18 18:41:11,226: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', '497af4f9-5dd0-454b-b18f-f7089ce5104c', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': '497af4f9-5dd0-454b-b18f-f7089ce5104c', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '497af4f9-5dd0-454b-b18f-f7089ce5104c', 'parent_id': None, 'argsrepr': '(9,)', 'kwargsrepr': '{\'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request \\\'$request_path\\\'\n ... kwargs:{}) [2026-09-18 18:41:11,241: DEBUG/main] (9) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/9 [2026-09-18 18:41:11,267: DEBUG/main] Job wrapper for Job [9] prepared (11.226 ms) [2026-09-18 18:41:11,267: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (39.838 ms) [2026-09-18 18:41:11,271: INFO/main] Task galaxy.setup_fetch_data[497af4f9-5dd0-454b-b18f-f7089ce5104c] succeeded in 0.044127125293016434s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/9', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/9/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-18 18:41:11,315 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58439 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:11,599 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58441 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:11,862 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58443 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:12,137 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58445 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 [2026-09-18 18:41:12,237: INFO/main] Task galaxy.fetch_data[803b61d9-b29e-4c24-9528-66f019f99a62] received [2026-09-18 18:41:12,238: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '803b61d9-b29e-4c24-9528-66f019f99a62', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '803b61d9-b29e-4c24-9528-66f019f99a62', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '497af4f9-5dd0-454b-b18f-f7089ce5104c', 'parent_id': '497af4f9-5dd0-454b-b18f-f7089ce5104c', 'argsrepr': "(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/9', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/9/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 9}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '803b61d9-b29e-4c24-9528-66f019f99a62', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{}) [2026-09-18 18:41:12,295: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (56.983 ms) [2026-09-18 18:41:12,299: INFO/main] Task galaxy.fetch_data[803b61d9-b29e-4c24-9528-66f019f99a62] succeeded in 0.06120899971574545s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/9' uvicorn.access INFO 2026-09-18 18:41:12,406 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58447 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:12,679 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58449 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:12,971 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58451 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:13,244 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58453 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 [2026-09-18 18:41:13,254: INFO/main] Task galaxy.set_job_metadata[880f4cb1-b197-4785-a66d-448177a635c6] received [2026-09-18 18:41:13,254: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '880f4cb1-b197-4785-a66d-448177a635c6', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '880f4cb1-b197-4785-a66d-448177a635c6', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '497af4f9-5dd0-454b-b18f-f7089ce5104c', 'parent_id': '803b61d9-b29e-4c24-9528-66f019f99a62', 'argsrepr': "('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/9',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 9}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '880f4cb1-b197-4785-a66d-448177a635c6', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': 'f95cf450-e86e-4584-b264-e570d96105fe'}, 'reply_to':... kwargs:{}) [2026-09-18 18:41:13,308: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (53.177 ms) [2026-09-18 18:41:13,312: INFO/main] Task galaxy.set_job_metadata[880f4cb1-b197-4785-a66d-448177a635c6] succeeded in 0.057640207931399345s: None uvicorn.access INFO 2026-09-18 18:41:13,518 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58455 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:13,791 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58457 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:14,064 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58459 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 [2026-09-18 18:41:14,273: INFO/main] Task galaxy.finish_job[dbd684aa-df59-45f3-b9c3-e8d42e40612c] received [2026-09-18 18:41:14,274: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', 'dbd684aa-df59-45f3-b9c3-e8d42e40612c', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': 'dbd684aa-df59-45f3-b9c3-e8d42e40612c', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '497af4f9-5dd0-454b-b18f-f7089ce5104c', 'parent_id': '880f4cb1-b197-4785-a66d-448177a635c6', 'argsrepr': '()', 'kwargsrepr': '{\'job_id\': 9, \'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request... kwargs:{}) [2026-09-18 18:41:14,287: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/9/outputs/dataset_b888659a-0928-47dc-90ba-18f2b3fa96a5.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/files/b/8/8/dataset_b888659a-0928-47dc-90ba-18f2b3fa96a5.dat [2026-09-18 18:41:14,289: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'AR0382_tnSWI1_A_1.fastq.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [{'hash_function': 'SHA-1', 'hash_value': '3b6109b5392bba5cb75f312fd7c078b67346013c'}], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/9/working/gxupload_0', 'object_id': 9}]}]}] uvicorn.access INFO 2026-09-18 18:41:14,333 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58461 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 [2026-09-18 18:41:14,360: INFO/main] Collecting metrics for Job 9 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/9 [2026-09-18 18:41:14,363: DEBUG/main] job_wrapper.finish for job 9 executed (83.518 ms) [2026-09-18 18:41:14,363: INFO/main] Successfully executed Celery task finish_job finish_job (89.078 ms) [2026-09-18 18:41:14,365: INFO/main] Task galaxy.finish_job[dbd684aa-df59-45f3-b9c3-e8d42e40612c] succeeded in 0.09121458232402802s: None uvicorn.access INFO 2026-09-18 18:41:14,611 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58463 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 galaxy.tools INFO 2026-09-18 18:41:14,622 [pN:main.1,p:72534,tN:AnyIO worker thread] Validated and populated state for tool request (0.071 ms) uvicorn.access INFO 2026-09-18 18:41:14,650 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58465 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:14,658 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58467 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:14,942 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58469 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:15,222 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58472 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 [2026-09-18 18:41:15,293: INFO/main] Task galaxy.setup_fetch_data[cb20f58a-f003-46a6-9374-c7d83586a75a] received [2026-09-18 18:41:15,293: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', 'cb20f58a-f003-46a6-9374-c7d83586a75a', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': 'cb20f58a-f003-46a6-9374-c7d83586a75a', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'cb20f58a-f003-46a6-9374-c7d83586a75a', 'parent_id': None, 'argsrepr': '(10,)', 'kwargsrepr': '{\'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request \\\'$request_path\\\'\n ... kwargs:{}) [2026-09-18 18:41:15,306: DEBUG/main] (10) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/10 [2026-09-18 18:41:15,330: DEBUG/main] Job wrapper for Job [10] prepared (8.712 ms) [2026-09-18 18:41:15,330: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (36.239 ms) [2026-09-18 18:41:15,334: INFO/main] Task galaxy.setup_fetch_data[cb20f58a-f003-46a6-9374-c7d83586a75a] succeeded in 0.04000591766089201s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/10', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/10/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-18 18:41:15,492 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58475 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:15,769 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58477 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:16,051 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58479 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 [2026-09-18 18:41:16,310: INFO/main] Task galaxy.fetch_data[37a47b08-1e7b-4d94-b824-bcc7d2d982b7] received [2026-09-18 18:41:16,310: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '37a47b08-1e7b-4d94-b824-bcc7d2d982b7', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '37a47b08-1e7b-4d94-b824-bcc7d2d982b7', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'cb20f58a-f003-46a6-9374-c7d83586a75a', 'parent_id': 'cb20f58a-f003-46a6-9374-c7d83586a75a', 'argsrepr': "(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/10', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/10/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 10}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '37a47b08-1e7b-4d94-b824-bcc7d2d982b7', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{}) uvicorn.access INFO 2026-09-18 18:41:16,317 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58481 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 [2026-09-18 18:41:16,368: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (57.247 ms) [2026-09-18 18:41:16,372: INFO/main] Task galaxy.fetch_data[37a47b08-1e7b-4d94-b824-bcc7d2d982b7] succeeded in 0.06144712492823601s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/10' uvicorn.access INFO 2026-09-18 18:41:16,586 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58483 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:16,863 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58485 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:17,154 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58487 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 [2026-09-18 18:41:17,325: INFO/main] Task galaxy.set_job_metadata[1ef09842-fc84-413d-9616-d504ca2df979] received [2026-09-18 18:41:17,325: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '1ef09842-fc84-413d-9616-d504ca2df979', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '1ef09842-fc84-413d-9616-d504ca2df979', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'cb20f58a-f003-46a6-9374-c7d83586a75a', 'parent_id': '37a47b08-1e7b-4d94-b824-bcc7d2d982b7', 'argsrepr': "('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/10',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 10}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '1ef09842-fc84-413d-9616-d504ca2df979', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '2ec8e658-3df5-474a-8db4-3326629c2297'}, 'reply_to':... kwargs:{}) [2026-09-18 18:41:17,370: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (43.606 ms) [2026-09-18 18:41:17,373: INFO/main] Task galaxy.set_job_metadata[1ef09842-fc84-413d-9616-d504ca2df979] succeeded in 0.04742983262985945s: None uvicorn.access INFO 2026-09-18 18:41:17,424 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58489 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:17,696 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58491 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:17,967 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58493 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:18,248 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58495 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 [2026-09-18 18:41:18,345: INFO/main] Task galaxy.finish_job[45937ede-93fd-44d5-bc4a-2a304b9944ce] received [2026-09-18 18:41:18,345: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '45937ede-93fd-44d5-bc4a-2a304b9944ce', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '45937ede-93fd-44d5-bc4a-2a304b9944ce', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'cb20f58a-f003-46a6-9374-c7d83586a75a', 'parent_id': '1ef09842-fc84-413d-9616-d504ca2df979', 'argsrepr': '()', 'kwargsrepr': '{\'job_id\': 10, \'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n ... kwargs:{}) [2026-09-18 18:41:18,358: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/10/outputs/dataset_a7395174-c96d-4f6f-8bef-68562d303b69.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/files/a/7/3/dataset_a7395174-c96d-4f6f-8bef-68562d303b69.dat [2026-09-18 18:41:18,360: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'AR0382_tnSWI1_A_2.fastq.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [{'hash_function': 'SHA-1', 'hash_value': 'e5599b61d6ec223f9cd88e7eb7e7877c6d7cf29c'}], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/10/working/gxupload_0', 'object_id': 10}]}]}] [2026-09-18 18:41:18,441: INFO/main] Collecting metrics for Job 10 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/10 [2026-09-18 18:41:18,444: DEBUG/main] job_wrapper.finish for job 10 executed (92.017 ms) [2026-09-18 18:41:18,444: INFO/main] Successfully executed Celery task finish_job finish_job (98.362 ms) [2026-09-18 18:41:18,447: INFO/main] Task galaxy.finish_job[45937ede-93fd-44d5-bc4a-2a304b9944ce] succeeded in 0.10099145770072937s: None uvicorn.access INFO 2026-09-18 18:41:18,520 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58498 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 galaxy.tools INFO 2026-09-18 18:41:18,526 [pN:main.1,p:72534,tN:AnyIO worker thread] Validated and populated state for tool request (0.037 ms) uvicorn.access INFO 2026-09-18 18:41:18,546 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58500 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:18,553 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58502 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:18,829 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58504 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:19,112 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58506 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 [2026-09-18 18:41:19,372: INFO/main] Task galaxy.setup_fetch_data[53b8c3eb-0aa9-4ef3-ac0f-31a81e178290] received [2026-09-18 18:41:19,373: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', '53b8c3eb-0aa9-4ef3-ac0f-31a81e178290', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': '53b8c3eb-0aa9-4ef3-ac0f-31a81e178290', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '53b8c3eb-0aa9-4ef3-ac0f-31a81e178290', 'parent_id': None, 'argsrepr': '(11,)', 'kwargsrepr': '{\'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request \\\'$request_path\\\'\n ... kwargs:{}) [2026-09-18 18:41:19,394: DEBUG/main] (11) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/11 uvicorn.access INFO 2026-09-18 18:41:19,402 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58509 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 [2026-09-18 18:41:19,429: DEBUG/main] Job wrapper for Job [11] prepared (12.010 ms) [2026-09-18 18:41:19,429: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (55.634 ms) [2026-09-18 18:41:19,434: INFO/main] Task galaxy.setup_fetch_data[53b8c3eb-0aa9-4ef3-ac0f-31a81e178290] succeeded in 0.06072662491351366s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/11', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/11/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-18 18:41:19,678 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58511 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:19,948 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58513 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:20,234 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58515 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 [2026-09-18 18:41:20,387: INFO/main] Task galaxy.fetch_data[c9505295-9b6b-4704-92c4-7184e02ad85b] received [2026-09-18 18:41:20,388: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', 'c9505295-9b6b-4704-92c4-7184e02ad85b', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': 'c9505295-9b6b-4704-92c4-7184e02ad85b', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '53b8c3eb-0aa9-4ef3-ac0f-31a81e178290', 'parent_id': '53b8c3eb-0aa9-4ef3-ac0f-31a81e178290', 'argsrepr': "(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/11', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/11/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 11}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'c9505295-9b6b-4704-92c4-7184e02ad85b', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{}) [2026-09-18 18:41:20,472: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (82.850 ms) [2026-09-18 18:41:20,476: INFO/main] Task galaxy.fetch_data[c9505295-9b6b-4704-92c4-7184e02ad85b] succeeded in 0.08713825047016144s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/11' uvicorn.access INFO 2026-09-18 18:41:20,503 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58517 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:20,779 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58519 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:21,076 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58521 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:21,350 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58523 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 [2026-09-18 18:41:21,399: INFO/main] Task galaxy.set_job_metadata[cbfff784-39c6-4dbb-9f52-64741eb3cc41] received [2026-09-18 18:41:21,400: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', 'cbfff784-39c6-4dbb-9f52-64741eb3cc41', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': 'cbfff784-39c6-4dbb-9f52-64741eb3cc41', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '53b8c3eb-0aa9-4ef3-ac0f-31a81e178290', 'parent_id': 'c9505295-9b6b-4704-92c4-7184e02ad85b', 'argsrepr': "('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/11',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 11}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'cbfff784-39c6-4dbb-9f52-64741eb3cc41', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': 'c83217b3-7bfc-4726-b731-8fae3a831825'}, 'reply_to':... kwargs:{}) [2026-09-18 18:41:21,442: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (41.498 ms) [2026-09-18 18:41:21,445: INFO/main] Task galaxy.set_job_metadata[cbfff784-39c6-4dbb-9f52-64741eb3cc41] succeeded in 0.045483749359846115s: None uvicorn.access INFO 2026-09-18 18:41:21,619 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58525 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:21,905 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58527 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:22,207 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58529 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 [2026-09-18 18:41:22,425: INFO/main] Task galaxy.finish_job[9b6cdea3-9c8d-4395-825e-2fc6c2d6ab8f] received [2026-09-18 18:41:22,426: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '9b6cdea3-9c8d-4395-825e-2fc6c2d6ab8f', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '9b6cdea3-9c8d-4395-825e-2fc6c2d6ab8f', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '53b8c3eb-0aa9-4ef3-ac0f-31a81e178290', 'parent_id': 'cbfff784-39c6-4dbb-9f52-64741eb3cc41', 'argsrepr': '()', 'kwargsrepr': '{\'job_id\': 11, \'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n ... kwargs:{}) [2026-09-18 18:41:22,449: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/11/outputs/dataset_6a4a4b70-5297-41d5-87b7-bdc038d338a8.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/files/6/a/4/dataset_6a4a4b70-5297-41d5-87b7-bdc038d338a8.dat [2026-09-18 18:41:22,452: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'AR0382_tnSWI1_B_1.fastq.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [{'hash_function': 'SHA-1', 'hash_value': 'f803a1ee765bd35a575ab66f80133ad09e50a4ea'}], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/11/working/gxupload_0', 'object_id': 11}]}]}] uvicorn.access INFO 2026-09-18 18:41:22,475 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58531 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 [2026-09-18 18:41:22,533: INFO/main] Collecting metrics for Job 11 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/11 [2026-09-18 18:41:22,536: DEBUG/main] job_wrapper.finish for job 11 executed (97.338 ms) [2026-09-18 18:41:22,536: INFO/main] Successfully executed Celery task finish_job finish_job (108.186 ms) [2026-09-18 18:41:22,538: INFO/main] Task galaxy.finish_job[9b6cdea3-9c8d-4395-825e-2fc6c2d6ab8f] succeeded in 0.11059804167598486s: None uvicorn.access INFO 2026-09-18 18:41:22,745 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58533 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 galaxy.tools INFO 2026-09-18 18:41:22,755 [pN:main.1,p:72534,tN:AnyIO worker thread] Validated and populated state for tool request (0.058 ms) uvicorn.access INFO 2026-09-18 18:41:22,782 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58535 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:22,791 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58537 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:23,055 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58539 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:23,350 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58541 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 [2026-09-18 18:41:23,442: INFO/main] Task galaxy.setup_fetch_data[a517ac46-1284-4b1c-84f2-d1f011509c93] received [2026-09-18 18:41:23,442: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', 'a517ac46-1284-4b1c-84f2-d1f011509c93', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': 'a517ac46-1284-4b1c-84f2-d1f011509c93', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'a517ac46-1284-4b1c-84f2-d1f011509c93', 'parent_id': None, 'argsrepr': '(12,)', 'kwargsrepr': '{\'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request \\\'$request_path\\\'\n ... kwargs:{}) [2026-09-18 18:41:23,455: DEBUG/main] (12) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/12 [2026-09-18 18:41:23,480: DEBUG/main] Job wrapper for Job [12] prepared (11.994 ms) [2026-09-18 18:41:23,480: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (36.962 ms) [2026-09-18 18:41:23,484: INFO/main] Task galaxy.setup_fetch_data[a517ac46-1284-4b1c-84f2-d1f011509c93] succeeded in 0.04162654187530279s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/12', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/12/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-18 18:41:23,619 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58544 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:23,921 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58546 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:24,216 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58548 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 [2026-09-18 18:41:24,453: INFO/main] Task galaxy.fetch_data[c6fb3d89-ff5c-4ad8-bead-106593ef3538] received [2026-09-18 18:41:24,454: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', 'c6fb3d89-ff5c-4ad8-bead-106593ef3538', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': 'c6fb3d89-ff5c-4ad8-bead-106593ef3538', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'a517ac46-1284-4b1c-84f2-d1f011509c93', 'parent_id': 'a517ac46-1284-4b1c-84f2-d1f011509c93', 'argsrepr': "(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/12', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/12/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 12}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'c6fb3d89-ff5c-4ad8-bead-106593ef3538', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{}) uvicorn.access INFO 2026-09-18 18:41:24,485 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58550 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 [2026-09-18 18:41:24,695: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (240.274 ms) [2026-09-18 18:41:24,699: INFO/main] Task galaxy.fetch_data[c6fb3d89-ff5c-4ad8-bead-106593ef3538] succeeded in 0.24469412490725517s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/12' uvicorn.access INFO 2026-09-18 18:41:24,756 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58552 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:25,020 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58554 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:25,281 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58556 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 [2026-09-18 18:41:25,466: INFO/main] Task galaxy.set_job_metadata[a58ae737-04ce-43ed-8235-109f50bc0ad1] received [2026-09-18 18:41:25,466: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', 'a58ae737-04ce-43ed-8235-109f50bc0ad1', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': 'a58ae737-04ce-43ed-8235-109f50bc0ad1', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'a517ac46-1284-4b1c-84f2-d1f011509c93', 'parent_id': 'c6fb3d89-ff5c-4ad8-bead-106593ef3538', 'argsrepr': "('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/12',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 12}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'a58ae737-04ce-43ed-8235-109f50bc0ad1', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '19cb50f7-dde1-4df5-b80a-0f4ffb88fc66'}, 'reply_to':... kwargs:{}) [2026-09-18 18:41:25,503: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (37.088 ms) [2026-09-18 18:41:25,507: INFO/main] Task galaxy.set_job_metadata[a58ae737-04ce-43ed-8235-109f50bc0ad1] succeeded in 0.04129833448678255s: None uvicorn.access INFO 2026-09-18 18:41:25,550 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58558 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:25,824 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58562 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:26,100 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58564 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:26,378 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58566 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 [2026-09-18 18:41:26,475: INFO/main] Task galaxy.finish_job[2c0a7a96-7a5a-46bf-b5cb-4fbd9ff4b8be] received [2026-09-18 18:41:26,475: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '2c0a7a96-7a5a-46bf-b5cb-4fbd9ff4b8be', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '2c0a7a96-7a5a-46bf-b5cb-4fbd9ff4b8be', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'a517ac46-1284-4b1c-84f2-d1f011509c93', 'parent_id': 'a58ae737-04ce-43ed-8235-109f50bc0ad1', 'argsrepr': '()', 'kwargsrepr': '{\'job_id\': 12, \'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n ... kwargs:{}) [2026-09-18 18:41:26,487: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/12/outputs/dataset_64da08a0-cfb9-461c-b5d7-62f68c065799.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/files/6/4/d/dataset_64da08a0-cfb9-461c-b5d7-62f68c065799.dat [2026-09-18 18:41:26,489: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'AR0382_tnSWI1_B_2.fastq.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [{'hash_function': 'SHA-1', 'hash_value': '97a623f6a006e90740a44d6391685ede0157acf4'}], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/12/working/gxupload_0', 'object_id': 12}]}]}] [2026-09-18 18:41:26,554: INFO/main] Collecting metrics for Job 12 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/12 [2026-09-18 18:41:26,557: DEBUG/main] job_wrapper.finish for job 12 executed (75.999 ms) [2026-09-18 18:41:26,557: INFO/main] Successfully executed Celery task finish_job finish_job (80.858 ms) [2026-09-18 18:41:26,559: INFO/main] Task galaxy.finish_job[2c0a7a96-7a5a-46bf-b5cb-4fbd9ff4b8be] succeeded in 0.0831195842474699s: None uvicorn.access INFO 2026-09-18 18:41:26,646 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58568 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:26,691 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58570 - "POST /api/dataset_collections HTTP/1.1" 200 galaxy.tools INFO 2026-09-18 18:41:26,964 [pN:main.1,p:72534,tN:AnyIO worker thread] Validated and populated state for tool request (0.050 ms) uvicorn.access INFO 2026-09-18 18:41:26,985 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58572 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:27,002 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58574 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:27,280 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58576 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 [2026-09-18 18:41:27,495: INFO/main] Task galaxy.setup_fetch_data[e8703ec8-a2f2-4da5-86d6-4ef2b8fb41af] received [2026-09-18 18:41:27,495: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', 'e8703ec8-a2f2-4da5-86d6-4ef2b8fb41af', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': 'e8703ec8-a2f2-4da5-86d6-4ef2b8fb41af', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'e8703ec8-a2f2-4da5-86d6-4ef2b8fb41af', 'parent_id': None, 'argsrepr': '(13,)', 'kwargsrepr': '{\'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request \\\'$request_path\\\'\n ... kwargs:{}) [2026-09-18 18:41:27,509: DEBUG/main] (13) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/13 [2026-09-18 18:41:27,536: DEBUG/main] Job wrapper for Job [13] prepared (9.307 ms) [2026-09-18 18:41:27,536: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (40.240 ms) [2026-09-18 18:41:27,540: INFO/main] Task galaxy.setup_fetch_data[e8703ec8-a2f2-4da5-86d6-4ef2b8fb41af] succeeded in 0.04447091743350029s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/13', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/13/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-18 18:41:27,544 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58578 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:27,833 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58580 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:28,120 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58582 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:28,391 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58585 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 [2026-09-18 18:41:28,511: INFO/main] Task galaxy.fetch_data[18dfebcd-2f55-497d-8a93-2a754618aff5] received [2026-09-18 18:41:28,511: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '18dfebcd-2f55-497d-8a93-2a754618aff5', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '18dfebcd-2f55-497d-8a93-2a754618aff5', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'e8703ec8-a2f2-4da5-86d6-4ef2b8fb41af', 'parent_id': 'e8703ec8-a2f2-4da5-86d6-4ef2b8fb41af', 'argsrepr': "(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/13', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/13/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 13}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '18dfebcd-2f55-497d-8a93-2a754618aff5', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{}) /Users/mvandenb/src/worktrees/.planemo-home/.planemo/gx_venv_3.12_release_26.1/lib/python3.12/site-packages/fs/__init__.py:4: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. __import__("pkg_resources").declare_namespace(__name__) # type: ignore uvicorn.access INFO 2026-09-18 18:41:28,656 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58587 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:28,936 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58590 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:29,203 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58592 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:29,476 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58594 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:29,745 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58596 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 [2026-09-18 18:41:29,854: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (1342.232 ms) [2026-09-18 18:41:29,858: INFO/main] Task galaxy.fetch_data[18dfebcd-2f55-497d-8a93-2a754618aff5] succeeded in 1.3464263752102852s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/13' uvicorn.access INFO 2026-09-18 18:41:30,019 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58598 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:30,297 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58600 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 [2026-09-18 18:41:30,539: INFO/main] Task galaxy.set_job_metadata[396a5d3a-7bc8-4972-bb99-e1a4bbe55144] received [2026-09-18 18:41:30,539: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '396a5d3a-7bc8-4972-bb99-e1a4bbe55144', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '396a5d3a-7bc8-4972-bb99-e1a4bbe55144', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'e8703ec8-a2f2-4da5-86d6-4ef2b8fb41af', 'parent_id': '18dfebcd-2f55-497d-8a93-2a754618aff5', 'argsrepr': "('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/13',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 13}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '396a5d3a-7bc8-4972-bb99-e1a4bbe55144', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '1fdd6b62-6b43-4220-ae7a-b6991a60f9f8'}, 'reply_to':... kwargs:{}) uvicorn.access INFO 2026-09-18 18:41:30,565 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58606 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 [2026-09-18 18:41:30,577: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (37.233 ms) [2026-09-18 18:41:30,581: INFO/main] Task galaxy.set_job_metadata[396a5d3a-7bc8-4972-bb99-e1a4bbe55144] succeeded in 0.04102674964815378s: None uvicorn.access INFO 2026-09-18 18:41:30,834 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58609 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:31,114 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58611 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:31,399 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58613 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 [2026-09-18 18:41:31,555: INFO/main] Task galaxy.finish_job[09633c92-83ab-4a66-9c9f-f5e3594b09dd] received [2026-09-18 18:41:31,556: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '09633c92-83ab-4a66-9c9f-f5e3594b09dd', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '09633c92-83ab-4a66-9c9f-f5e3594b09dd', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'e8703ec8-a2f2-4da5-86d6-4ef2b8fb41af', 'parent_id': '396a5d3a-7bc8-4972-bb99-e1a4bbe55144', 'argsrepr': '()', 'kwargsrepr': '{\'job_id\': 13, \'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n ... kwargs:{}) [2026-09-18 18:41:31,568: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/13/outputs/dataset_41de4ba9-305e-4151-958f-7c54946b4314.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/files/4/1/d/dataset_41de4ba9-305e-4151-958f-7c54946b4314.dat [2026-09-18 18:41:31,571: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'GCA_002759435.2_Cand_auris_B8441_V2_genomic.fna.gz', 'dbkey': '?', 'ext': 'fasta', 'link_data_only': False, 'sources': [{'source_uri': 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/759/435/GCA_002759435.2_Cand_auris_B8441_V2/GCA_002759435.2_Cand_auris_B8441_V2_genomic.fna.gz', 'requested_transform': [{'action': 'datatype_groom'}, {'action': 'to_posix_lines'}]}], 'hashes': [], 'info': 'uploaded fasta file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/13/working/data_fetch_upload_n74ua_dx', 'object_id': 13}]}]}] [2026-09-18 18:41:31,645: INFO/main] Collecting metrics for Job 13 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/13 [2026-09-18 18:41:31,648: DEBUG/main] job_wrapper.finish for job 13 executed (85.324 ms) [2026-09-18 18:41:31,648: INFO/main] Successfully executed Celery task finish_job finish_job (91.120 ms) [2026-09-18 18:41:31,650: INFO/main] Task galaxy.finish_job[09633c92-83ab-4a66-9c9f-f5e3594b09dd] succeeded in 0.09335062466561794s: None uvicorn.access INFO 2026-09-18 18:41:31,670 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58615 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 galaxy.tools INFO 2026-09-18 18:41:31,679 [pN:main.1,p:72534,tN:AnyIO worker thread] Validated and populated state for tool request (0.029 ms) uvicorn.access INFO 2026-09-18 18:41:31,698 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58617 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:31,705 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58619 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:31,972 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58621 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:32,239 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58623 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:32,518 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58625 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 [2026-09-18 18:41:32,574: INFO/main] Task galaxy.compute_dataset_hash[7e420c06-0120-414e-8277-14362f85e046] received [2026-09-18 18:41:32,575: DEBUG/main] TaskPool: Apply (args:('galaxy.compute_dataset_hash', '7e420c06-0120-414e-8277-14362f85e046', {'lang': 'py', 'task': 'galaxy.compute_dataset_hash', 'id': '7e420c06-0120-414e-8277-14362f85e046', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'e8703ec8-a2f2-4da5-86d6-4ef2b8fb41af', 'parent_id': '09633c92-83ab-4a66-9c9f-f5e3594b09dd', 'argsrepr': '()', 'kwargsrepr': "{'request': ComputeDatasetHashTaskRequest(dataset_id=13, extra_files_path=None, hash_function='SHA-256', user=None)}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '7e420c06-0120-414e-8277-14362f85e046', 'reply_to': '01881f92-a07d-38e0-98e8-5b53ce2282ab', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '917b056e-58b5-4d74-a6c4-6f86956b6178'}, 'reply_to':... kwargs:{}) [2026-09-18 18:41:32,582: INFO/main] Task galaxy.setup_fetch_data[25edfcce-8a7e-4055-af30-03857c42a34d] received [2026-09-18 18:41:32,582: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', '25edfcce-8a7e-4055-af30-03857c42a34d', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': '25edfcce-8a7e-4055-af30-03857c42a34d', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '25edfcce-8a7e-4055-af30-03857c42a34d', 'parent_id': None, 'argsrepr': '(14,)', 'kwargsrepr': '{\'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n --request \\\'$request_path\\\'\n ... kwargs:{}) [2026-09-18 18:41:32,593: DEBUG/main] (14) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/14 [2026-09-18 18:41:32,601: INFO/main] Successfully executed Celery task compute_dataset_hash to compute dataset hash and store in database compute_dataset_hash to compute dataset hash and store in database (25.753 ms) [2026-09-18 18:41:32,603: INFO/main] Task galaxy.compute_dataset_hash[7e420c06-0120-414e-8277-14362f85e046] succeeded in 0.028330917470157146s: None [2026-09-18 18:41:32,620: DEBUG/main] Job wrapper for Job [14] prepared (8.704 ms) [2026-09-18 18:41:32,620: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (38.317 ms) [2026-09-18 18:41:32,633: INFO/main] Task galaxy.setup_fetch_data[25edfcce-8a7e-4055-af30-03857c42a34d] succeeded in 0.05069554224610329s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/14', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/14/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-18 18:41:32,788 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58627 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:33,090 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58629 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:33,368 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58631 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 [2026-09-18 18:41:33,591: INFO/main] Task galaxy.fetch_data[ac4ddcbd-0ac6-49dc-becd-a89a08d80f70] received [2026-09-18 18:41:33,592: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', 'ac4ddcbd-0ac6-49dc-becd-a89a08d80f70', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': 'ac4ddcbd-0ac6-49dc-becd-a89a08d80f70', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '25edfcce-8a7e-4055-af30-03857c42a34d', 'parent_id': '25edfcce-8a7e-4055-af30-03857c42a34d', 'argsrepr': "(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/14', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/14/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 14}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'ac4ddcbd-0ac6-49dc-becd-a89a08d80f70', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{}) uvicorn.access INFO 2026-09-18 18:41:33,637 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58633 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:33,908 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58636 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:34,195 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58639 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:34,486 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58641 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 [2026-09-18 18:41:34,526: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (933.474 ms) [2026-09-18 18:41:34,531: INFO/main] Task galaxy.fetch_data[ac4ddcbd-0ac6-49dc-becd-a89a08d80f70] succeeded in 0.939151500351727s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/14' [2026-09-18 18:41:34,605: INFO/main] Task galaxy.set_job_metadata[f63c5bba-64e3-4ce8-ac3f-c24ce6577abc] received [2026-09-18 18:41:34,605: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', 'f63c5bba-64e3-4ce8-ac3f-c24ce6577abc', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': 'f63c5bba-64e3-4ce8-ac3f-c24ce6577abc', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '25edfcce-8a7e-4055-af30-03857c42a34d', 'parent_id': 'ac4ddcbd-0ac6-49dc-becd-a89a08d80f70', 'argsrepr': "('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/14',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 14}", 'origin': 'gen72528@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'f63c5bba-64e3-4ce8-ac3f-c24ce6577abc', 'reply_to': '8213afa5-048d-30fb-be73-93fd9febb41e', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': 'd0b3beb0-70c1-4bd5-b000-e825803f2be0'}, 'reply_to':... kwargs:{}) [2026-09-18 18:41:34,655: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (48.544 ms) [2026-09-18 18:41:34,658: INFO/main] Task galaxy.set_job_metadata[f63c5bba-64e3-4ce8-ac3f-c24ce6577abc] succeeded in 0.052581749856472015s: None uvicorn.access INFO 2026-09-18 18:41:34,757 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58643 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:35,039 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58645 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:35,308 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58647 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:35,575 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58649 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 [2026-09-18 18:41:35,616: INFO/main] Task galaxy.finish_job[7d91bccc-d01a-4b3e-ab00-d0ca1b300e27] received [2026-09-18 18:41:35,616: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '7d91bccc-d01a-4b3e-ab00-d0ca1b300e27', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '7d91bccc-d01a-4b3e-ab00-d0ca1b300e27', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '25edfcce-8a7e-4055-af30-03857c42a34d', 'parent_id': 'f63c5bba-64e3-4ce8-ac3f-c24ce6577abc', 'argsrepr': '()', 'kwargsrepr': '{\'job_id\': 14, \'raw_tool_source\': \'\n \n \n operation_0224\n \n \n python \\\'$__tool_directory__/data_fetch.py\\\'\n --galaxy-root \\\'$GALAXY_ROOT_DIR\\\'\n --datatypes-registry \\\'$GALAXY_DATATYPES_CONF_FILE\\\'\n --request-version \\\'$request_version\\\'\n ... kwargs:{}) [2026-09-18 18:41:35,623: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/14/outputs/dataset_a469545a-6e8b-4e1b-b5f2-0773b2802235.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/files/a/4/6/dataset_a469545a-6e8b-4e1b-b5f2-0773b2802235.dat [2026-09-18 18:41:35,624: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'GCA_002759435.2_Cand_auris_B8441_V2_genomic.gtf.gz', 'dbkey': '?', 'ext': 'gtf', 'link_data_only': False, 'sources': [{'source_uri': 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/759/435/GCA_002759435.2_Cand_auris_B8441_V2/GCA_002759435.2_Cand_auris_B8441_V2_genomic.gtf.gz', 'requested_transform': [{'action': 'datatype_groom'}, {'action': 'to_posix_lines'}]}], 'hashes': [], 'info': 'uploaded gtf file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/14/working/data_fetch_upload_9w86fggp', 'object_id': 14}]}]}] uvicorn.access INFO 2026-09-18 18:41:35,842 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58651 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 [2026-09-18 18:41:35,943: INFO/main] Collecting metrics for Job 14 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpiga46cve/job_working_directory/000/14 [2026-09-18 18:41:35,946: DEBUG/main] job_wrapper.finish for job 14 executed (327.311 ms) [2026-09-18 18:41:35,946: INFO/main] Successfully executed Celery task finish_job finish_job (329.931 ms) [2026-09-18 18:41:35,948: INFO/main] Task galaxy.finish_job[7d91bccc-d01a-4b3e-ab00-d0ca1b300e27] succeeded in 0.33206700067967176s: None uvicorn.access INFO 2026-09-18 18:41:36,106 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58653 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,115 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58655 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,122 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58657 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,130 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58659 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,141 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58661 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,148 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58663 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,155 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58665 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,162 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58667 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,169 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58669 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,176 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58671 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,183 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58673 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,190 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58675 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,198 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58677 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,205 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58679 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,212 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58681 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,219 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58683 - "GET /api/jobs/ebe71a73e20b643c?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,233 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58685 - "GET /api/datasets/ebe71a73e20b643c?hda_ldda=hda HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,240 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58687 - "GET /api/jobs/d16afb8e60ade1b4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,247 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58689 - "GET /api/datasets/d16afb8e60ade1b4?hda_ldda=hda HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,254 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58691 - "GET /api/jobs/98132c307fbf1c2f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,262 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58693 - "GET /api/datasets/98132c307fbf1c2f?hda_ldda=hda HTTP/1.1" 200 Failed to execute Galaxy activity, throwing ErrorRunResponse uvicorn.access INFO 2026-09-18 18:41:36,268 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58695 - "GET /api/jobs/d7d72322b2370e36?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,276 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58697 - "GET /api/datasets/d7d72322b2370e36?hda_ldda=hda HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,284 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58699 - "GET /api/jobs/743e042bb792309d?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,292 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58701 - "GET /api/datasets/743e042bb792309d?hda_ldda=hda HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,299 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58703 - "GET /api/jobs/f34ad1a46fc30f17?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,307 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58705 - "GET /api/datasets/f34ad1a46fc30f17?hda_ldda=hda HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,314 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58707 - "GET /api/jobs/720e9da47f83a408?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,322 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58709 - "GET /api/datasets/720e9da47f83a408?hda_ldda=hda HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,329 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58711 - "GET /api/jobs/e0ff396d312edcc6?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,337 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58713 - "GET /api/datasets/e0ff396d312edcc6?hda_ldda=hda HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,344 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58715 - "GET /api/jobs/a086d9e31496090f?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,351 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58717 - "GET /api/datasets/a086d9e31496090f?hda_ldda=hda HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,358 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58719 - "GET /api/jobs/0ef806e6cd7be31e?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,366 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58721 - "GET /api/datasets/0ef806e6cd7be31e?hda_ldda=hda HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,373 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58723 - "GET /api/jobs/19a1c21c98eb6de4?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,380 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58725 - "GET /api/datasets/19a1c21c98eb6de4?hda_ldda=hda HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,387 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58727 - "GET /api/jobs/104993baf792ad06?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,395 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58729 - "GET /api/datasets/104993baf792ad06?hda_ldda=hda HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,402 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58731 - "GET /api/jobs/92a4647b5675fca8?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,414 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58733 - "GET /api/datasets/92a4647b5675fca8?hda_ldda=hda HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,421 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58735 - "GET /api/jobs/2c6217a6349ce645?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,431 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58737 - "GET /api/datasets/2c6217a6349ce645?hda_ldda=hda HTTP/1.1" 200 uvicorn.access INFO 2026-09-18 18:41:36,498 [pN:main.1,p:72534,tN:MainThread] 127.0.0.1:58739 - "POST /api/workflows/ebe71a73e20b643c/invocations HTTP/1.1" 400 There were problems with 1 test(s) - out of 1 test(s) executed. See /Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/interview-driven-workflows/case_studies/auris-scf1-rnaseq/tool_test_output.html for detailed breakdown. Traceback (most recent call last): File "/Users/mvandenb/.local/share/uv/tools/planemo/lib/python3.13/site-packages/planemo/galaxy/activity.py", line 89, in execute return _execute(ctx, config, runnable, job_path, fail_fast=fail_fast, **kwds) File "/Users/mvandenb/.local/share/uv/tools/planemo/lib/python3.13/site-packages/planemo/galaxy/activity.py", line 315, in _execute invocation = user_gi.workflows.invoke_workflow( workflow_id, ...<4 lines>... use_cached_job=kwds.get("use_cache", False), ) File "/Users/mvandenb/.local/share/uv/tools/planemo/lib/python3.13/site-packages/bioblend/galaxy/workflows/__init__.py", line 593, in invoke_workflow return self._post(payload, url=url) ~~~~~~~~~~^^^^^^^^^^^^^^^^^^ File "/Users/mvandenb/.local/share/uv/tools/planemo/lib/python3.13/site-packages/bioblend/galaxy/client.py", line 196, in _post return self.gi.make_post_request(url, payload=payload, files_attached=files_attached) ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/mvandenb/.local/share/uv/tools/planemo/lib/python3.13/site-packages/bioblend/galaxyclient.py", line 206, in make_post_request raise ConnectionError( ...<3 lines>... ) bioblend.ConnectionError: Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (version 5.2+galaxy2), toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param (version 0.1.1), toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value (version 0.2.0), toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc (version 0.74+galaxy1), toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star (version 2.7.11b+galaxy1), toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts (version 2.1.1+galaxy1), toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2 (version 2.11.40.8+galaxy4)","err_code":0} galaxy-workflow.gxwf.yml_1: failed === PLANEMO_EXIT=1 2026-09-18T16:41:41Z ===