/Users/scottcain/.local/share/uv/tools/planemo/lib/python3.13/site-packages/pydantic/_internal/_generate_schema.py:2249: UnsupportedFieldAttributeWarning: The 'default' attribute with value None was provided to the `Field()` function, which has no effect in the context it was used. 'default' is field-specific metadata, and can only be attached to a model field using `Annotated` metadata or by assignment. This may have happened because an `Annotated` type alias using the `type` statement was used, or if the `Field()` function was attached to a single member of a union type. warnings.warn( git --git-dir /Users/scottcain/.planemo/gx_repo config remote.origin.fetch '+refs/*:refs/*' git --git-dir /Users/scottcain/.planemo/gx_repo config remote.origin.mirror true git --git-dir /Users/scottcain/.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 master --depth 1 file:///Users/scottcain/.planemo/gx_repo /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev Cloning into '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev'... if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/Users/scottcain/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /opt/homebrew/Caskroom/miniconda/base/bin/python3 -m venv $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$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 ${COMMON_STARTUP_ARGS} galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input Activated a virtualenv for Galaxy /Users/scottcain/.planemo/gx_venv_3 Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample Activating Conda environment: _galaxy_ Activating virtualenv at /Users/scottcain/.planemo/gx_venv_3 Using Python 3.13.5 environment at: /Users/scottcain/.planemo/gx_venv_3 Audited 313 packages in 2.13s Trying to resolve path for the 'email_ban_file' option but it's empty/None Using Python 3.13.5 environment at: /Users/scottcain/.planemo/gx_venv_3 Using Python 3.13.5 environment at: /Users/scottcain/.planemo/gx_venv_3 Audited 1 package in 28ms The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable. Starting Galaxy with command [cd /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev && if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/Users/scottcain/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /opt/homebrew/Caskroom/miniconda/base/bin/python3 -m venv $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$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/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/run.sh $COMMON_STARTUP_ARGS --server-name main] Activated a virtualenv for Galaxy /Users/scottcain/.planemo/gx_venv_3 Activating Conda environment: _galaxy_ Activating virtualenv at /Users/scottcain/.planemo/gx_venv_3 Using Python 3.13.5 environment at: /Users/scottcain/.planemo/gx_venv_3 Audited 313 packages in 77ms 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 3.13.5 environment at: /Users/scottcain/.planemo/gx_venv_3 Using Python 3.13.5 environment at: /Users/scottcain/.planemo/gx_venv_3 Audited 2 packages in 194ms The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable. Activating Conda environment: _galaxy_ Activating virtualenv at /Users/scottcain/.planemo/gx_venv_3 Executing: galaxy Working directory: /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev Working directory: /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev Executing: PYTHONPATH=lib GALAXY_CONFIG_FILE=/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy.yml celery --app galaxy.celery beat --loglevel DEBUG --schedule /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/gravity/celerybeat-schedule Working directory: /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev Executing: npm_config_yes=true npx @galaxyproject/gx-it-proxy@>=0.0.6 --ip localhost --port 54496 --sessions /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/database/interactivetools_map.sqlite --verbose --proxyPathPrefix /interactivetool/ep Executing: PYTHONPATH=lib GALAXY_CONFIG_FILE=/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy.yml celery --app galaxy.celery worker --concurrency 2 --loglevel DEBUG --pool threads --queues celery,galaxy.internal,galaxy.external Working directory: /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev Executing: PYTHONPATH=lib GALAXY_CONFIG_FILE=/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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:54467 --workers=1 --config python:galaxy.web_stack.gunicorn_config --no-control-socket [2026-09-17 11:45:54 -0500] [86625] [INFO] Starting gunicorn 26.0.0 [2026-09-17 11:45:54 -0500] [86625] [INFO] Listening at: http://127.0.0.1:54467 (86625) [2026-09-17 11:45:54 -0500] [86625] [INFO] Using worker: galaxy.webapps.galaxy.workers.Worker [2026-09-17 11:45:54 -0500] [86630] [INFO] Booting worker with pid: 86630 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 '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 'data_manager_config_file' option but it's empty/None Watching path /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/database/interactivetools_map.sqlite Listening on localhost:54496 [galaxy-wait] Still waiting for Galaxy at http://127.0.0.1:54467 after 34s (30 attempts) 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 [2026-09-17 11:46:11,256: DEBUG/MainProcess] | Worker: Preparing bootsteps. [2026-09-17 11:46:11,261: DEBUG/MainProcess] | Worker: Building graph... [2026-09-17 11:46:11,262: DEBUG/MainProcess] | Worker: New boot order: {StateDB, Beat, Timer, Hub, Pool, Autoscaler, Consumer} [2026-09-17 11:46:11,265: DEBUG/MainProcess] Setting default socket timeout to 30 [2026-09-17 11:46:11,265: INFO/MainProcess] beat: Starting... [2026-09-17 11:46:11,291: DEBUG/MainProcess] Current schedule: [2026-09-17 11:46:11,291: DEBUG/MainProcess] beat: Ticking with max interval->5.00 minutes [2026-09-17 11:46:11,291: DEBUG/MainProcess] beat: Waking up in 5.00 minutes. [2026-09-17 11:46:11,292: DEBUG/MainProcess] | Consumer: Preparing bootsteps. [2026-09-17 11:46:11,296: DEBUG/MainProcess] | Consumer: Building graph... [2026-09-17 11:46:11,319: DEBUG/MainProcess] | Consumer: New boot order: {Connection, Events, Heart, Mingle, Tasks, DelayedDelivery, Agent, Gossip, Control, event loop} -------------- celery@e1-055847.science.psu.edu v5.6.3 (recovery) --- ***** ----- -- ******* ---- macOS-26.6.2-arm64-arm-64bit-Mach-O 2026-09-17 11:46:11 - *** --- * --- - ** ---------- [config] - ** ---------- .> app: galaxy:0x13ae91a90 - ** ---------- .> transport: sqlalchemy+sqlite:////private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/celery_broker.sqlite - ** ---------- .> results: sqlite:////private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 [2026-09-17 11:46:11,351: DEBUG/MainProcess] | Worker: Starting Pool [2026-09-17 11:46:11,351: DEBUG/MainProcess] ^-- substep ok [2026-09-17 11:46:11,351: DEBUG/MainProcess] | Worker: Starting Consumer [2026-09-17 11:46:11,351: DEBUG/MainProcess] | Consumer: Starting Connection [2026-09-17 11:46:11,353: INFO/MainProcess] Connected to sqlalchemy+sqlite:////private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/celery_broker.sqlite [2026-09-17 11:46:11,353: DEBUG/MainProcess] ^-- substep ok [2026-09-17 11:46:11,353: DEBUG/MainProcess] | Consumer: Starting Events [2026-09-17 11:46:11,353: DEBUG/MainProcess] ^-- substep ok [2026-09-17 11:46:11,353: DEBUG/MainProcess] | Consumer: Starting Heart [2026-09-17 11:46:11,353: DEBUG/MainProcess] ^-- substep ok [2026-09-17 11:46:11,354: DEBUG/MainProcess] | Consumer: Starting Tasks [2026-09-17 11:46:11,373: DEBUG/MainProcess] ^-- substep ok [2026-09-17 11:46:11,373: DEBUG/MainProcess] | Consumer: Starting event loop [2026-09-17 11:46:11,373: INFO/MainProcess] celery@e1-055847.science.psu.edu ready. DEBUG:yacman.yacman:Using yacman version 1.0.0 /Users/scottcain/.planemo/gx_venv_3/lib/python3.13/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/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev, /Users/scottcain/.planemo/gx_venv_3/bin, /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/lib, /opt/homebrew/Caskroom/miniconda/base/lib/python313.zip, /opt/homebrew/Caskroom/miniconda/base/lib/python3.13, /opt/homebrew/Caskroom/miniconda/base/lib/python3.13/lib-dynload, /Users/scottcain/.planemo/gx_venv_3/lib/python3.13/site-packages, /Users/scottcain/.planemo/gx_venv_3/lib/python3.13/site-packages/setuptools/_vendor DEBUG:galaxy.config:Configuration directory is /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5 DEBUG:galaxy.config:Data directory is /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/database DEBUG:galaxy.config:Managed config directory is /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5 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/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/version.json INFO:galaxy.model.migrations:Creating database for URI [sqlite:////private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:13,360 [pN:main,p:86630,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 2026-09-17 11:46:13,361 [pN:main,p:86630,tN:MainThread] Job handler assignment methods set to: db-transaction-isolation galaxy.config.url_headers WARNING 2026-09-17 11:46:13,363 [pN:main,p:86630,tN:MainThread] URL headers configuration file not found: /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/url_headers_conf.yml. Using null configuration. galaxy.queue_worker INFO 2026-09-17 11:46:13,366 [pN:main,p:86630,tN:MainThread] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/celery_broker.sqlite galaxy.datatypes.registry ERROR 2026-09-17 11:46:15,630 [pN:main,p:86630,tN:MainThread] Error importing datatype module galaxy.datatypes.html Traceback (most recent call last): File "/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:16,284 [pN:main.1,p:86630,tN:MainThread] Error reading twobit.loc Traceback (most recent call last): File "/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/tool-data/twobit.loc' galaxy.util WARNING 2026-09-17 11:46:16,425 [pN:main.1,p:86630,tN:MainThread] directory not found: /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/config/plugins/activities galaxy.tools WARNING 2026-09-17 11:46:16,425 [pN:main.1,p:86630,tN:MainThread] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:16,425 [pN:main.1,p:86630,tN:MainThread] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/tool_conf.xml galaxy.tools WARNING 2026-09-17 11:46:16,505 [pN:main.1,p:86630,tN:MainThread] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:16,505 [pN:main.1,p:86630,tN:MainThread] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/shed_tools_conf.xml galaxy.tools WARNING 2026-09-17 11:46:16,506 [pN:main.1,p:86630,tN:MainThread] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:16,506 [pN:main.1,p:86630,tN:MainThread] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/empty_tool_conf.xml galaxy.tools.search WARNING 2026-09-17 11:46:18,325 [pN:main.1,p:86630,tN:MainThread] Index at '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/database/tool_search_index/default' uses outdated schema, creating a new index galaxy.tools.search WARNING 2026-09-17 11:46:18,346 [pN:main.1,p:86630,tN:MainThread] Index at '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/database/tool_search_index/my_panel' uses outdated schema, creating a new index galaxy.tools.search WARNING 2026-09-17 11:46:18,351 [pN:main.1,p:86630,tN:MainThread] Index at '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/database/tool_search_index/ontology:edam_operations' uses outdated schema, creating a new index galaxy.tools.search WARNING 2026-09-17 11:46:18,358 [pN:main.1,p:86630,tN:MainThread] Index at '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/database/tool_search_index/ontology:edam_topics' uses outdated schema, creating a new index galaxy.datatypes.display_applications.application ERROR 2026-09-17 11:46:18,390 [pN:main.1,p:86630,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 2026-09-17 11:46:18,398 [pN:main.1,p:86630,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 2026-09-17 11:46:18,425 [pN:main.1,p:86630,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 2026-09-17 11:46:18,432 [pN:main.1,p:86630,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 2026-09-17 11:46:18,446 [pN:main.1,p:86630,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 2026-09-17 11:46:18,470 [pN:main.1,p:86630,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 2026-09-17 11:46:18,478 [pN:main.1,p:86630,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 2026-09-17 11:46:18,480 [pN:main.1,p:86630,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 2026-09-17 11:46:18,496 [pN:main.1,p:86630,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 2026-09-17 11:46:18,503 [pN:main.1,p:86630,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 2026-09-17 11:46:18,509 [pN:main.1,p:86630,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 2026-09-17 11:46:18,517 [pN:main.1,p:86630,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 2026-09-17 11:46:18,521 [pN:main.1,p:86630,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 2026-09-17 11:46:18,525 [pN:main.1,p:86630,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 2026-09-17 11:46:18,527 [pN:main.1,p:86630,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 2026-09-17 11:46:18,528 [pN:main.1,p:86630,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 2026-09-17 11:46:19,219 [pN:main.1,p:86630,tN:MainThread] VisualizationsRegistry, loaded plugin: example galaxy.tours._impl INFO 2026-09-17 11:46:19,231 [pN:main.1,p:86630,tN:MainThread] Loaded tour 'core.galaxy_ui' galaxy.tours._impl INFO 2026-09-17 11:46:19,240 [pN:main.1,p:86630,tN:MainThread] Loaded tour 'core.deferred' galaxy.tours._impl INFO 2026-09-17 11:46:19,250 [pN:main.1,p:86630,tN:MainThread] Loaded tour 'core.windows' galaxy.tours._impl INFO 2026-09-17 11:46:19,256 [pN:main.1,p:86630,tN:MainThread] Loaded tour 'core.visualizations' galaxy.tours._impl INFO 2026-09-17 11:46:19,267 [pN:main.1,p:86630,tN:MainThread] Loaded tour 'core.history' galaxy.workflow.scheduling_manager INFO 2026-09-17 11:46:19,344 [pN:main.1,p:86630,tN:MainThread] No workflow schedulers plugin config file defined, using default scheduler. galaxy.web_stack.handlers INFO 2026-09-17 11:46:19,345 [pN:main.1,p:86630,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 2026-09-17 11:46:19,351 [pN:main.1,p:86630,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 2026-09-17 11:46:19,368 [pN:main.1,p:86630,tN:MainThread] Enabling workflow completion hook: send_notification galaxy.workflow.completion_hooks INFO 2026-09-17 11:46:19,369 [pN:main.1,p:86630,tN:MainThread] Enabling workflow completion hook: export_to_file_source galaxy.workflow.completion_monitor INFO 2026-09-17 11:46:19,369 [pN:main.1,p:86630,tN:MainThread] Starting workflow completion monitor galaxy.jobs INFO 2026-09-17 11:46:19,370 [pN:main.1,p:86630,tN:MainThread] Handler 'main.1' will load all configured runner plugins galaxy.jobs.handler INFO 2026-09-17 11:46:19,409 [pN:main.1,p:86630,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 2026-09-17 11:46:19,410 [pN:main.1,p:86630,tN:MainThread] job handler queue started galaxy.jobs.handler INFO 2026-09-17 11:46:19,411 [pN:main.1,p:86630,tN:MainThread] job handler stop queue started galaxy.queue_worker INFO 2026-09-17 11:46:19,412 [pN:main.1,p:86630,tN:MainThread] Binding and starting galaxy control worker for main.1 galaxy.queue_worker INFO 2026-09-17 11:46:19,414 [pN:main.1,p:86630,tN:MainThread] Queuing async task rebuild_toolbox_search_index for main.1. galaxy.app INFO 2026-09-17 11:46:19,438 [pN:main.1,p:86630,tN:MainThread] Galaxy app startup finished (6986.832 ms) galaxy.queue_worker INFO 2026-09-17 11:46:19,449 [pN:main.1,p:86630,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. galaxy.web_stack INFO 2026-09-17 11:46:23,995 [pN:main.1,p:86630,tN:MainThread] Galaxy server instance 'main.1' is running Serving on http://127.0.0.1:54467 [2026-09-17 11:46:27 -0500] [86630] [INFO] Started server process [86630] [2026-09-17 11:46:27 -0500] [86630] [INFO] Waiting for application startup. [2026-09-17 11:46:27 -0500] [86630] [INFO] Application startup complete. uvicorn.access INFO 2026-09-17 11:46:28,256 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54660 - "GET /api/version HTTP/1.1" 200 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 uvicorn.access INFO 2026-09-17 11:46:28,308 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54662 - "GET /api/tools?in_panel=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:46:28,314 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54664 - "GET /api/tools?in_panel=False HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:46:28,320 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54666 - "GET /api/tool_shed_repositories HTTP/1.1" 200 galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-17 11:46:29,597 [pN:main.1,p:86630,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/nml/collapse_collections' at 7:90981f86000f galaxy.queue_worker INFO 2026-09-17 11:46:31,749 [pN:main.1,p:86630,tN:Thread-5 (check)] Queuing sync task reload_toolbox for main.1. galaxy.queue_worker INFO 2026-09-17 11:46:32,363 [pN:main.1,p:86630,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now. galaxy.util WARNING 2026-09-17 11:46:32,366 [pN:main.1,p:86630,tN:Thread-2] directory not found: /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/config/plugins/activities galaxy.tools WARNING 2026-09-17 11:46:32,384 [pN:main.1,p:86630,tN:Thread-2] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:32,385 [pN:main.1,p:86630,tN:Thread-2] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/tool_conf.xml galaxy.tools WARNING 2026-09-17 11:46:32,391 [pN:main.1,p:86630,tN:Thread-2] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:32,392 [pN:main.1,p:86630,tN:Thread-2] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/shed_tools_conf.xml galaxy.tools WARNING 2026-09-17 11:46:32,393 [pN:main.1,p:86630,tN:Thread-2] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:32,394 [pN:main.1,p:86630,tN:Thread-2] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/empty_tool_conf.xml galaxy.queue_worker INFO 2026-09-17 11:46:32,424 [pN:main.1,p:86630,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. galaxy.queue_worker INFO 2026-09-17 11:46:32,440 [pN:main.1,p:86630,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. uvicorn.access INFO 2026-09-17 11:46:32,516 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54668 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.queue_worker INFO 2026-09-17 11:46:32,784 [pN:main.1,p:86630,tN:Thread-5 (check)] Sending reload_toolbox control task. galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-17 11:46:33,959 [pN:main.1,p:86630,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/kmindex' at 5:b6fa25b6b436 galaxy.queue_worker INFO 2026-09-17 11:46:36,830 [pN:main.1,p:86630,tN:Thread-5 (check)] Queuing sync task reload_toolbox for main.1. galaxy.queue_worker INFO 2026-09-17 11:46:37,696 [pN:main.1,p:86630,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now. galaxy.util WARNING 2026-09-17 11:46:37,699 [pN:main.1,p:86630,tN:Thread-2] directory not found: /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/config/plugins/activities galaxy.tools WARNING 2026-09-17 11:46:37,709 [pN:main.1,p:86630,tN:Thread-2] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:37,710 [pN:main.1,p:86630,tN:Thread-2] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/tool_conf.xml galaxy.tools WARNING 2026-09-17 11:46:37,714 [pN:main.1,p:86630,tN:Thread-2] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:37,715 [pN:main.1,p:86630,tN:Thread-2] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/shed_tools_conf.xml galaxy.tools WARNING 2026-09-17 11:46:37,716 [pN:main.1,p:86630,tN:Thread-2] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:37,717 [pN:main.1,p:86630,tN:Thread-2] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/empty_tool_conf.xml galaxy.queue_worker INFO 2026-09-17 11:46:37,743 [pN:main.1,p:86630,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. galaxy.queue_worker INFO 2026-09-17 11:46:37,758 [pN:main.1,p:86630,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. galaxy.queue_worker INFO 2026-09-17 11:46:37,858 [pN:main.1,p:86630,tN:Thread-5 (check)] Sending reload_toolbox control task. uvicorn.access INFO 2026-09-17 11:46:37,875 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54677 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager INFO 2026-09-17 11:46:38,903 [pN:main.1,p:86630,tN:WSGI_0] Skipping installation of revision 90981f86000f of repository 'collapse_collections' because it was installed with the (possibly updated) revision 90981f86000f and its current installation status is 'Installed'. uvicorn.access INFO 2026-09-17 11:46:38,905 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54688 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-17 11:46:40,133 [pN:main.1,p:86630,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/lexicmap' at 7:bcb6caec41eb galaxy.queue_worker INFO 2026-09-17 11:46:42,914 [pN:main.1,p:86630,tN:Thread-5 (check)] Queuing sync task reload_toolbox for main.1. galaxy.queue_worker INFO 2026-09-17 11:46:43,277 [pN:main.1,p:86630,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now. galaxy.util WARNING 2026-09-17 11:46:43,278 [pN:main.1,p:86630,tN:Thread-2] directory not found: /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/config/plugins/activities galaxy.tools WARNING 2026-09-17 11:46:43,292 [pN:main.1,p:86630,tN:Thread-2] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:43,292 [pN:main.1,p:86630,tN:Thread-2] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/tool_conf.xml galaxy.tools WARNING 2026-09-17 11:46:43,295 [pN:main.1,p:86630,tN:Thread-2] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:43,295 [pN:main.1,p:86630,tN:Thread-2] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/shed_tools_conf.xml galaxy.tools WARNING 2026-09-17 11:46:43,296 [pN:main.1,p:86630,tN:Thread-2] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:43,296 [pN:main.1,p:86630,tN:Thread-2] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/empty_tool_conf.xml galaxy.queue_worker INFO 2026-09-17 11:46:43,314 [pN:main.1,p:86630,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. galaxy.queue_worker INFO 2026-09-17 11:46:43,321 [pN:main.1,p:86630,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. uvicorn.access INFO 2026-09-17 11:46:43,356 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54693 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 galaxy.queue_worker INFO 2026-09-17 11:46:43,945 [pN:main.1,p:86630,tN:Thread-5 (check)] Sending reload_toolbox control task. galaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-17 11:46:44,725 [pN:main.1,p:86630,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join' at 5:3ddd99c7efee galaxy.queue_worker INFO 2026-09-17 11:46:45,982 [pN:main.1,p:86630,tN:Thread-5 (check)] Queuing sync task reload_toolbox for main.1. galaxy.queue_worker INFO 2026-09-17 11:46:46,528 [pN:main.1,p:86630,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now. galaxy.util WARNING 2026-09-17 11:46:46,531 [pN:main.1,p:86630,tN:Thread-2] directory not found: /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/config/plugins/activities galaxy.tools WARNING 2026-09-17 11:46:46,545 [pN:main.1,p:86630,tN:Thread-2] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:46,546 [pN:main.1,p:86630,tN:Thread-2] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/tool_conf.xml galaxy.tools WARNING 2026-09-17 11:46:46,550 [pN:main.1,p:86630,tN:Thread-2] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:46,551 [pN:main.1,p:86630,tN:Thread-2] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/shed_tools_conf.xml galaxy.tools WARNING 2026-09-17 11:46:46,552 [pN:main.1,p:86630,tN:Thread-2] The default shed tool config file (/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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 2026-09-17 11:46:46,552 [pN:main.1,p:86630,tN:Thread-2] Parsing the tool configuration /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/empty_tool_conf.xml galaxy.queue_worker INFO 2026-09-17 11:46:46,578 [pN:main.1,p:86630,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1. galaxy.queue_worker INFO 2026-09-17 11:46:46,595 [pN:main.1,p:86630,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now. galaxy.queue_worker INFO 2026-09-17 11:46:47,002 [pN:main.1,p:86630,tN:Thread-5 (check)] Sending reload_toolbox control task. Retrieving notices: ...working... done Channels: - conda-forge - bioconda Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed PackagesNotFoundError: The following packages are not available from current channels: - coreutils=8.25 Current channels: - https://conda.anaconda.org/conda-forge - https://conda.anaconda.org/bioconda To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. Retrieving notices: ...working... done Channels: - conda-forge - bioconda Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed PackagesNotFoundError: The following packages are not available from current channels: - coreutils=8.25 Current channels: - https://conda.anaconda.org/conda-forge - https://conda.anaconda.org/bioconda To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. Retrieving notices: ...working... done Channels: - conda-forge - bioconda Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed PackagesNotFoundError: The following packages are not available from current channels: - coreutils=8.25 Current channels: - https://conda.anaconda.org/conda-forge - https://conda.anaconda.org/bioconda To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. Retrieving notices: ...working... done Channels: - conda-forge - bioconda Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed PackagesNotFoundError: The following packages are not available from current channels: - coreutils=8.25 Current channels: - https://conda.anaconda.org/conda-forge - https://conda.anaconda.org/bioconda To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. Retrieving notices: ...working... done Channels: - conda-forge - bioconda Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed PackagesNotFoundError: The following packages are not available from current channels: - coreutils=8.25 Current channels: - https://conda.anaconda.org/conda-forge - https://conda.anaconda.org/bioconda To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. Retrieving notices: ...working... done Channels: - conda-forge - bioconda Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed PackagesNotFoundError: The following packages are not available from current channels: - coreutils=8.25 Current channels: - https://conda.anaconda.org/conda-forge - https://conda.anaconda.org/bioconda To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. Retrieving notices: ...working... done Channels: - conda-forge - bioconda Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed PackagesNotFoundError: The following packages are not available from current channels: - coreutils=8.25 Current channels: - https://conda.anaconda.org/conda-forge - https://conda.anaconda.org/bioconda To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. Retrieving notices: ...working... done Channels: - conda-forge - bioconda Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed PackagesNotFoundError: The following packages are not available from current channels: - coreutils=8.25 Current channels: - https://conda.anaconda.org/conda-forge - https://conda.anaconda.org/bioconda To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. uvicorn.access INFO 2026-09-17 11:47:15,480 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54702 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:15,490 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54797 - "GET /api/users HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:15,493 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54799 - "GET /api/configuration HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:15,530 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54801 - "POST /api/users HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:15,538 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54803 - "POST /api/users/c0417687166904cb/api_key HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:15,606 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54805 - "POST /api/workflows/upload HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:15,626 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54807 - "POST /api/histories HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:15,629 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54809 - "GET /api/version HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:15,633 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54811 - "GET /api/configuration HTTP/1.1" 200 galaxy.tools INFO 2026-09-17 11:47:15,647 [pN:main.1,p:86630,tN:AnyIO worker thread] Validated and populated state for tool request (0.051 ms) uvicorn.access INFO 2026-09-17 11:47:15,710 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54813 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:15,728 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54815 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 [2026-09-17 11:47:15,840: INFO/MainProcess] Task galaxy.setup_fetch_data[5ddef49d-d77d-4669-b5de-639f6cc11008] received [2026-09-17 11:47:15,840: DEBUG/MainProcess] TaskPool: Apply (args:('galaxy.setup_fetch_data', '5ddef49d-d77d-4669-b5de-639f6cc11008', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': '5ddef49d-d77d-4669-b5de-639f6cc11008', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '5ddef49d-d77d-4669-b5de-639f6cc11008', '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 2026-09-17 11:47:15,989 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54817 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 [2026-09-17 11:47:16,168: INFO/MainProcess] setup plugin alembic.autogenerate.schemas [2026-09-17 11:47:16,168: INFO/MainProcess] setup plugin alembic.autogenerate.tables [2026-09-17 11:47:16,168: INFO/MainProcess] setup plugin alembic.autogenerate.types [2026-09-17 11:47:16,168: INFO/MainProcess] setup plugin alembic.autogenerate.constraints [2026-09-17 11:47:16,168: INFO/MainProcess] setup plugin alembic.autogenerate.defaults [2026-09-17 11:47:16,168: INFO/MainProcess] setup plugin alembic.autogenerate.comments uvicorn.access INFO 2026-09-17 11:47:16,253 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54819 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 [2026-09-17 11:47:16,497: DEBUG/MainProcess] python path is: /Users/scottcain/.planemo/gx_venv_3/bin, /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/lib, /opt/homebrew/Caskroom/miniconda/base/lib/python313.zip, /opt/homebrew/Caskroom/miniconda/base/lib/python3.13, /opt/homebrew/Caskroom/miniconda/base/lib/python3.13/lib-dynload, /Users/scottcain/.planemo/gx_venv_3/lib/python3.13/site-packages [2026-09-17 11:47:16,498: DEBUG/MainProcess] Configuration directory is /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5 [2026-09-17 11:47:16,498: DEBUG/MainProcess] Data directory is /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/database [2026-09-17 11:47:16,498: DEBUG/MainProcess] Managed config directory is /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5 uvicorn.access INFO 2026-09-17 11:47:16,519 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54821 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 [2026-09-17 11:47:16,678: WARNING/MainProcess] Option master_api_key has been deprecated in favor of bootstrap_admin_api_key [2026-09-17 11:47:16,678: WARNING/MainProcess] Trying to resolve path for the 'email_ban_file' option but it's empty/None [2026-09-17 11:47:16,678: WARNING/MainProcess] Trying to resolve path for the 'data_manager_config_file' option but it's empty/None [2026-09-17 11:47:16,678: DEBUG/MainProcess] No extra version JSON file detected at /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/version.json [2026-09-17 11:47:16,679: INFO/MainProcess] Install database targeting Galaxy's database configuration. [2026-09-17 11:47:16,684: DEBUG/main] WeblessApplicationStack initialized [2026-09-17 11:47:16,734: DEBUG/main] Read job configuration from file: /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_conf.yml [2026-09-17 11:47:16,735: DEBUG/main] Database does not support WITH FOR UPDATE statement, cannot use DB-SKIP-LOCKED handler assignment [2026-09-17 11:47:16,735: 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 [2026-09-17 11:47:16,735: INFO/main] Job handler assignment methods set to: db-transaction-isolation [2026-09-17 11:47:16,735: DEBUG/main] default set to child with id or tag 'local' [2026-09-17 11:47:16,735: DEBUG/main] Done loading job configuration [2026-09-17 11:47:16,736: WARNING/main] URL headers configuration file not found: /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/url_headers_conf.yml. Using null configuration. [2026-09-17 11:47:16,737: INFO/main] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/celery_broker.sqlite uvicorn.access INFO 2026-09-17 11:47:16,785 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54823 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 [2026-09-17 11:47:16,800: WARNING/main] /Users/scottcain/.planemo/gx_venv_3/lib/python3.13/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 2026-09-17 11:47:17,049 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54825 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 [2026-09-17 11:47:17,242: DEBUG/main] Loading datatypes from /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/lib/galaxy/config/sample/datatypes_conf.xml.sample [2026-09-17 11:47:17,242: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.h. [2026-09-17 11:47:17,243: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.c. [2026-09-17 11:47:17,243: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cpp. [2026-09-17 11:47:17,243: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.py. [2026-09-17 11:47:17,243: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.go. [2026-09-17 11:47:17,243: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.rs. [2026-09-17 11:47:17,243: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cs. [2026-09-17 11:47:17,243: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markdown. [2026-09-17 11:47:17,243: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension rmd. [2026-09-17 11:47:17,243: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hep.root. [2026-09-17 11:47:17,243: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:JP2 from the datatype registry for extension jp2. [2026-09-17 11:47:17,243: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry for extension ab1. [2026-09-17 11:47:17,243: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension a2m. [2026-09-17 11:47:17,246: DEBUG/main] Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry for extension afg. [2026-09-17 11:47:17,248: DEBUG/main] Retrieved datatype module galaxy.datatypes.goldenpath:GoldenPath from the datatype registry for extension agp. [2026-09-17 11:47:17,248: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension alto. [2026-09-17 11:47:17,248: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension page.xml. [2026-09-17 11:47:17,248: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension abbyy.xml. [2026-09-17 11:47:17,248: ERROR/main] Error importing datatype module galaxy.datatypes.html Traceback (most recent call last): File "/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/lib/galaxy/datatypes/registry.py", line 235, in load_datatypes module = __import__(datatype_module) ModuleNotFoundError: No module named 'galaxy.datatypes.html' [2026-09-17 11:47:17,251: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_cog_profile. [2026-09-17 11:47:17,251: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_composite. [2026-09-17 11:47:17,251: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension anvio_classifier. [2026-09-17 11:47:17,251: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioContigsDB from the datatype registry for extension anvio_contigs_db. [2026-09-17 11:47:17,251: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioDB from the datatype registry for extension anvio_db. [2026-09-17 11:47:17,251: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioGenomesDB from the datatype registry for extension anvio_genomes_db. [2026-09-17 11:47:17,251: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioPanDB from the datatype registry for extension anvio_pan_db. [2026-09-17 11:47:17,251: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_pfam_profile. [2026-09-17 11:47:17,251: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioProfileDB from the datatype registry for extension anvio_profile_db. [2026-09-17 11:47:17,251: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioSamplesDB from the datatype registry for extension anvio_samples_db. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension anvio_state. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioStructureDB from the datatype registry for extension anvio_structure_db. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension anvio_variability. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry for extension arff. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Paf from the datatype registry for extension paf. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Taf from the datatype registry for extension taf. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Gfa1 from the datatype registry for extension gfa1. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Gfa2 from the datatype registry for extension gfa2. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension asn1. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension asn1-binary. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry for extension axt. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry for extension fli. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry for extension bam. [2026-09-17 11:47:17,252: DEBUG/main] Loaded preferred visualization definition: bam -> igv [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bai. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BamInputSorted from the datatype registry for extension qname_input_sorted.bam. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BamQuerynameSorted from the datatype registry for extension qname_sorted.bam. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BamNative from the datatype registry for extension unsorted.bam. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ProBam from the datatype registry for extension probam. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry for extension cram. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry for extension bed. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry for extension bedgraph. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry for extension bedstrict. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry for extension bed6. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry for extension bed12. [2026-09-17 11:47:17,252: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:ProBed from the datatype registry for extension probed. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry for extension len. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:DAA from the datatype registry for extension daa. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RMA6 from the datatype registry for extension rma6. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:DMND from the datatype registry for extension dmnd. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Parquet from the datatype registry for extension parquet. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension arrow. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Idat from the datatype registry for extension idat. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry for extension bigbed. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry for extension bigwig. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cxb. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry for extension chrint. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension csv. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:GeoCSV from the datatype registry for extension geocsv. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension tsv. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension intermine_tabular. [2026-09-17 11:47:17,254: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry for extension customtrack. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry for extension bowtie_color_index. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry for extension bowtie_base_index. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry for extension csfasta. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension data. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gz. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension binary. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension las. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension laz. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension pnts. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension d3_hierarchy. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:CytoscapeJson from the datatype registry for extension cytoscapejson. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension freq.json. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:ImgtJson from the datatype registry for extension imgt.json. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:GeoJson from the datatype registry for extension geojson. [2026-09-17 11:47:17,257: DEBUG/main] Loaded preferred visualization definition: geojson -> openlayers [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:VitessceJson from the datatype registry for extension vitessce.json. [2026-09-17 11:47:17,257: DEBUG/main] Loaded preferred visualization definition: vitessce.json -> vitessce [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:AuspiceJson from the datatype registry for extension auspice.json. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:DataManagerJson from the datatype registry for extension data_manager_json. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry for extension dbn. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension fai. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension fasta. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fastg from the datatype registry for extension fastg. [2026-09-17 11:47:17,257: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry for extension fastq. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry for extension fastqsanger. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry for extension fastqsolexa. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry for extension fastqcssanger. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry for extension fastqillumina. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry for extension fqtoc. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry for extension eland. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry for extension elandmulti. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry for extension genetrack. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension a3m. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry for extension gff. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry for extension gff3. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry for extension gif. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry for extension gmaj.zip. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension graph_dot. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry for extension gtf. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension toolshed.gz. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hdf4. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension h5. [2026-09-17 11:47:17,258: DEBUG/main] Loaded preferred visualization definition: h5 -> h5web [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension scool. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Grib from the datatype registry for extension grib. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Loom from the datatype registry for extension loom. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Anndata from the datatype registry for extension h5ad. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension h5mu. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Visium from the datatype registry for extension visium.tar.gz. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mz5. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mzmlb. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mbi. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hyphy_results.json. [2026-09-17 11:47:17,258: DEBUG/main] Loaded preferred visualization definition: hyphy_results.json -> hyphyvision [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hivtrace. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Hic from the datatype registry for extension hic. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Cool from the datatype registry for extension cool. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MCool from the datatype registry for extension mcool. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5MLM from the datatype registry for extension h5mlm. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:LudwigModel from the datatype registry for extension ludwig_model. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension html. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension ludwig_report.html. [2026-09-17 11:47:17,258: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry for extension interval. [2026-09-17 11:47:17,259: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension jellyfish. [2026-09-17 11:47:17,259: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_ktab. [2026-09-17 11:47:17,259: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_hist. [2026-09-17 11:47:17,259: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_prof. [2026-09-17 11:47:17,259: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension fastk_ktab_tar. [2026-09-17 11:47:17,259: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Numpy from the datatype registry for extension npy. uvicorn.access INFO 2026-09-17 11:47:17,310 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54827 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 [2026-09-17 11:47:17,394: DEBUG/main] Retrieved datatype module galaxy.datatypes.isa:IsaTab from the datatype registry for extension isa-tab. [2026-09-17 11:47:17,394: DEBUG/main] Retrieved datatype module galaxy.datatypes.isa:IsaJson from the datatype registry for extension isa-json. [2026-09-17 11:47:17,394: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension picard_interval_list. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_interval. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_report. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_dbsnp. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_tranche. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_recal. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cnn. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cns. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cnr. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hhr. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry for extension jpg. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tiff. [2026-09-17 11:47:17,395: DEBUG/main] Loaded preferred visualization definition: tiff -> tiffviewer [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf2. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf8. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension btf. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tif. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension svs. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension scn. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension bif. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:OMETiff from the datatype registry for extension ome.tiff. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Dicom from the datatype registry for extension dcm. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vms. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vmu. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension ndpi. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry for extension mrxs. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry for extension svslide. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry for extension bmp. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry for extension im. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry for extension pcd. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry for extension pcx. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry for extension ppm. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry for extension psd. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry for extension xbm. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry for extension xpm. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry for extension rgb. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry for extension pbm. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry for extension pgm. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nrrd. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nhdr. [2026-09-17 11:47:17,395: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry for extension rna_eps. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Artifact from the datatype registry for extension qza. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Visualization from the datatype registry for extension qzv. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Metadata from the datatype registry for extension qiime2.tabular. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension zip. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension ncbi_genome_dataset.zip. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedZarrZipArchive from the datatype registry for extension zarr.zip. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedOMEZarrZipArchive from the datatype registry for extension ome_zarr.zip. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:SpatialData from the datatype registry for extension spatialdata.zip. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension tar. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension directory. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension bwa_index. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension bwa_mem2_index. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension egapx_local_cache. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension lexicmap_index. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension kmindex. [2026-09-17 11:47:17,402: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:ZarrDirectory from the datatype registry for extension zarr. [2026-09-17 11:47:17,403: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:OMEZarr from the datatype registry for extension ome_zarr. [2026-09-17 11:47:17,403: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension yaml. [2026-09-17 11:47:17,403: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mrm. [2026-09-17 11:47:17,407: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Dta from the datatype registry for extension dta. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Dta2d from the datatype registry for extension dta2d. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Edta from the datatype registry for extension edta. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension pepxml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension raw_pepxml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension peptideprophet_pepxml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension interprophet_pepxml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry for extension protxml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ParamXml from the datatype registry for extension paramxml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Kroenik from the datatype registry for extension kroenik. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepList from the datatype registry for extension peplist. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PSMS from the datatype registry for extension psms. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry for extension pepxml.tsv. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry for extension protxml.tsv. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry for extension mascotdat. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry for extension mzid. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry for extension idxml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry for extension tandem. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sirius.ms. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry for extension thermo.raw. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BafTar from the datatype registry for extension brukerbaf.d.tar. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:YepTar from the datatype registry for extension agilentbrukeryep.d.tar. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:TdfTar from the datatype registry for extension brukertdf.d.tar. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MassHunterTar from the datatype registry for extension agilentmasshunter.d.tar. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MassLynxTar from the datatype registry for extension watersmasslynx.raw.tar. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:WiffTar from the datatype registry for extension wiff.tar. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Wiff2Tar from the datatype registry for extension wiff2.tar. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MascotXML from the datatype registry for extension mascotxml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzTab from the datatype registry for extension mztab. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzTab2 from the datatype registry for extension mztab2. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry for extension mzml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:NmrML from the datatype registry for extension nmrml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Meryldb from the datatype registry for extension meryldb. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Bref3 from the datatype registry for extension bref3. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry for extension mgf. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry for extension wiff. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Wiff2 from the datatype registry for extension wiff2. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry for extension mzxml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry for extension mzdata. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry for extension ms2. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry for extension mzq. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry for extension sqlite. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry for extension mz.sqlite. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OSW from the datatype registry for extension osw. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:PQP from the datatype registry for extension pqp. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry for extension traml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:TrafoXML from the datatype registry for extension trafoxml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry for extension featurexml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry for extension consensusxml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry for extension uniprotxml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:XquestXML from the datatype registry for extension xquest.xml. [2026-09-17 11:47:17,408: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:XquestSpecXML from the datatype registry for extension spec.xml. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:QCML from the datatype registry for extension qcml. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension mzqc. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry for extension msp. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry for extension splib_noindex. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry for extension splib. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BlibSQlite from the datatype registry for extension blib. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:DlibSQlite from the datatype registry for extension dlib. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ElibSQlite from the datatype registry for extension elib. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry for extension hlf. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry for extension idpdb. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry for extension sf3. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cps. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry for extension ct. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:PostgresqlArchive from the datatype registry for extension postgresql. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MongoDBArchive from the datatype registry for extension mongodb. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GeneNoteBook from the datatype registry for extension genenotebook. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry for extension searchgui_archive. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry for extension fast5.tar. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry for extension fast5.tar.gz. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry for extension fast5.tar.bz2. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveXz from the datatype registry for extension fast5.tar.xz. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Pod5 from the datatype registry for extension pod5. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension peptideshaker_archive. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension percin. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension percout. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hardklor. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension kronik. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry for extension imzml. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Analyze75 from the datatype registry for extension analyze75. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Nifti1 from the datatype registry for extension nii1. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Nifti2 from the datatype registry for extension nii2. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Gifti from the datatype registry for extension gii. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tck from the datatype registry for extension tck. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Trk from the datatype registry for extension trk. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Mrc2014 from the datatype registry for extension mrc. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Star from the datatype registry for extension star. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PEFF from the datatype registry for extension peff. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension toml. [2026-09-17 11:47:17,409: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension colab.tar. [2026-09-17 11:47:17,414: DEBUG/main] Retrieved datatype module galaxy.datatypes.flow:FCS from the datatype registry for extension fcs. [2026-09-17 11:47:17,414: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowtext. [2026-09-17 11:47:17,414: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowclr. [2026-09-17 11:47:17,414: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowmfi. [2026-09-17 11:47:17,414: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat1. [2026-09-17 11:47:17,414: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat2. [2026-09-17 11:47:17,414: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat3. [2026-09-17 11:47:17,414: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowscore. [2026-09-17 11:47:17,414: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowframe. [2026-09-17 11:47:17,414: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension fsom. [2026-09-17 11:47:17,414: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowset. [2026-09-17 11:47:17,414: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension amnisflow.cif. [2026-09-17 11:47:17,414: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension metacyto_clr.txt. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.metacyto:mSummary from the datatype registry for extension metacyto_summary.txt. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.metacyto:mStats from the datatype registry for extension metacyto_stats.txt. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_compute_matrix_archive. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_coverage_matrix. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry for extension netcdf. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry for extension eps. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry for extension rast. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry for extension laj. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry for extension lav. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry for extension maf. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry for extension mafcustomtrack. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:MatrixMarket from the datatype registry for extension mtx. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CMAP from the datatype registry for extension cmap. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry for extension encodepeak. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:FourDNPairs from the datatype registry for extension 4dn_pairs. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:FourDNPairsam from the datatype registry for extension 4dn_pairsam. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry for extension pdf. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry for extension pileup. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Psl from the datatype registry for extension psl. [2026-09-17 11:47:17,418: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry for extension obo. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry for extension owl. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry for extension png. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry for extension qual. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry for extension qualsolexa. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry for extension qualillumina. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry for extension qualsolid. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry for extension qual454. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry for extension roadmaps. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry for extension sam. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry for extension scf. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry for extension sequences. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry for extension snpeffdb. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry for extension snpsiftdbnsfp. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dbnsfp.tabular. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry for extension sff. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry for extension sra. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:SraManifest from the datatype registry for extension sra_manifest.tabular. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension svg. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry for extension taxonomy. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension tabular. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry for extension twobit. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:SQmass from the datatype registry for extension sqmass. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry for extension gemini.sqlite. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ChiraSQLite from the datatype registry for extension chira.sqlite. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CuffDiffSQlite from the datatype registry for extension cuffdiff.sqlite. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GAFASQLite from the datatype registry for extension gafa.sqlite. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:NcbiTaxonomySQlite from the datatype registry for extension ncbitaxonomy.sqlite. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension txt. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry for extension linecount. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry for extension memepsp. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry for extension memexml. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry for extension cisml. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Tei from the datatype registry for extension tei. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xml. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xsd. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Dzi from the datatype registry for extension dzi. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry for extension vcf. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf_bgzip. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry for extension bcf_uncompressed. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry for extension velvet. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry for extension wig. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension interval_index. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension odgi. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension vg. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.loci. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.dist. [2026-09-17 11:47:17,419: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.snarls. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.gamp. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.min. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.zipcodes. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.gg. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gbz. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gbwt. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hal. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hal.pg. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hal.hg. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension xg. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gam. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf2. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf3. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension onnx. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tabix. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:IntervalTabix from the datatype registry for extension interval_tabix.gz. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:JuicerMediumTabix from the datatype registry for extension juicer_medium_tabix.gz. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:BedTabix from the datatype registry for extension bed_tabix.gz. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:GffTabix from the datatype registry for extension gff_tabix.gz. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension bgzip. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension gwas_bgzip. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension gwas_tabix.gz. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry for extension vcf_bgzip. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bus. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension kallisto.idx. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry for extension phyloxml. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension newick. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension nhx. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry for extension nex. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:IQTree from the datatype registry for extension iqtree. [2026-09-17 11:47:17,420: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension beast.trees. [2026-09-17 11:47:17,425: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mldist. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry for extension affybatch. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry for extension eigenstratgeno. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry for extension eigenstratpca. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry for extension eset. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry for extension fped. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry for extension fphe. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry for extension gg. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry for extension ldindep. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry for extension malist. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry for extension lped. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry for extension pbed. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry for extension pheno. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry for extension pphe. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry for extension rexpbase. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry for extension rgenetics. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry for extension snptest. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry for extension snpmatrix. [2026-09-17 11:47:17,429: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension xls. [2026-09-17 11:47:17,430: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry for extension ipynb. [2026-09-17 11:47:17,430: DEBUG/main] Loaded preferred visualization definition: ipynb -> jupyterlite [2026-09-17 11:47:17,430: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension json. [2026-09-17 11:47:17,430: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Text from the datatype registry for extension tool_markdown. [2026-09-17 11:47:17,430: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:ExpressionJson from the datatype registry for extension expression.json. [2026-09-17 11:47:17,438: DEBUG/main] Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry for extension xgmml. [2026-09-17 11:47:17,438: DEBUG/main] Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry for extension sif. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry for extension triples. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry for extension hdt. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry for extension nt. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry for extension n3. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry for extension ttl. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry for extension rdf. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry for extension jsonld. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Sbol from the datatype registry for extension sbol. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension excel.xls. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry for extension xlsx. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Docx from the datatype registry for extension docx. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Pptx from the datatype registry for extension pptx. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension btwisted. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cai. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cat_db. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension charge. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension checktrans. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension chips. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codcmp. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension coderet. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension compseq. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgplot. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgreport. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cusp. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cut. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dan. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension digest. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dreg. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension einverted. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension epestfind. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension equicktandem. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension est2genome. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension etandem. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension freak. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzznuc. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzzpro. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzztran. [2026-09-17 11:47:17,443: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gaf. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension garnier. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension geecee. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension helixturnhelix. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hmoment. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension isochore. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension match. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nametable. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension needle. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgreport. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgseek. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension noreturn. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension palindrome. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepcoil. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepinfo. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepstats. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension polydot. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension preg. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prettyseq. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension primersearch. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showfeat. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showorf. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sixpack. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension strider. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension supermatcher. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension syco. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension textsearch. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension vectorstrip. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wobble. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wordcount. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dbmotif. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension diffseq. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension excel. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feattable. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension motif. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension regions. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension seqtable. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension simple. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension table. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension tagseq. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension acedb. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension clustal. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codata. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension embl. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fitch. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gcg. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry for extension genbank. [2026-09-17 11:47:17,444: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hennig86. [2026-09-17 11:47:17,445: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ig. [2026-09-17 11:47:17,445: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifer. [2026-09-17 11:47:17,445: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifernon. [2026-09-17 11:47:17,445: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mega. [2026-09-17 11:47:17,445: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension meganon. [2026-09-17 11:47:17,445: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ncbi. [2026-09-17 11:47:17,445: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexus. [2026-09-17 11:47:17,445: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexusnon. [2026-09-17 11:47:17,449: DEBUG/main] Retrieved datatype module galaxy.datatypes.phylip:Phylip from the datatype registry for extension phylip. [2026-09-17 11:47:17,449: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension phylipnon. [2026-09-17 11:47:17,449: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pir. [2026-09-17 11:47:17,449: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension staden. [2026-09-17 11:47:17,449: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension swiss. [2026-09-17 11:47:17,454: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:Msf from the datatype registry for extension msf. [2026-09-17 11:47:17,454: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx0. [2026-09-17 11:47:17,454: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx1. [2026-09-17 11:47:17,454: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx10. [2026-09-17 11:47:17,454: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx2. [2026-09-17 11:47:17,454: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx3. [2026-09-17 11:47:17,454: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pair. [2026-09-17 11:47:17,454: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension score. [2026-09-17 11:47:17,454: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srs. [2026-09-17 11:47:17,454: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srspair. [2026-09-17 11:47:17,459: DEBUG/main] Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry for extension snaphmm. [2026-09-17 11:47:17,459: DEBUG/main] Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry for extension augustus. [2026-09-17 11:47:17,459: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ICM from the datatype registry for extension icm. [2026-09-17 11:47:17,459: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:InfernalCM from the datatype registry for extension cm. [2026-09-17 11:47:17,459: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry for extension hmm2. [2026-09-17 11:47:17,459: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry for extension hmm3. [2026-09-17 11:47:17,459: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry for extension stockholm. [2026-09-17 11:47:17,459: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry for extension xmfa. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.microarrays:Cel from the datatype registry for extension cel. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.microarrays:Gpr from the datatype registry for extension gpr. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.microarrays:Gal from the datatype registry for extension gal. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension rds. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension phyloseq. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.sce. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.raw. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.msnbase.raw. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.findchrompeaks. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.group. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.retcor. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.fillpeaks. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.positive. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.negative. [2026-09-17 11:47:17,463: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.quick. [2026-09-17 11:47:17,471: DEBUG/main] Retrieved datatype module galaxy.datatypes.hdf5:HDF5SummarizedExperiment from the datatype registry for extension rdata.se. [2026-09-17 11:47:17,471: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rdock_as. [2026-09-17 11:47:17,471: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rrd. [2026-09-17 11:47:17,471: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Prm from the datatype registry for extension prm. [2026-09-17 11:47:17,471: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry for extension oxlicg. [2026-09-17 11:47:17,471: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry for extension oxling. [2026-09-17 11:47:17,471: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry for extension oxlits. [2026-09-17 11:47:17,471: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry for extension oxlist. [2026-09-17 11:47:17,471: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry for extension oxliss. [2026-09-17 11:47:17,471: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry for extension oxligl. [2026-09-17 11:47:17,475: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry for extension stl. [2026-09-17 11:47:17,476: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry for extension plyascii. [2026-09-17 11:47:17,476: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry for extension plybinary. [2026-09-17 11:47:17,476: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry for extension vtkascii. [2026-09-17 11:47:17,476: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry for extension vtkbinary. [2026-09-17 11:47:17,476: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtpAscii from the datatype registry for extension vtpascii. [2026-09-17 11:47:17,476: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtpBinary from the datatype registry for extension vtpbinary. [2026-09-17 11:47:17,476: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry for extension biom1. [2026-09-17 11:47:17,476: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry for extension biom2. [2026-09-17 11:47:17,476: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MashSketch from the datatype registry for extension msh. [2026-09-17 11:47:17,476: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:SourmashSignature from the datatype registry for extension sourmash.sig. [2026-09-17 11:47:17,476: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry for extension scidx. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry for extension smi. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry for extension sdf. [2026-09-17 11:47:17,480: DEBUG/main] Loaded preferred visualization definition: sdf -> molstar [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry for extension inchi. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry for extension mol. [2026-09-17 11:47:17,480: DEBUG/main] Loaded preferred visualization definition: mol -> molstar [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry for extension mol2. [2026-09-17 11:47:17,480: DEBUG/main] Loaded preferred visualization definition: mol2 -> molstar [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry for extension cml. [2026-09-17 11:47:17,480: DEBUG/main] Loaded preferred visualization definition: cml -> molstar [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry for extension fps. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry for extension obfs. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry for extension drf. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry for extension phar. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry for extension pdb. [2026-09-17 11:47:17,480: DEBUG/main] Loaded preferred visualization definition: pdb -> molstar [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry for extension pdbqt. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:PQR from the datatype registry for extension pqr. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:Cell from the datatype registry for extension cell. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:CIF from the datatype registry for extension cif. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:XYZ from the datatype registry for extension xyz. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:ExtendedXYZ from the datatype registry for extension extxyz. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:Magres from the datatype registry for extension magres. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Trr from the datatype registry for extension trr. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Dcd from the datatype registry for extension dcd. [2026-09-17 11:47:17,480: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension top. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prmtop. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension itp. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mdp. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ndx. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension xvg. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Xtc from the datatype registry for extension xtc. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Cpt from the datatype registry for extension cpt. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Edr from the datatype registry for extension edr. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tpr. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:GRO from the datatype registry for extension gro. [2026-09-17 11:47:17,481: DEBUG/main] Loaded preferred visualization definition: gro -> molstar [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension inpcrd. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Vel from the datatype registry for extension vel. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry for extension grd. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry for extension grd.tgz. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.otu. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.list. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.sabund. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.rabund. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.shared. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.relabund. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry for extension mothur.names. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.design. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry for extension mothur.summary. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.groups. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry for extension mothur.oligos. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension mothur.align. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.accnos. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.otulabels. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mothur.otu.corr. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry for extension mothur.map. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry for extension mothur.align.check. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry for extension mothur.align.report. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry for extension mothur.filter. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry for extension mothur.dist. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mothur.tre. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry for extension mothur.pair.dist. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mothur.square.dist. [2026-09-17 11:47:17,481: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry for extension mothur.lower.dist. [2026-09-17 11:47:17,482: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.ref.taxonomy. [2026-09-17 11:47:17,482: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.seq.taxonomy. [2026-09-17 11:47:17,482: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.rdp.taxonomy. [2026-09-17 11:47:17,482: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry for extension mothur.cons.taxonomy. [2026-09-17 11:47:17,482: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry for extension mothur.tax.summary. [2026-09-17 11:47:17,482: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry for extension mothur.freq. [2026-09-17 11:47:17,482: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.quan. [2026-09-17 11:47:17,482: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.quan. [2026-09-17 11:47:17,482: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.masked.quan. [2026-09-17 11:47:17,482: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.masked.quan. [2026-09-17 11:47:17,482: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry for extension mothur.axes. [2026-09-17 11:47:17,482: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry for extension mothur.sff.flow. [2026-09-17 11:47:17,482: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry for extension mothur.count_table. [2026-09-17 11:47:17,486: DEBUG/main] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry for extension neostore. [2026-09-17 11:47:17,486: DEBUG/main] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDBzip from the datatype registry for extension neostore.zip. [2026-09-17 11:47:17,486: DEBUG/main] Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry for extension trackhub. [2026-09-17 11:47:17,490: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry for extension blastxml. [2026-09-17 11:47:17,490: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry for extension blastdbn. [2026-09-17 11:47:17,490: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry for extension blastdbp. [2026-09-17 11:47:17,490: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry for extension blastdbd. [2026-09-17 11:47:17,490: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:LastDb from the datatype registry for extension lastdb. [2026-09-17 11:47:17,490: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb5 from the datatype registry for extension blastdbn5. [2026-09-17 11:47:17,490: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb5 from the datatype registry for extension blastdbp5. [2026-09-17 11:47:17,490: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb5 from the datatype registry for extension blastdbd5. [2026-09-17 11:47:17,490: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension maskinfo-asn1. [2026-09-17 11:47:17,490: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension maskinfo-asn1-binary. [2026-09-17 11:47:17,490: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension pssm-asn1. [2026-09-17 11:47:17,495: DEBUG/main] Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry for extension ptkscmp. [2026-09-17 11:47:17,495: DEBUG/main] Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry for extension smat. [2026-09-17 11:47:17,495: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:GenotypeMatrix from the datatype registry for extension alohomora_gts. [2026-09-17 11:47:17,495: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_map. [2026-09-17 11:47:17,495: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_maf. [2026-09-17 11:47:17,495: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_ped. [2026-09-17 11:47:17,495: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension linkage_pedin. [2026-09-17 11:47:17,495: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:DataIn from the datatype registry for extension linkage_datain. [2026-09-17 11:47:17,495: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:MarkerMap from the datatype registry for extension linkage_map. [2026-09-17 11:47:17,495: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_ihaplo. [2026-09-17 11:47:17,495: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_descent. [2026-09-17 11:47:17,495: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:AllegroLOD from the datatype registry for extension allegro_fparam. [2026-09-17 11:47:17,495: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:IdeasPre from the datatype registry for extension ideaspre. [2026-09-17 11:47:17,495: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Sbml from the datatype registry for extension sbml. [2026-09-17 11:47:17,499: DEBUG/main] Retrieved datatype module galaxy.datatypes.spaln:SpalnNuclDb from the datatype registry for extension spalndbnp. [2026-09-17 11:47:17,499: DEBUG/main] Retrieved datatype module galaxy.datatypes.spaln:SpalnProtDb from the datatype registry for extension spalndba. [2026-09-17 11:47:17,499: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_dada. [2026-09-17 11:47:17,499: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_errorrates. [2026-09-17 11:47:17,499: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_mergepairs. [2026-09-17 11:47:17,499: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_sequencetable. [2026-09-17 11:47:17,499: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_uniques. [2026-09-17 11:47:17,499: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension ampvis2. [2026-09-17 11:47:17,499: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension ckpt. [2026-09-17 11:47:17,499: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tgz. [2026-09-17 11:47:17,504: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Wav from the datatype registry for extension wav. [2026-09-17 11:47:17,504: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mp3 from the datatype registry for extension mp3. [2026-09-17 11:47:17,504: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Ogg from the datatype registry for extension ogg. [2026-09-17 11:47:17,504: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Wma from the datatype registry for extension wma. [2026-09-17 11:47:17,504: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mkv from the datatype registry for extension mkv. [2026-09-17 11:47:17,504: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mp4 from the datatype registry for extension mp4. [2026-09-17 11:47:17,504: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:M4a from the datatype registry for extension m4a. [2026-09-17 11:47:17,504: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Flv from the datatype registry for extension flv. [2026-09-17 11:47:17,504: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Flac from the datatype registry for extension flac. [2026-09-17 11:47:17,504: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Webm from the datatype registry for extension webm. [2026-09-17 11:47:17,504: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mpg from the datatype registry for extension mpg. [2026-09-17 11:47:17,504: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mov from the datatype registry for extension mov. [2026-09-17 11:47:17,504: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Avi from the datatype registry for extension avi. [2026-09-17 11:47:17,504: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Wmv from the datatype registry for extension wmv. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.speech:TextGrid from the datatype registry for extension textgrid. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.speech:BPF from the datatype registry for extension par. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension ffindex. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension ffdata. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Pretext from the datatype registry for extension pretext. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension immuneml_receptors.html. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:HexrdMaterials from the datatype registry for extension hexrd.materials.h5. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension npz. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:HexrdImagesNpz from the datatype registry for extension hexrd.images.npz. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:HexrdEtaOmeNpz from the datatype registry for extension hexrd.eta_ome.npz. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension hexrd.scored_orientations.npz. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hexrd.accepted_orientations. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension hexrd.yml. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTess from the datatype registry for extension neper.tess. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTesr from the datatype registry for extension neper.tesr. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPoints from the datatype registry for extension neper.points. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPointsTabular from the datatype registry for extension neper.points.tsv. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperMultiScaleCell from the datatype registry for extension neper.mscell. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshMsh from the datatype registry for extension gmsh.msh. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshGeo from the datatype registry for extension gmsh.geo. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:ZsetGeof from the datatype registry for extension zset.geof. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkXml from the datatype registry for extension vtkxml. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GocadSGrid from the datatype registry for extension gocad.sg. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:FeflowFem from the datatype registry for extension feflow.fem. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:AsciiRaster from the datatype registry for extension raster.asc. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension stl. [2026-09-17 11:47:17,509: DEBUG/main] Overriding conflicting datatype with extension 'stl', using datatype from /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/lib/galaxy/config/sample/datatypes_conf.xml.sample. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Text from the datatype registry for extension pov. [2026-09-17 11:47:17,509: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:PithyaResult from the datatype registry for extension pithya.result. [2026-09-17 11:47:17,510: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:PithyaProperty from the datatype registry for extension pithya.property. [2026-09-17 11:47:17,510: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:PithyaModel from the datatype registry for extension pithya.model. [2026-09-17 11:47:17,510: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:BCSLts from the datatype registry for extension bcsl.ts. [2026-09-17 11:47:17,510: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:BCSLmodel from the datatype registry for extension bcsl.model. [2026-09-17 11:47:17,510: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:StormSample from the datatype registry for extension storm.sample. [2026-09-17 11:47:17,510: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:StormCheck from the datatype registry for extension storm.check. [2026-09-17 11:47:17,510: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:CTLresult from the datatype registry for extension ctl.result. [2026-09-17 11:47:17,510: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Castep from the datatype registry for extension castep. [2026-09-17 11:47:17,510: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Param from the datatype registry for extension param. [2026-09-17 11:47:17,510: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:FormattedDensity from the datatype registry for extension den_fmt. [2026-09-17 11:47:17,513: DEBUG/main] Retrieved datatype module galaxy.datatypes.larch:AthenaProject from the datatype registry for extension prj. [2026-09-17 11:47:17,513: DEBUG/main] Retrieved datatype module galaxy.datatypes.larch:FEFFInput from the datatype registry for extension inp. [2026-09-17 11:47:17,513: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension sp. [2026-09-17 11:47:17,513: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension gds. [2026-09-17 11:47:17,513: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension feff. [2026-09-17 11:47:17,513: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feffit. [2026-09-17 11:47:17,513: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bil. [2026-09-17 11:47:17,513: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hdr. [2026-09-17 11:47:17,518: DEBUG/main] Retrieved datatype module galaxy.datatypes.gis:Shapefile from the datatype registry for extension shp. [2026-09-17 11:47:17,518: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:FITS from the datatype registry for extension fits. [2026-09-17 11:47:17,518: DEBUG/main] Loaded preferred visualization definition: fits -> aladin [2026-09-17 11:47:17,522: DEBUG/main] Retrieved datatype module galaxy.datatypes.chain:Chain from the datatype registry for extension chain. [2026-09-17 11:47:17,522: DEBUG/main] Retrieved datatype module galaxy.datatypes.chain:Net from the datatype registry for extension ucsc.net. [2026-09-17 11:47:17,522: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bcsp. [2026-09-17 11:47:17,522: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rd. [2026-09-17 11:47:17,522: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Safetensors from the datatype registry for extension safetensors. [2026-09-17 11:47:17,522: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension mlmodel. [2026-09-17 11:47:17,522: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension deacon.idx. [2026-09-17 11:47:17,523: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension rmsx.json. [2026-09-17 11:47:17,523: DEBUG/main] Loaded preferred visualization definition: rmsx.json -> rmsxflipbook [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtpAscii' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtpBinary' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkXml' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTess' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTesr' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:GmshMsh' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:GocadSGrid' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:FeflowFem' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:AsciiRaster' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.goldenpath:GoldenPath' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:JP2' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQmass' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OSW' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:PQP' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:ElibSQlite' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:DlibSQlite' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:BlibSQlite' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:ChiraSQLite' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CuffDiffSQlite' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:GAFASQLite' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:NcbiTaxonomySQlite' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5MLM' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Hic' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cool' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:MCool' [2026-09-17 11:47:17,523: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Loom' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Anndata' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdMaterials' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Grib' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdImagesNpz' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdEtaOmeNpz' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Npz' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamQuerynameSorted' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamNative' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:DAA' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:RMA6' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Parquet' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:BafTar' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:TdfTar' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassHunterTar' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassLynxTar' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:YepTar' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:WiffTar' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveXz' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pod5' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Meryldb' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bref3' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:PostgresqlArchive' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:ICM' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Idat' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Trr' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Dcd' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xtc' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cpt' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Edr' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Vel' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xlsx' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Docx' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pptx' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Numpy' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Metadata' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Artifact' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Visualization' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:SpatialData' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedOMEZarrZipArchive' [2026-09-17 11:47:17,524: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedZarrZipArchive' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedZipArchive' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pretext' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.chain:Chain' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.chain:Net' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Gifti' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:Dzi' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:Sbml' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Dta2d' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Edta' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ConsensusXML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:IdXML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:FeatureXML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MascotXML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Ms2' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab2' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ParamXml' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:NmrML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Kroenik' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepList' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PSMS' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TrafoXML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestXML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestSpecXML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:QCML' [2026-09-17 11:47:17,525: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Wiff' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PEFF' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:Sbol' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastg' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Cell' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CIF' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:ExtendedXYZ' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:XYZ' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Magres' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PQR' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:GRO' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.phylip:Phylip' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqCSSanger' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Html' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' [2026-09-17 11:47:17,526: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Psl' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Paf' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Taf' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:FourDNPairs' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:FourDNPairsam' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:IQTree' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:ImgtJson' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:CytoscapeJson' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:GeoJson' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:VitessceJson' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaResult' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLts' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Json' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.genetics:GenotypeMatrix' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.genetics:DataIn' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.genetics:MarkerMap' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.genetics:AllegroLOD' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CMAP' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:GeoCSV' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' [2026-09-17 11:47:17,527: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mSummary' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mStats' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:MatrixMarket' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:InfernalCM' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Cel' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gpr' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gal' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:RDS' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Mrc2014' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Png' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:OMETiff' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Dicom' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Im' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' [2026-09-17 11:47:17,528: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Tck' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Trk' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti1' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti2' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Star' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Wav' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp3' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp4' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:M4a' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Flv' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Ogg' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mpg' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mov' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Avi' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Wmv' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Wma' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Webm' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mkv' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.speech:TextGrid' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.speech:BPF' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.larch:FEFFInput' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.larch:AthenaProject' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Castep' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:CTLresult' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:FormattedDensity' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Param' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Yaml' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:FITS' [2026-09-17 11:47:17,529: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.neo4j:Neo4jDBzip' [2026-09-17 11:47:17,530: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaProperty' [2026-09-17 11:47:17,530: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaModel' [2026-09-17 11:47:17,530: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLmodel' [2026-09-17 11:47:17,530: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:StormSample' [2026-09-17 11:47:17,530: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:StormCheck' [2026-09-17 11:47:17,530: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:SourmashSignature' [2026-09-17 11:47:17,531: 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]. [2026-09-17 11:47:17,532: DEBUG/main] Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] [2026-09-17 11:47:17,532: 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'] [2026-09-17 11:47:17,532: DEBUG/main] Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt [2026-09-17 11:47:17,532: DEBUG/main] Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt [2026-09-17 11:47:17,532: 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]. [2026-09-17 11:47:17,532: DEBUG/main] Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample [2026-09-17 11:47:17,532: 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]. [2026-09-17 11:47:17,532: DEBUG/main] Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample [2026-09-17 11:47:17,543: DEBUG/main] Loaded 0 lines from '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/tool-data/shed/kmindex.loc' for 'kmindex' [2026-09-17 11:47:17,543: DEBUG/main] Loaded tool data table 'kmindex' from file '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/shed_tool_data_table_conf.xml' [2026-09-17 11:47:17,544: DEBUG/main] Loaded 0 lines from '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/tool-data/shed/lexicmap_index.loc' for 'lexicmap_index' [2026-09-17 11:47:17,544: DEBUG/main] Loaded tool data table 'lexicmap_index' from file '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/shed_tool_data_table_conf.xml' [2026-09-17 11:47:17,544: DEBUG/main] Loading references to tool sheds from /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/tool_sheds_conf.xml [2026-09-17 11:47:17,544: DEBUG/main] Loaded reference to tool shed: toolshed.g2.bx.psu.edu uvicorn.access INFO 2026-09-17 11:47:17,577 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54830 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 [2026-09-17 11:47:17,675: DEBUG/main] No parameter model for tool '__DATA_FETCH__': Cannot generate a tool parameter model for upload_dataset inputs [2026-09-17 11:47:17,707: DEBUG/main] (1) Working directory for job is: /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/1 [2026-09-17 11:47:17,778: DEBUG/main] Job wrapper for Job [1] prepared (15.993 ms) [2026-09-17 11:47:17,778: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (103.281 ms) [2026-09-17 11:47:17,805: INFO/main] Task galaxy.setup_fetch_data[5ddef49d-d77d-4669-b5de-639f6cc11008] succeeded in 1.964293291035574s: ('/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/1', '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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/scottcain/git/dms/draft-manuscript-galaxy/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-17 11:47:17,840 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54832 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 [2026-09-17 11:47:17,856: INFO/main] Task galaxy.fetch_data[61197ea8-744f-4893-b8a2-ea911293404c] received [2026-09-17 11:47:17,856: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '61197ea8-744f-4893-b8a2-ea911293404c', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '61197ea8-744f-4893-b8a2-ea911293404c', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '5ddef49d-d77d-4669-b5de-639f6cc11008', 'parent_id': '5ddef49d-d77d-4669-b5de-639f6cc11008', 'argsrepr': "(('/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/1', '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/1/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 1}", 'origin': 'gen86626@e1-055847.science.psu.edu', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '61197ea8-744f-4893-b8a2-ea911293404c', 'reply_to': '573f8ecf-1b34-33b8-97bc-9197ceb9f16c', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key':... kwargs:{}) uvicorn.access INFO 2026-09-17 11:47:18,105 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54834 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:18,368 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54836 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:18,632 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54840 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:18,893 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54842 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:19,157 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54844 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:19,416 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54846 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:19,679 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54848 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:19,944 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54851 - "GET /api/jobs/c0417687166904cb?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 '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 'data_manager_config_file' option but it's empty/None uvicorn.access INFO 2026-09-17 11:47:20,210 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54853 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:20,474 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54855 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:20,738 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54857 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:21,001 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54859 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:21,265 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54861 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:21,529 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54863 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:21,792 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54865 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:22,051 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54867 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:22,315 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54870 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:22,574 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54872 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:22,841 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54874 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:23,104 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54876 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:23,369 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54878 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:23,629 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54880 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 /Users/scottcain/.planemo/gx_venv_3/lib/python3.13/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 2026-09-17 11:47:23,890 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54882 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 Exception ignored in: <_io.BufferedWriter name='/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/1/working/gx_file_streamqjsz3lrq'> Traceback (most recent call last): File "/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/lib/galaxy/files/sources/__init__.py", line 612, in realize_to self._realize_to(source_path, native_path, resolved_config) OSError: [Errno 9] Bad file descriptor [2026-09-17 11:47:24,154: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (6297.929 ms) uvicorn.access INFO 2026-09-17 11:47:24,158 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54885 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 [2026-09-17 11:47:24,167: INFO/main] Task galaxy.fetch_data[61197ea8-744f-4893-b8a2-ea911293404c] succeeded in 6.3105882910313085s: '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/1' uvicorn.access INFO 2026-09-17 11:47:24,447 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54887 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:24,737 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54889 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 [2026-09-17 11:47:24,916: INFO/main] Task galaxy.set_job_metadata[8cfe5826-41e1-4918-9e21-8e69c43ae381] received [2026-09-17 11:47:24,916: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '8cfe5826-41e1-4918-9e21-8e69c43ae381', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '8cfe5826-41e1-4918-9e21-8e69c43ae381', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '5ddef49d-d77d-4669-b5de-639f6cc11008', 'parent_id': '61197ea8-744f-4893-b8a2-ea911293404c', 'argsrepr': "('/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/1',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 1}", 'origin': 'gen86626@e1-055847.science.psu.edu', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '8cfe5826-41e1-4918-9e21-8e69c43ae381', 'reply_to': '573f8ecf-1b34-33b8-97bc-9197ceb9f16c', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag':... kwargs:{}) uvicorn.access INFO 2026-09-17 11:47:25,005 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54891 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 [2026-09-17 11:47:25,146: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (227.751 ms) [2026-09-17 11:47:25,151: INFO/main] Task galaxy.set_job_metadata[8cfe5826-41e1-4918-9e21-8e69c43ae381] succeeded in 0.23317099997075275s: None uvicorn.access INFO 2026-09-17 11:47:25,273 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54893 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:25,555 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54895 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:25,842 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54897 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 [2026-09-17 11:47:25,941: INFO/main] Task galaxy.finish_job[f91117ff-ecfd-4f7b-889b-698dc9a5aa6b] received [2026-09-17 11:47:25,942: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', 'f91117ff-ecfd-4f7b-889b-698dc9a5aa6b', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': 'f91117ff-ecfd-4f7b-889b-698dc9a5aa6b', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '5ddef49d-d77d-4669-b5de-639f6cc11008', 'parent_id': '8cfe5826-41e1-4918-9e21-8e69c43ae381', '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:{}) [2026-09-17 11:47:25,967: DEBUG/main] finish(): Moved /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/1/outputs/dataset_6082e5f8-5e30-4435-8b7c-94623fdef7d4.dat to /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/files/6/0/8/dataset_6082e5f8-5e30-4435-8b7c-94623fdef7d4.dat [2026-09-17 11:47:25,972: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'query1.fasta', 'dbkey': '?', 'ext': 'fasta', 'link_data_only': False, 'sources': [{'source_uri': 'https://raw.githubusercontent.com/galaxyproject/tools-iuc/main/tools/kmindex/test-data/query1.fasta', 'requested_transform': [{'action': 'datatype_groom'}, {'action': 'to_posix_lines'}], 'transform': [{'action': 'to_posix_lines'}]}], 'hashes': [], 'info': 'uploaded fasta file', 'state': 'ok', 'filename': '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/1/working/data_fetch_upload_mvrq76t_', 'object_id': 1}]}]}] [2026-09-17 11:47:26,024: INFO/main] Collecting metrics for Job 1 in /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/1 [2026-09-17 11:47:26,032: DEBUG/main] job_wrapper.finish for job 1 executed (75.697 ms) [2026-09-17 11:47:26,032: INFO/main] Successfully executed Celery task finish_job finish_job (88.651 ms) [2026-09-17 11:47:26,037: INFO/main] Task galaxy.finish_job[f91117ff-ecfd-4f7b-889b-698dc9a5aa6b] succeeded in 0.0934675419703126s: None uvicorn.access INFO 2026-09-17 11:47:26,129 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54899 - "GET /api/jobs/c0417687166904cb?full=True HTTP/1.1" 200 galaxy.tools INFO 2026-09-17 11:47:26,146 [pN:main.1,p:86630,tN:AnyIO worker thread] Validated and populated state for tool request (0.071 ms) uvicorn.access INFO 2026-09-17 11:47:26,205 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54902 - "POST /api/tools/fetch HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:26,217 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54904 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:26,502 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54906 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:26,783 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54908 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 [2026-09-17 11:47:26,970: INFO/main] Task galaxy.compute_dataset_hash[a1134306-6e9a-4f08-abb9-c986a3c490f4] received [2026-09-17 11:47:26,970: DEBUG/main] TaskPool: Apply (args:('galaxy.compute_dataset_hash', 'a1134306-6e9a-4f08-abb9-c986a3c490f4', {'lang': 'py', 'task': 'galaxy.compute_dataset_hash', 'id': 'a1134306-6e9a-4f08-abb9-c986a3c490f4', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '5ddef49d-d77d-4669-b5de-639f6cc11008', 'parent_id': 'f91117ff-ecfd-4f7b-889b-698dc9a5aa6b', 'argsrepr': '()', 'kwargsrepr': "{'request': ComputeDatasetHashTaskRequest(dataset_id=1, extra_files_path=None, hash_function='SHA-256', user=None)}", 'origin': 'gen86626@e1-055847.science.psu.edu', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'a1134306-6e9a-4f08-abb9-c986a3c490f4', 'reply_to': '95e3666f-0b0e-3ffe-8919-207a881055f4', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': 'ffe6df34-1e51-4b73-927e-33e2e7e746ff'}, 'reply_to':... kwargs:{}) [2026-09-17 11:47:26,981: INFO/main] Task galaxy.setup_fetch_data[c2a8fc3a-d06d-4e39-8291-6221a7c9b650] received [2026-09-17 11:47:26,981: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', 'c2a8fc3a-d06d-4e39-8291-6221a7c9b650', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': 'c2a8fc3a-d06d-4e39-8291-6221a7c9b650', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'c2a8fc3a-d06d-4e39-8291-6221a7c9b650', '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:{}) [2026-09-17 11:47:26,991: 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 (18.777 ms) [2026-09-17 11:47:26,999: INFO/main] Task galaxy.compute_dataset_hash[a1134306-6e9a-4f08-abb9-c986a3c490f4] succeeded in 0.028018583019729704s: None [2026-09-17 11:47:27,005: DEBUG/main] (2) Working directory for job is: /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/2 uvicorn.access INFO 2026-09-17 11:47:27,054 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54910 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 [2026-09-17 11:47:27,068: DEBUG/main] Job wrapper for Job [2] prepared (14.174 ms) [2026-09-17 11:47:27,068: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (86.082 ms) [2026-09-17 11:47:27,095: INFO/main] Task galaxy.setup_fetch_data[c2a8fc3a-d06d-4e39-8291-6221a7c9b650] succeeded in 0.11310858401702717s: ('/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/2', '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/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/scottcain/git/dms/draft-manuscript-galaxy/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}}) uvicorn.access INFO 2026-09-17 11:47:27,337 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54930 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:27,613 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54933 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:27,879 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54935 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 [2026-09-17 11:47:28,001: INFO/main] Task galaxy.fetch_data[7083c436-50df-49e5-a750-74e9334bff8c] received [2026-09-17 11:47:28,002: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '7083c436-50df-49e5-a750-74e9334bff8c', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '7083c436-50df-49e5-a750-74e9334bff8c', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'c2a8fc3a-d06d-4e39-8291-6221a7c9b650', 'parent_id': 'c2a8fc3a-d06d-4e39-8291-6221a7c9b650', 'argsrepr': "(('/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/2', '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/2/request.json', {'file_sources': [...], 'config': {...}}),)", 'kwargsrepr': "{'job_id': 2}", 'origin': 'gen86626@e1-055847.science.psu.edu', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '7083c436-50df-49e5-a750-74e9334bff8c', 'reply_to': '573f8ecf-1b34-33b8-97bc-9197ceb9f16c', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key':... kwargs:{}) uvicorn.access INFO 2026-09-17 11:47:28,143 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54937 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:28,413 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54940 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 Exception ignored in: <_io.BufferedWriter name='/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/2/working/gx_file_stream1gt9nf1i'> Traceback (most recent call last): File "/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/galaxy-dev/lib/galaxy/files/sources/__init__.py", line 612, in realize_to self._realize_to(source_path, native_path, resolved_config) OSError: [Errno 9] Bad file descriptor [2026-09-17 11:47:28,496: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (493.489 ms) [2026-09-17 11:47:28,509: INFO/main] Task galaxy.fetch_data[7083c436-50df-49e5-a750-74e9334bff8c] succeeded in 0.5061589160468429s: '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/2' uvicorn.access INFO 2026-09-17 11:47:28,700 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54942 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:28,975 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54944 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 [2026-09-17 11:47:29,021: INFO/main] Task galaxy.set_job_metadata[93fbac2a-9666-45df-b5ef-3119c885ae49] received [2026-09-17 11:47:29,022: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '93fbac2a-9666-45df-b5ef-3119c885ae49', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '93fbac2a-9666-45df-b5ef-3119c885ae49', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'c2a8fc3a-d06d-4e39-8291-6221a7c9b650', 'parent_id': '7083c436-50df-49e5-a750-74e9334bff8c', 'argsrepr': "('/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/2',)", 'kwargsrepr': "{'extended_metadata_collection': False, 'job_id': 2}", 'origin': 'gen86626@e1-055847.science.psu.edu', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '93fbac2a-9666-45df-b5ef-3119c885ae49', 'reply_to': '573f8ecf-1b34-33b8-97bc-9197ceb9f16c', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag':... kwargs:{}) [2026-09-17 11:47:29,078: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (55.349 ms) [2026-09-17 11:47:29,085: INFO/main] Task galaxy.set_job_metadata[93fbac2a-9666-45df-b5ef-3119c885ae49] succeeded in 0.06175733299460262s: None uvicorn.access INFO 2026-09-17 11:47:29,261 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54947 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 Failed to execute Galaxy activity, throwing ErrorRunResponse uvicorn.access INFO 2026-09-17 11:47:29,543 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54949 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 uvicorn.access INFO 2026-09-17 11:47:29,824 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54951 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 [2026-09-17 11:47:30,043: INFO/main] Task galaxy.finish_job[16ef0409-d983-4e5a-8ed5-3e151ac121fb] received [2026-09-17 11:47:30,043: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '16ef0409-d983-4e5a-8ed5-3e151ac121fb', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '16ef0409-d983-4e5a-8ed5-3e151ac121fb', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'c2a8fc3a-d06d-4e39-8291-6221a7c9b650', 'parent_id': '93fbac2a-9666-45df-b5ef-3119c885ae49', '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:{}) [2026-09-17 11:47:30,067: DEBUG/main] finish(): Moved /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/2/outputs/dataset_4468f326-9d2e-490c-a625-bb6d7da9df6f.dat to /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/files/4/4/6/dataset_4468f326-9d2e-490c-a625-bb6d7da9df6f.dat [2026-09-17 11:47:30,073: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'lexicmap_query3.fasta', 'dbkey': '?', 'ext': 'fasta', 'link_data_only': False, 'sources': [{'source_uri': 'https://raw.githubusercontent.com/galaxyproject/tools-iuc/main/tools/lexicmap/test-data/lexicmap_query3.fasta', 'requested_transform': [{'action': 'datatype_groom'}, {'action': 'to_posix_lines'}]}], 'hashes': [], 'info': 'uploaded fasta file', 'state': 'ok', 'filename': '/private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/2/working/data_fetch_upload_85596nku', 'object_id': 2}]}]}] uvicorn.access INFO 2026-09-17 11:47:30,096 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54953 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 [2026-09-17 11:47:30,108: INFO/main] Collecting metrics for Job 2 in /private/var/folders/x8/_0hyg7fn13gb3b7qprwgq93m0000gp/T/tmpedicm8_5/job_working_directory/000/2 [2026-09-17 11:47:30,115: DEBUG/main] job_wrapper.finish for job 2 executed (60.607 ms) [2026-09-17 11:47:30,115: INFO/main] Successfully executed Celery task finish_job finish_job (69.746 ms) [2026-09-17 11:47:30,119: INFO/main] Task galaxy.finish_job[16ef0409-d983-4e5a-8ed5-3e151ac121fb] succeeded in 0.07424016698496416s: None uvicorn.access INFO 2026-09-17 11:47:30,375 [pN:main.1,p:86630,tN:MainThread] 127.0.0.1:54955 - "GET /api/jobs/e4160cfcb38bdd28?full=True HTTP/1.1" 200 There were problems with 1 test(s) - out of 1 test(s) executed. See /Users/scottcain/git/dms/draft-manuscript-galaxy/planemo-test1-output.html for detailed breakdown. Traceback (most recent call last): File "/Users/scottcain/.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/scottcain/.local/share/uv/tools/planemo/lib/python3.13/site-packages/planemo/galaxy/activity.py", line 270, in _execute job_dict, history_id = stage_in(ctx, runnable, config, job_path, **kwds) ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/scottcain/.local/share/uv/tools/planemo/lib/python3.13/site-packages/planemo/galaxy/activity.py", line 441, in stage_in job_dict, datasets = psi.stage( ~~~~~~~~~^ tool_or_workflow, ^^^^^^^^^^^^^^^^^ ...<3 lines>... to_posix_lines=to_posix_lines, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/Users/scottcain/.local/share/uv/tools/planemo/lib/python3.13/site-packages/galaxy/tool_util/client/staging.py", line 275, in stage return galactic_job_json( job, ...<4 lines>... resolve_data=resolve_data, ) File "/Users/scottcain/.local/share/uv/tools/planemo/lib/python3.13/site-packages/galaxy/tool_util/cwl/util.py", line 388, in galactic_job_json replace_keys[key] = replacement_item(value) ~~~~~~~~~~~~~~~~^^^^^^^ File "/Users/scottcain/.local/share/uv/tools/planemo/lib/python3.13/site-packages/galaxy/tool_util/cwl/util.py", line 234, in replacement_item return replacement_collection(value) File "/Users/scottcain/.local/share/uv/tools/planemo/lib/python3.13/site-packages/galaxy/tool_util/cwl/util.py", line 362, in replacement_collection kwds["rows"] = value["rows"] ~~~~~^^^^^^^^ KeyError: 'rows' galaxy-workflow.gxwf.yml_0: failed