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mvdbeek/gist:271b4189ad66b4d81d2f772684601f0b

Created February 21, 2024 11:34
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Hmm, those tests are passing, but if you look at the logs it appears that some functionality is actually broken ?
```
================================================================ test session starts =================================================================
platform darwin -- Python 3.11.7, pytest-7.4.4, pluggy-1.4.0 -- /Users/mvandenb/src/galaxy/.venv/bin/python3.11
cachedir: .pytest_cache
metadata: {'Python': '3.11.7', 'Platform': 'macOS-14.1.1-arm64-arm-64bit', 'Packages': {'pytest': '7.4.4', 'pluggy': '1.4.0'}, 'Plugins': {'cwltest': '2.4.20240129145612', 'asyncio': '0.23.5', 'postgresql': '5.1.0', 'instafail': '0.5.0', 'shard': '0.1.2', 'html': '4.1.1', 'json-report': '1.5.0', 'pytest_httpserver': '1.0.9', 'metadata': '3.1.1', 'cov': '4.1.0', 'playwright': '0.4.4', 'mock': '3.12.0', 'base-url': '2.1.0', 'anyio': '4.2.0', 'celery': '0.0.0'}, 'Base URL': ''}
rootdir: /Users/mvandenb/src/galaxy
configfile: pytest.ini
plugins: cwltest-2.4.20240129145612, asyncio-0.23.5, postgresql-5.1.0, instafail-0.5.0, shard-0.1.2, html-4.1.1, json-report-1.5.0, pytest_httpserver-1.0.9, metadata-3.1.1, cov-4.1.0, playwright-0.4.4, mock-3.12.0, base-url-2.1.0, anyio-4.2.0, celery-0.0.0
asyncio: mode=Mode.AUTO
collected 11 items
Running 11 items in this shard: test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_oidc_login_new_user, test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_oidc_login_existing_user, test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_oidc_login_account_linkup, test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_oidc_logout, test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_auth_by_access_token_logged_in_once, test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_auth_by_access_token_never_logged_in, test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_auth_with_expired_token, test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_auth_with_another_authorized_client, test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_auth_with_authorized_client_but_unauthorized_audience, test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_auth_with_unauthorized_client, test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_auth_without_required_scopes
test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_oidc_login_new_user DEBUG:celery.utils.functional:
def cleanup_expired_notifications(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def ping():
return 1
DEBUG:celery.utils.functional:
def set_metadata(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def import_data_bundle(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def set_job_metadata(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def backend_cleanup():
return 1
DEBUG:celery.utils.functional:
def write_history_content_to(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def purge_hda(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def accumulate(self, *args, **kwargs):
return 1
DEBUG:celery.utils.functional:
def prepare_invocation_download(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def prepare_pdf_download(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def unlock_chord(self, group_id, callback, interval=0, max_retries=1, result=2, Result=3, GroupResult=4, result_from_tuple=5, **kwargs):
return 1
DEBUG:celery.utils.functional:
def fetch_data(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def clean_object_store_caches(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def xmap(task, it):
return 1
DEBUG:celery.utils.functional:
def prune_history_audit_table(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def change_datatype(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def xstarmap(task, it):
return 1
DEBUG:celery.utils.functional:
def setup_fetch_data(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def import_model_store(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def purge_datasets(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def chunks(task, it, n):
return 1
DEBUG:celery.utils.functional:
def write_invocation_to(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def prepare_history_download(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def group(self, tasks, result, group_id, partial_args, add_to_parent=0):
return 1
DEBUG:celery.utils.functional:
def export_history(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def chain(*args, **kwargs):
return 1
DEBUG:celery.utils.functional:
def cleanup_short_term_storage(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def touch(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def chord(self, header, body, partial_args=0, interval=1, countdown=2, max_retries=3, eager=4, **kwargs):
return 1
DEBUG:celery.utils.functional:
def finish_job(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def compute_dataset_hash(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def recalculate_user_disk_usage(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def materialize(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def write_history_to(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def prepare_history_content_download(*args, **kwds):
return 1
DEBUG:celery.utils.functional:
def prepare_dataset_collection_download(*args, **kwds):
return 1
WARNING:kombu.connection:No hostname was supplied. Reverting to default 'localhost'
WARNING:kombu.connection:No hostname was supplied. Reverting to default 'localhost'
Unable to find image 'keycloak/keycloak:22.0.1' locally
22.0.1: Pulling from keycloak/keycloak
d1da3ca59af4: Pull complete
67c43f3eefa9: Pull complete
4d216e602406: Pull complete
f557d650c4c1: Pull complete
Digest: sha256:89b37fa67c6d48b08637f5b6fb891785bd679e0bc15ee6c68eaab479c1cef7b1
Status: Downloaded newer image for keycloak/keycloak:22.0.1
e59070b5e1acca367ae9c0f7f371b2532e6dc314244bf4b28b4727a486238c27
bash: until curl --silent --output /dev/null http://localhost:9443; do sleep 0.5; done: No such file or directory
galaxy.jobs WARNING 2024-02-21 12:20:43,024 [pN:main,p:38658,tN:MainThread] Job configuration "/Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq" does not exist, using default job configuration
galaxy.web_stack.handlers INFO 2024-02-21 12:20:43,151 [pN:main,p:38658,tN:MainThread] JobConfiguration: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on <handlers> to override the default
galaxy.jobs DEBUG 2024-02-21 12:20:43,151 [pN:main,p:38658,tN:MainThread] Done loading job configuration
py.warnings WARNING 2024-02-21 12:20:43,187 [pN:main,p:38658,tN:MainThread] /Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fs/__init__.py:4: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('fs')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
__import__("pkg_resources").declare_namespace(__name__) # type: ignore
py.warnings WARNING 2024-02-21 12:20:43,203 [pN:main,p:38658,tN:MainThread] /Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fs/opener/__init__.py:6: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('fs.opener')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
__import__("pkg_resources").declare_namespace(__name__) # type: ignore
py.warnings WARNING 2024-02-21 12:20:43,205 [pN:main,p:38658,tN:MainThread] /Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/pkg_resources/__init__.py:2331: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('fs')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
declare_namespace(parent)
galaxy.security.vault WARNING 2024-02-21 12:20:43,604 [pN:main,p:38658,tN:MainThread] No vault configured. We recommend defining the vault_config_file setting in galaxy.yml
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,966 [pN:main,p:38658,tN:MainThread] Loading datatypes from /Users/mvandenb/src/galaxy/lib/galaxy/config/sample/datatypes_conf.xml.sample
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,968 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.h.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,968 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.c.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,968 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cpp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,968 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.py.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,968 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.go.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,968 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.rs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,968 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,969 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hep.root.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,969 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:JP2 from the datatype registry for extension jp2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,969 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry for extension ab1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,974 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry for extension afg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,983 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.goldenpath:GoldenPath from the datatype registry for extension agp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,987 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_cog_profile.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,987 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_composite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,987 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension anvio_classifier.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,987 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioContigsDB from the datatype registry for extension anvio_contigs_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,987 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioDB from the datatype registry for extension anvio_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,987 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioGenomesDB from the datatype registry for extension anvio_genomes_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,987 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioPanDB from the datatype registry for extension anvio_pan_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,987 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_pfam_profile.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,987 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioProfileDB from the datatype registry for extension anvio_profile_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,987 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioSamplesDB from the datatype registry for extension anvio_samples_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,987 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension anvio_state.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,987 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioStructureDB from the datatype registry for extension anvio_structure_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,987 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension anvio_variability.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,987 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry for extension arff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Paf from the datatype registry for extension paf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa1 from the datatype registry for extension gfa1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa2 from the datatype registry for extension gfa2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension asn1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension asn1-binary.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry for extension axt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry for extension fli.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry for extension bam.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bai.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamInputSorted from the datatype registry for extension qname_input_sorted.bam.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamQuerynameSorted from the datatype registry for extension qname_sorted.bam.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamNative from the datatype registry for extension unsorted.bam.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ProBam from the datatype registry for extension probam.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry for extension cram.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry for extension bed.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry for extension bedgraph.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry for extension bedstrict.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry for extension bed6.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry for extension bed12.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,988 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ProBed from the datatype registry for extension probed.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,989 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry for extension len.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,989 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DAA from the datatype registry for extension daa.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,989 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RMA6 from the datatype registry for extension rma6.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,989 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DMND from the datatype registry for extension dmnd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,989 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Parquet from the datatype registry for extension parquet.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,989 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Idat from the datatype registry for extension idat.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,989 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry for extension bigbed.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,989 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry for extension bigwig.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,989 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cxb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,989 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry for extension chrint.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,989 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension csv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,989 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension tsv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,989 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension intermine_tabular.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,989 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry for extension customtrack.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,991 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry for extension bowtie_color_index.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,991 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry for extension bowtie_base_index.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,991 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry for extension csfasta.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,991 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension data.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,991 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,991 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension binary.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,991 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension d3_hierarchy.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,991 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:ImgtJson from the datatype registry for extension imgt.json.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,991 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:GeoJson from the datatype registry for extension geojson.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,991 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:DataManagerJson from the datatype registry for extension data_manager_json.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,992 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry for extension dbn.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,992 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension fai.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,992 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension fasta.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,992 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastg from the datatype registry for extension fastg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,992 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry for extension fastq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,992 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry for extension fastqsanger.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,993 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry for extension fastqsolexa.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,993 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry for extension fastqcssanger.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,993 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry for extension fastqillumina.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,993 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry for extension fqtoc.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,993 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry for extension eland.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,994 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry for extension elandmulti.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,994 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry for extension genetrack.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,994 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension a3m.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,994 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry for extension gff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,994 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry for extension gff3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,994 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry for extension gif.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,994 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry for extension gmaj.zip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,994 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension graph_dot.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,994 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry for extension gtf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,995 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension toolshed.gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,997 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hdf4.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,997 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension h5.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,997 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension scool.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,998 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Grib from the datatype registry for extension grib.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,998 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Loom from the datatype registry for extension loom.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,998 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Anndata from the datatype registry for extension h5ad.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,998 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Visium from the datatype registry for extension visium.tar.gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,998 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mz5.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,998 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hyphy_results.json.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,998 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hivtrace.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,998 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Cool from the datatype registry for extension cool.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,998 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MCool from the datatype registry for extension mcool.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,998 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5MLM from the datatype registry for extension h5mlm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,999 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:LudwigModel from the datatype registry for extension ludwig_model.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,999 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension html.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,999 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension ludwig_report.html.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,999 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry for extension interval.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,999 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension jellyfish.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,999 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension ktab.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,999 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:43,999 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension prof.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,650 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaTab from the datatype registry for extension isa-tab.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,651 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaJson from the datatype registry for extension isa-json.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,651 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension picard_interval_list.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,651 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_interval.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,651 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_report.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,652 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_dbsnp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,652 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_tranche.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,652 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_recal.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,652 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cnn.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,652 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cns.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,652 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cnr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,652 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hhr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,652 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry for extension jpg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,652 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tiff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,652 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,652 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf8.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,652 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension btf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,652 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tif.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,652 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension svs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension scn.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension bif.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:OMETiff from the datatype registry for extension ome.tiff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vms.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vmu.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension ndpi.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry for extension mrxs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry for extension svslide.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry for extension bmp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry for extension im.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry for extension pcd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry for extension pcx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry for extension ppm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry for extension psd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry for extension xbm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry for extension xpm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,653 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry for extension rgb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,654 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry for extension pbm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,654 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry for extension pgm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,654 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nrrd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,654 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nhdr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,654 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry for extension rna_eps.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,656 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Artifact from the datatype registry for extension qza.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,656 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Visualization from the datatype registry for extension qzv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,656 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Metadata from the datatype registry for extension qiime2.tabular.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,656 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension zip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,656 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension ncbi_genome_dataset.zip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,657 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,657 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension directory.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,657 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension yaml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,657 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mrm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Dta from the datatype registry for extension dta.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Dta2d from the datatype registry for extension dta2d.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Edta from the datatype registry for extension edta.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension pepxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension raw_pepxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension peptideprophet_pepxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension interprophet_pepxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry for extension protxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ParamXml from the datatype registry for extension paramxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Kroenik from the datatype registry for extension kroenik.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepList from the datatype registry for extension peplist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PSMS from the datatype registry for extension psms.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry for extension pepxml.tsv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry for extension protxml.tsv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry for extension mascotdat.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry for extension mzid.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry for extension idxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry for extension tandem.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sirius.ms.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry for extension thermo.raw.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BafTar from the datatype registry for extension brukerbaf.d.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,666 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:YepTar from the datatype registry for extension agilentbrukeryep.d.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:TdfTar from the datatype registry for extension brukertdf.d.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MassHunterTar from the datatype registry for extension agilentmasshunter.d.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MassLynxTar from the datatype registry for extension watersmasslynx.raw.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:WiffTar from the datatype registry for extension wiff.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Wiff2Tar from the datatype registry for extension wiff2.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotXML from the datatype registry for extension mascotxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzTab from the datatype registry for extension mztab.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzTab2 from the datatype registry for extension mztab2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry for extension mzml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:NmrML from the datatype registry for extension nmrml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Meryldb from the datatype registry for extension meryldb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bref3 from the datatype registry for extension bref3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry for extension mgf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry for extension wiff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff2 from the datatype registry for extension wiff2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry for extension mzxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry for extension mzdata.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry for extension ms2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry for extension mzq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry for extension sqlite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry for extension mz.sqlite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OSW from the datatype registry for extension osw.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:PQP from the datatype registry for extension pqp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry for extension traml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TrafoXML from the datatype registry for extension trafoxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry for extension featurexml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry for extension consensusxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry for extension uniprotxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XquestXML from the datatype registry for extension xquest.xml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XquestSpecXML from the datatype registry for extension spec.xml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:QCML from the datatype registry for extension qcml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,667 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension mzqc.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry for extension msp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry for extension splib_noindex.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry for extension splib.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BlibSQlite from the datatype registry for extension blib.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DlibSQlite from the datatype registry for extension dlib.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ElibSQlite from the datatype registry for extension elib.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry for extension hlf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry for extension idpdb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry for extension sf3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cps.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry for extension ct.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:PostgresqlArchive from the datatype registry for extension postgresql.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MongoDBArchive from the datatype registry for extension mongodb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GeneNoteBook from the datatype registry for extension genenotebook.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry for extension searchgui_archive.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry for extension fast5.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry for extension fast5.tar.gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,668 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry for extension fast5.tar.bz2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,669 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension peptideshaker_archive.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,669 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension percin.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,669 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension percout.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,669 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hardklor.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,669 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension kronik.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,669 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry for extension imzml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,672 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Analyze75 from the datatype registry for extension analyze75.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,672 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nifti1 from the datatype registry for extension nii1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,672 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nifti2 from the datatype registry for extension nii2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,672 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gifti from the datatype registry for extension gii.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,672 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tck from the datatype registry for extension tck.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,672 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Trk from the datatype registry for extension trk.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,672 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Mrc2014 from the datatype registry for extension mrc.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,672 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Star from the datatype registry for extension star.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,672 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PEFF from the datatype registry for extension peff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,672 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension toml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,673 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.flow:FCS from the datatype registry for extension fcs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,673 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowtext.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,673 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowclr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,673 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowmfi.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,673 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,673 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,673 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,673 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowscore.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,673 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowframe.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,675 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension fsom.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,675 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowset.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,675 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension metacyto_clr.txt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,675 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.metacyto:mSummary from the datatype registry for extension metacyto_summary.txt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,675 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.metacyto:mStats from the datatype registry for extension metacyto_stats.txt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,675 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_compute_matrix_archive.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,675 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_coverage_matrix.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,675 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry for extension netcdf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry for extension eps.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry for extension rast.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry for extension laj.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry for extension lav.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry for extension maf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry for extension mafcustomtrack.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:MatrixMarket from the datatype registry for extension mtx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CMAP from the datatype registry for extension cmap.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry for extension encodepeak.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry for extension pdf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry for extension pileup.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Psl from the datatype registry for extension psl.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry for extension obo.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry for extension owl.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry for extension png.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry for extension qual.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry for extension qualsolexa.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry for extension qualillumina.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry for extension qualsolid.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry for extension qual454.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry for extension roadmaps.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry for extension sam.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry for extension scf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry for extension sequences.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry for extension snpeffdb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry for extension snpsiftdbnsfp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dbnsfp.tabular.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry for extension sff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry for extension sra.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:SraManifest from the datatype registry for extension sra_manifest.tabular.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension svg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,676 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry for extension taxonomy.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,677 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension tabular.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,677 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry for extension twobit.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,677 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SQmass from the datatype registry for extension sqmass.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,677 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry for extension gemini.sqlite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,677 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ChiraSQLite from the datatype registry for extension chira.sqlite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,677 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CuffDiffSQlite from the datatype registry for extension cuffdiff.sqlite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,677 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GAFASQLite from the datatype registry for extension gafa.sqlite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,677 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:NcbiTaxonomySQlite from the datatype registry for extension ncbitaxonomy.sqlite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension txt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry for extension linecount.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry for extension memepsp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry for extension memexml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry for extension cisml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xsd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Dzi from the datatype registry for extension dzi.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry for extension vcf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf_bgzip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry for extension bcf_uncompressed.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry for extension velvet.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry for extension wig.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension interval_index.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension odgi.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension vg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,678 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension xg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension onnx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tabix.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:IntervalTabix from the datatype registry for extension interval_tabix.gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:JuicerMediumTabix from the datatype registry for extension juicer_medium_tabix.gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedTabix from the datatype registry for extension bed_tabix.gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:GffTabix from the datatype registry for extension gff_tabix.gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bgzip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry for extension vcf_bgzip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bus.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension kallisto.idx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry for extension phyloxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension newick.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension nhx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry for extension nex.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,679 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:IQTree from the datatype registry for extension iqtree.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,683 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mldist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,689 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry for extension affybatch.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,689 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry for extension eigenstratgeno.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,689 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry for extension eigenstratpca.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,689 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry for extension eset.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,689 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry for extension fped.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,689 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry for extension fphe.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,689 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry for extension gg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,689 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry for extension ldindep.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,689 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry for extension malist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,689 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry for extension lped.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,689 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry for extension pbed.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,689 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry for extension pheno.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,689 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry for extension pphe.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,689 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry for extension rexpbase.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,690 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry for extension rgenetics.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,690 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry for extension snptest.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,690 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry for extension snpmatrix.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,690 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension xls.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,690 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry for extension ipynb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,690 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension json.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,690 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:ExpressionJson from the datatype registry for extension expression.json.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,692 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry for extension xgmml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,693 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry for extension sif.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,694 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry for extension triples.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,694 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry for extension hdt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,694 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry for extension nt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,694 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry for extension n3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,694 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry for extension ttl.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,694 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry for extension rdf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,694 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry for extension jsonld.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,694 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension excel.xls.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,694 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry for extension xlsx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,694 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension docx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,694 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension btwisted.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cai.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cat_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension charge.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension checktrans.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension chips.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codcmp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension coderet.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension compseq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgplot.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgreport.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cusp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cut.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dan.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension digest.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dreg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension einverted.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension epestfind.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension equicktandem.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension est2genome.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension etandem.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension freak.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzznuc.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,695 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzzpro.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzztran.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension garnier.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension geecee.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension helixturnhelix.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hmoment.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension isochore.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension match.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nametable.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension needle.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgreport.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgseek.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension noreturn.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension palindrome.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepcoil.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepinfo.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepstats.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension polydot.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension preg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prettyseq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension primersearch.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showfeat.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showorf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sixpack.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension strider.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,696 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension supermatcher.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,697 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension syco.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,697 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension textsearch.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,697 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension vectorstrip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,697 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wobble.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,697 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wordcount.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,697 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dbmotif.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,697 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension diffseq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,697 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension excel.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,697 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feattable.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,697 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension motif.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,698 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension regions.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,698 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension seqtable.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,698 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension simple.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,698 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension table.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,698 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension tagseq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,698 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension acedb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,698 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension clustal.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,698 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codata.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,698 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension embl.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,698 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fitch.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,698 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gcg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,698 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry for extension genbank.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,698 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hennig86.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,699 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ig.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,699 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifer.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,699 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifernon.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,699 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mega.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,699 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension meganon.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,699 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ncbi.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,699 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexus.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,699 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexusnon.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,703 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.phylip:Phylip from the datatype registry for extension phylip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,703 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension phylipnon.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,703 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pir.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,703 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension staden.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,703 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension swiss.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,708 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Msf from the datatype registry for extension msf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,708 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx0.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,708 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,708 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx10.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,708 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,708 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,708 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pair.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,708 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension score.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,709 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,709 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srspair.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,711 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry for extension snaphmm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,712 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry for extension augustus.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,712 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ICM from the datatype registry for extension icm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,712 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:InfernalCM from the datatype registry for extension cm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,712 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry for extension hmm2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,712 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry for extension hmm3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,712 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry for extension stockholm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,712 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry for extension xmfa.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,713 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Cel from the datatype registry for extension cel.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,713 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gpr from the datatype registry for extension gpr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,713 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gal from the datatype registry for extension gal.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,713 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension rds.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,713 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension phyloseq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,713 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,713 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.sce.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,714 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.raw.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,714 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.msnbase.raw.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,714 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.findchrompeaks.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,714 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.group.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,714 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.retcor.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,714 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.fillpeaks.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,714 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.positive.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,714 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.negative.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,714 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.quick.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,715 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.hdf5:HDF5SummarizedExperiment from the datatype registry for extension rdata.se.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,715 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rdock_as.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,715 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry for extension oxlicg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,715 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry for extension oxling.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,715 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry for extension oxlits.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,715 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry for extension oxlist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,715 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry for extension oxliss.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,715 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry for extension oxligl.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,719 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry for extension stl.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,719 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry for extension plyascii.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,719 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry for extension plybinary.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,720 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry for extension vtkascii.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,720 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry for extension vtkbinary.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,720 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry for extension biom1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,720 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry for extension biom2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,720 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MashSketch from the datatype registry for extension msh.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,720 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry for extension scidx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry for extension smi.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry for extension sdf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry for extension inchi.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry for extension mol.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry for extension mol2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry for extension cml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry for extension fps.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry for extension obfs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry for extension drf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry for extension phar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry for extension pdb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry for extension pdbqt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PQR from the datatype registry for extension pqr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:Cell from the datatype registry for extension cell.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:CIF from the datatype registry for extension cif.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:XYZ from the datatype registry for extension xyz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:ExtendedXYZ from the datatype registry for extension extxyz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,756 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:Magres from the datatype registry for extension magres.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Trr from the datatype registry for extension trr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Dcd from the datatype registry for extension dcd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension top.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prmtop.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension itp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mdp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ndx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension xvg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Xtc from the datatype registry for extension xtc.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Cpt from the datatype registry for extension cpt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Edr from the datatype registry for extension edr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tpr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:GRO from the datatype registry for extension gro.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension inpcrd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Vel from the datatype registry for extension vel.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry for extension grd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry for extension grd.tgz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.otu.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.list.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.sabund.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.rabund.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.shared.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.relabund.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry for extension mothur.names.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,757 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.design.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry for extension mothur.summary.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.groups.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry for extension mothur.oligos.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension mothur.align.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.accnos.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.otulabels.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mothur.otu.corr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry for extension mothur.map.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry for extension mothur.align.check.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry for extension mothur.align.report.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry for extension mothur.filter.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry for extension mothur.dist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mothur.tre.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry for extension mothur.pair.dist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mothur.square.dist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,758 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry for extension mothur.lower.dist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,759 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.ref.taxonomy.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,759 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.seq.taxonomy.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,759 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.rdp.taxonomy.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,759 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry for extension mothur.cons.taxonomy.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,759 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry for extension mothur.tax.summary.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,759 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry for extension mothur.freq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,759 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.quan.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,759 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.quan.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,759 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.masked.quan.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,760 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.masked.quan.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,760 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry for extension mothur.axes.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,760 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry for extension mothur.sff.flow.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,760 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry for extension mothur.count_table.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,761 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry for extension neostore.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,761 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDBzip from the datatype registry for extension neostore.zip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,761 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry for extension trackhub.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,764 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry for extension blastxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,764 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry for extension blastdbn.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,764 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry for extension blastdbp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,764 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry for extension blastdbd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,764 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:LastDb from the datatype registry for extension lastdb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,764 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb5 from the datatype registry for extension blastdbn5.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,764 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb5 from the datatype registry for extension blastdbp5.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,764 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb5 from the datatype registry for extension blastdbd5.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,764 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension maskinfo-asn1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,764 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension maskinfo-asn1-binary.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,764 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension pssm-asn1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,765 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry for extension ptkscmp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,766 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry for extension smat.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,766 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenotypeMatrix from the datatype registry for extension alohomora_gts.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,766 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_map.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,766 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_maf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,766 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_ped.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,766 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension linkage_pedin.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,766 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:DataIn from the datatype registry for extension linkage_datain.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,766 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:MarkerMap from the datatype registry for extension linkage_map.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,766 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_ihaplo.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,766 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_descent.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,766 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:AllegroLOD from the datatype registry for extension allegro_fparam.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,766 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:IdeasPre from the datatype registry for extension ideaspre.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,766 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Sbml from the datatype registry for extension sbml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,767 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnNuclDb from the datatype registry for extension spalndbnp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,767 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnProtDb from the datatype registry for extension spalndba.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,768 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_dada.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,768 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_errorrates.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,768 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_mergepairs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,768 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_sequencetable.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,768 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_uniques.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,768 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension ampvis2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,768 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension ckpt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,768 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tgz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,771 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Wav from the datatype registry for extension wav.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,771 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mp3 from the datatype registry for extension mp3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,771 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mkv from the datatype registry for extension mkv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,771 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mp4 from the datatype registry for extension mp4.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,771 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Flv from the datatype registry for extension flv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,771 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mpg from the datatype registry for extension mpg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,772 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.speech:TextGrid from the datatype registry for extension textgrid.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,772 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.speech:BPF from the datatype registry for extension par.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,772 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension ffindex.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,772 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension ffdata.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,772 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Pretext from the datatype registry for extension pretext.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,772 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension immuneml_receptors.html.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,772 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdMaterials from the datatype registry for extension hexrd.materials.h5.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,772 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension npz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,772 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdImagesNpz from the datatype registry for extension hexrd.images.npz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,772 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdEtaOmeNpz from the datatype registry for extension hexrd.eta_ome.npz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,772 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension hexrd.scored_orientations.npz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,773 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hexrd.accepted_orientations.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,773 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension hexrd.yml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,773 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTess from the datatype registry for extension neper.tess.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,773 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTesr from the datatype registry for extension neper.tesr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,773 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPoints from the datatype registry for extension neper.points.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,773 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPointsTabular from the datatype registry for extension neper.points.tsv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,773 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperMultiScaleCell from the datatype registry for extension neper.mscell.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,774 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshMsh from the datatype registry for extension gmsh.msh.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,774 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshGeo from the datatype registry for extension gmsh.geo.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,774 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:ZsetGeof from the datatype registry for extension zset.geof.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,774 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension stl.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,774 [pN:main,p:38658,tN:MainThread] Overriding conflicting datatype with extension 'stl', using datatype from /Users/mvandenb/src/galaxy/lib/galaxy/config/sample/datatypes_conf.xml.sample.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,774 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Text from the datatype registry for extension pov.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,774 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaResult from the datatype registry for extension pithya.result.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,774 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaProperty from the datatype registry for extension pithya.property.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,774 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaModel from the datatype registry for extension pithya.model.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,774 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:BCSLts from the datatype registry for extension bcsl.ts.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,774 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:BCSLmodel from the datatype registry for extension bcsl.model.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,774 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:StormSample from the datatype registry for extension storm.sample.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,775 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:StormCheck from the datatype registry for extension storm.check.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,775 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:CTLresult from the datatype registry for extension ctl.result.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,775 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Castep from the datatype registry for extension castep.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,775 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Param from the datatype registry for extension param.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,775 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:FormattedDensity from the datatype registry for extension den_fmt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,776 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.larch:AthenaProject from the datatype registry for extension prj.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,776 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.larch:FEFFInput from the datatype registry for extension inp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,776 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension sp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,776 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension gds.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,776 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension feff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,776 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feffit.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,776 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bil.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,777 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hdr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,778 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.gis:Shapefile from the datatype registry for extension shp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,778 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:FITS from the datatype registry for extension fits.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.chain:Chain from the datatype registry for extension chain.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTess'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTesr'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:GmshMsh'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.goldenpath:GoldenPath'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:JP2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQmass'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OSW'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PQP'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ElibSQlite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DlibSQlite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BlibSQlite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ChiraSQLite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CuffDiffSQlite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GAFASQLite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NcbiTaxonomySQlite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,779 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5MLM'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cool'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MCool'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Loom'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Anndata'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdMaterials'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Grib'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdImagesNpz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdEtaOmeNpz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Npz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamQuerynameSorted'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamNative'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DAA'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RMA6'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Parquet'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BafTar'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TdfTar'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassHunterTar'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassLynxTar'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:YepTar'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:WiffTar'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Meryldb'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,780 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bref3'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PostgresqlArchive'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ICM'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Idat'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Trr'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Dcd'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xtc'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cpt'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Edr'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Vel'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xlsx'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Metadata'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Artifact'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Visualization'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedZipArchive'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pretext'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.chain:Chain'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gifti'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Dzi'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Sbml'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Dta2d'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Edta'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ConsensusXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:IdXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:FeatureXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MascotXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Ms2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ParamXml'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,781 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:NmrML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Kroenik'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepList'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PSMS'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TrafoXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestSpecXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:QCML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Wiff'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PEFF'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastg'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Cell'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CIF'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:ExtendedXYZ'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:XYZ'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Magres'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PQR'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,782 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:GRO'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.phylip:Phylip'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqCSSanger'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Html'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Psl'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Paf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Newick'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:IQTree'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Obo'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Arff'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:ImgtJson'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:GeoJson'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaResult'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLts'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Json'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:GenotypeMatrix'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:DataIn'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:MarkerMap'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:AllegroLOD'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,783 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CMAP'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mSummary'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mStats'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:MatrixMarket'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:InfernalCM'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Cel'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gpr'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gal'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RData'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RDS'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Mrc2014'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Png'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:OMETiff'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gif'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Im'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Psd'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Eps'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rast'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,784 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tck'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Trk'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti1'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Star'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Wav'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mkv'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp3'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp4'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Flv'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mpg'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:TextGrid'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:BPF'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.larch:FEFFInput'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.larch:AthenaProject'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Castep'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:CTLresult'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:FormattedDensity'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Param'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Yaml'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:FITS'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.neo4j:Neo4jDBzip'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaProperty'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaModel'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLmodel'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormSample'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,785 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormCheck'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,787 [pN:main,p:38658,tN:MainThread] Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample].
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,787 [pN:main,p:38658,tN:MainThread] Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla']
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,788 [pN:main,p:38658,tN:MainThread] 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']
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,788 [pN:main,p:38658,tN:MainThread] Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,788 [pN:main,p:38658,tN:MainThread] Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,788 [pN:main,p:38658,tN:MainThread] Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample].
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,788 [pN:main,p:38658,tN:MainThread] Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,788 [pN:main,p:38658,tN:MainThread] Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample].
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:45,788 [pN:main,p:38658,tN:MainThread] Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample
galaxy.util.tool_shed.tool_shed_registry DEBUG 2024-02-21 12:20:45,789 [pN:main,p:38658,tN:MainThread] Loading references to tool sheds from internal default config
galaxy.util.tool_shed.tool_shed_registry DEBUG 2024-02-21 12:20:45,789 [pN:main,p:38658,tN:MainThread] Loaded reference to tool shed: Galaxy Main Tool Shed
galaxy.web_stack DEBUG 2024-02-21 12:20:45,792 [pN:main,p:38658,tN:MainThread] server_name set to: main
galaxy.queue_worker INFO 2024-02-21 12:20:45,802 [pN:main,p:38658,tN:MainThread] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/tmpo1ompzky/database/control.sqlite?isolation_level=IMMEDIATE
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,821 [pN:main,p:38658,tN:MainThread] Loaded 11 lines from 'all_fasta.loc' for 'all_fasta'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,821 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'all_fasta' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:45,821 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/bfast_indexes.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,822 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/bfast_indexes.loc.sample' for 'bfast_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,822 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'bfast_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:45,822 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/blastdb.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,822 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/blastdb.loc.sample' for 'blastdb'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,822 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'blastdb' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:45,822 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/blastdb_p.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,822 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/blastdb_p.loc.sample' for 'blastdb_p'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,822 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'blastdb_p' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:45,822 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/blastdb_d.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,823 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/blastdb_d.loc.sample' for 'blastdb_d'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,823 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'blastdb_d' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data WARNING 2024-02-21 12:20:45,823 [pN:main,p:38658,tN:MainThread] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,823 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'bwa_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data WARNING 2024-02-21 12:20:45,823 [pN:main,p:38658,tN:MainThread] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,823 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'bwa_indexes_color' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/maf_index.loc' for 'indexed_maf_files'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'indexed_maf_files' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/ngs_sim_fasta.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'ngs_sim_fasta' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/perm_base_index.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/perm_base_index.loc.sample' for 'perm_base_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'perm_base_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/perm_color_index.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/perm_color_index.loc.sample' for 'perm_color_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'perm_color_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/picard_index.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/picard_index.loc.sample' for 'picard_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'picard_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/picard_index.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,824 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/picard_index.loc.sample' for 'srma_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,825 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'srma_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:45,825 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/mosaik_index.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,825 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/mosaik_index.loc.sample' for 'mosaik_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,825 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'mosaik_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:45,825 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/twobit.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,825 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/twobit.loc.sample' for 'twobit'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:45,825 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'twobit' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,186 [pN:main,p:38658,tN:MainThread] Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/Users/mvandenb/tmp/TTDT_URL_igv_broad_genomes-4c596e_p".
galaxy.tool_util.data WARNING 2024-02-21 12:20:46,187 [pN:main,p:38658,tN:MainThread] Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields):
<Server-Side Genome List>
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,187 [pN:main,p:38658,tN:MainThread] Loaded 156 lines from '/Users/mvandenb/tmp/TTDT_URL_igv_broad_genomes-4c596e_p' for 'igv_broad_genomes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,187 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'igv_broad_genomes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,189 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/tool-data/liftOver.loc' for 'liftOver'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,189 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'liftOver' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:46,190 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/bam_iobio.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,191 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/tool-data/bam_iobio.loc.sample' for 'bam_iobio'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,191 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'bam_iobio' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:46,192 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/vcf_iobio.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,193 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/tool-data/vcf_iobio.loc.sample' for 'vcf_iobio'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,193 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'vcf_iobio' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:46,193 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/biom_simple_display.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,194 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/tool-data/biom_simple_display.loc.sample' for 'biom_simple_display'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,194 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'biom_simple_display' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:46,194 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/intermine_simple_display.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,194 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/tool-data/intermine_simple_display.loc.sample' for 'intermine_simple_display'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,194 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'intermine_simple_display' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:46,195 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/icn3d_simple_display.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,195 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/tool-data/icn3d_simple_display.loc.sample' for 'icn3d_simple_display'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,195 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'icn3d_simple_display' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table '__dbkeys__'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table '__dbkeys__'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Loaded tool data table '__dbkeys__' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'all_fasta'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'all_fasta'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'fasta_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'fasta_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'fasta_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'bowtie2_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'bowtie2_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'bowtie2_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'bwa_mem_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'bwa_mem_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'bwa_mem_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'hisat2_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'hisat2_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'hisat2_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/q2view_display.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/tool-data/q2view_display.loc.sample' for 'q2view_display'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,196 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'q2view_display' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,197 [pN:main,p:38658,tN:MainThread] Loaded 2 lines from '/Users/mvandenb/src/galaxy/test/functional/tool-data/testalpha.loc' for 'testalpha'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,197 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'testalpha' from file '/Users/mvandenb/src/galaxy/test/functional/tool-data/sample_tool_data_tables.xml'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,197 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/test/functional/tool-data/testbeta.loc' for 'testbeta'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,197 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'testbeta' from file '/Users/mvandenb/src/galaxy/test/functional/tool-data/sample_tool_data_tables.xml'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,197 [pN:main,p:38658,tN:MainThread] Loaded 3 lines from '/Users/mvandenb/src/galaxy/test/functional/tool-data/fasta_indexes.loc' for 'test_fasta_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:46,197 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'test_fasta_indexes' from file '/Users/mvandenb/src/galaxy/test/functional/tool-data/sample_tool_data_tables.xml'
galaxy.util WARNING 2024-02-21 12:20:46,242 [pN:main,p:38658,tN:MainThread] directory not found: /Users/mvandenb/src/galaxy/lib/galaxy/util/../../../config/plugins/activities
galaxy.tools WARNING 2024-02-21 12:20:46,242 [pN:main,p:38658,tN:MainThread] The default shed tool config file (/Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/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 2024-02-21 12:20:46,242 [pN:main,p:38658,tN:MainThread] Parsing the tool configuration /Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_conf.xml.sample
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,242 [pN:main,p:38658,tN:MainThread] Tool path for tool configuration /Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_conf.xml.sample is None
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,258 [pN:main,p:38658,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,259 [pN:main,p:38658,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,260 [pN:main,p:38658,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,261 [pN:main,p:38658,tN:MainThread] Loaded tool id: ncbi_datasets_source, version: 13.14.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,261 [pN:main,p:38658,tN:MainThread] Loaded tool id: sra_source, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,261 [pN:main,p:38658,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,262 [pN:main,p:38658,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,262 [pN:main,p:38658,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,263 [pN:main,p:38658,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,263 [pN:main,p:38658,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,263 [pN:main,p:38658,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,264 [pN:main,p:38658,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,264 [pN:main,p:38658,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,264 [pN:main,p:38658,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,264 [pN:main,p:38658,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,265 [pN:main,p:38658,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,265 [pN:main,p:38658,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,265 [pN:main,p:38658,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,266 [pN:main,p:38658,tN:MainThread] Loaded tool id: send_to_cloud, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,267 [pN:main,p:38658,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,267 [pN:main,p:38658,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,268 [pN:main,p:38658,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,268 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,269 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,269 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,271 [pN:main,p:38658,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,273 [pN:main,p:38658,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,273 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,274 [pN:main,p:38658,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,275 [pN:main,p:38658,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,275 [pN:main,p:38658,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,276 [pN:main,p:38658,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,277 [pN:main,p:38658,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.2.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,277 [pN:main,p:38658,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,278 [pN:main,p:38658,tN:MainThread] Loaded tool id: __DUPLICATE_FILE_TO_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,279 [pN:main,p:38658,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,280 [pN:main,p:38658,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,281 [pN:main,p:38658,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,281 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,282 [pN:main,p:38658,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,283 [pN:main,p:38658,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,284 [pN:main,p:38658,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,284 [pN:main,p:38658,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,284 [pN:main,p:38658,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,285 [pN:main,p:38658,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,286 [pN:main,p:38658,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,286 [pN:main,p:38658,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,287 [pN:main,p:38658,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,288 [pN:main,p:38658,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,288 [pN:main,p:38658,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,289 [pN:main,p:38658,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,289 [pN:main,p:38658,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,290 [pN:main,p:38658,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,290 [pN:main,p:38658,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,291 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,292 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,294 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,294 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,295 [pN:main,p:38658,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,296 [pN:main,p:38658,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,296 [pN:main,p:38658,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,298 [pN:main,p:38658,tN:MainThread] Loaded tool id: Filter1, version: 1.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,298 [pN:main,p:38658,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,299 [pN:main,p:38658,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,300 [pN:main,p:38658,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,301 [pN:main,p:38658,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,301 [pN:main,p:38658,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,302 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,302 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,303 [pN:main,p:38658,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,304 [pN:main,p:38658,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,304 [pN:main,p:38658,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,306 [pN:main,p:38658,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,307 [pN:main,p:38658,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,307 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,308 [pN:main,p:38658,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,309 [pN:main,p:38658,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,310 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,311 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,311 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,312 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,313 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,313 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,314 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,314 [pN:main,p:38658,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,315 [pN:main,p:38658,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,316 [pN:main,p:38658,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,316 [pN:main,p:38658,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,317 [pN:main,p:38658,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,318 [pN:main,p:38658,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base ERROR 2024-02-21 12:20:46,318 [pN:main,p:38658,tN:MainThread] Error reading tool from path: phenotype_association/sift.xml
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 873, in _load_tool_tag_set
tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 1100, in load_tool
tool = self.create_tool(
^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 547, in create_tool
return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 563, in _create_tool_from_source
return create_tool_from_source(self.app, tool_source, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 355, in create_tool_from_source
tool = ToolClass(config_file, tool_source, app, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 820, in __init__
raise e
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 817, in __init__
self.parse(tool_source, guid=guid, dynamic=dynamic)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 1142, in parse
self.parse_inputs(self.tool_source)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 1427, in parse_inputs
inputs = self.parse_input_elem(page_source, enctypes)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 1622, in parse_input_elem
param = self.parse_param_elem(input_source, enctypes, context)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 1635, in parse_param_elem
param = ToolParameter.build(self, input_source)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/basic.py", line 329, in build
return parameter_types[param_type](tool, input_source)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/basic.py", line 2054, in __init__
super().__init__(tool, input_source, trans)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/basic.py", line 1845, in __init__
super().__init__(tool, input_source)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/basic.py", line 185, in __init__
self.validators.append(validation.Validator.from_element(self, elem))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/validation.py", line 45, in from_element
return validator_types[_type].from_element(param, elem)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/validation.py", line 397, in from_element
assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found"
AssertionError: File /Users/mvandenb/src/galaxy/tool-data/sift_db.loc specified by the 'filename' attribute not found
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,322 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,323 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,323 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,324 [pN:main,p:38658,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel..
galaxy.tools WARNING 2024-02-21 12:20:46,324 [pN:main,p:38658,tN:MainThread] The default shed tool config file (/Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/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 2024-02-21 12:20:46,324 [pN:main,p:38658,tN:MainThread] Parsing the tool configuration /Users/mvandenb/src/galaxy/test/functional/tools/sample_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,324 [pN:main,p:38658,tN:MainThread] Tool path for tool configuration /Users/mvandenb/src/galaxy/test/functional/tools/sample_tool_conf.xml is ${tool_conf_dir}
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,327 [pN:main,p:38658,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,328 [pN:main,p:38658,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,329 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_data_optional, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,329 [pN:main,p:38658,tN:MainThread] Loaded tool id: paths_as_file, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,330 [pN:main,p:38658,tN:MainThread] Loaded tool id: param_text_option, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,330 [pN:main,p:38658,tN:MainThread] Loaded tool id: column_param, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,331 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_format_input, version: 1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,332 [pN:main,p:38658,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,332 [pN:main,p:38658,tN:MainThread] Loaded tool id: test_data_source, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,333 [pN:main,p:38658,tN:MainThread] Loaded tool id: simple_constructs, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,334 [pN:main,p:38658,tN:MainThread] Loaded tool id: color_param, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,334 [pN:main,p:38658,tN:MainThread] Loaded tool id: inheritance_simple, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,335 [pN:main,p:38658,tN:MainThread] Loaded tool id: boolean_conditional, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,336 [pN:main,p:38658,tN:MainThread] Loaded tool id: composite, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,336 [pN:main,p:38658,tN:MainThread] Loaded tool id: environment_variables, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,337 [pN:main,p:38658,tN:MainThread] Loaded tool id: environment_variables_inject, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,337 [pN:main,p:38658,tN:MainThread] Loaded tool id: code_file, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,338 [pN:main,p:38658,tN:MainThread] Loaded tool id: disambiguate_cond, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,339 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_repeats, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,339 [pN:main,p:38658,tN:MainThread] Loaded tool id: remove_value, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,340 [pN:main,p:38658,tN:MainThread] Loaded tool id: bibtex, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,340 [pN:main,p:38658,tN:MainThread] Loaded tool id: select_from_url, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,341 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_select, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,341 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_output, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,342 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_output_configured, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,342 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_output_assign_primary, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,343 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_output_assign_primary_ext_dbkey, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,344 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_output_recurse, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,345 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_output_recurse_collection, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,346 [pN:main,p:38658,tN:MainThread] Loaded tool id: galaxy_json_sleep, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,346 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,346 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_2, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,347 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_3, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,347 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_4, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,347 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_5, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,348 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_6, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,348 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_7, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,348 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_8, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,349 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_9, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,349 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_10, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,349 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_11, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,350 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_12, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,350 [pN:main,p:38658,tN:MainThread] Loaded tool id: empty_datasets, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,350 [pN:main,p:38658,tN:MainThread] Loaded tool id: is_of_type, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,351 [pN:main,p:38658,tN:MainThread] Loaded tool id: data_optional, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,352 [pN:main,p:38658,tN:MainThread] Loaded tool id: inputs_as_json, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,352 [pN:main,p:38658,tN:MainThread] Loaded tool id: inputs_as_json_profile, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,353 [pN:main,p:38658,tN:MainThread] Loaded tool id: inputs_as_json_with_paths, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,354 [pN:main,p:38658,tN:MainThread] Loaded tool id: inputs_as_json_with_staging_paths, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,354 [pN:main,p:38658,tN:MainThread] Loaded tool id: filter_multiple_splitter, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,355 [pN:main,p:38658,tN:MainThread] Loaded tool id: filter_param_value, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,355 [pN:main,p:38658,tN:MainThread] Loaded tool id: filter_param_value_ref_attribute, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,356 [pN:main,p:38658,tN:MainThread] Loaded tool id: filter_static_regexp, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,357 [pN:main,p:38658,tN:MainThread] Loaded tool id: select_from_dataset, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,358 [pN:main,p:38658,tN:MainThread] Loaded tool id: select_from_csvdataset, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,358 [pN:main,p:38658,tN:MainThread] Loaded tool id: select_from_dataset_optional, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,359 [pN:main,p:38658,tN:MainThread] Loaded tool id: drill_down, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,360 [pN:main,p:38658,tN:MainThread] Loaded tool id: dbkey_filter_input, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,360 [pN:main,p:38658,tN:MainThread] Loaded tool id: dbkey_filter_multi_input, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,361 [pN:main,p:38658,tN:MainThread] Loaded tool id: dbkey_filter_collection_input, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,361 [pN:main,p:38658,tN:MainThread] Loaded tool id: dbkey_output_action, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,362 [pN:main,p:38658,tN:MainThread] Loaded tool id: composite_output, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,362 [pN:main,p:38658,tN:MainThread] Loaded tool id: composite_output_tests, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,363 [pN:main,p:38658,tN:MainThread] Loaded tool id: unicode_stream, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,363 [pN:main,p:38658,tN:MainThread] Loaded tool id: vcf_bgzip_test, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,364 [pN:main,p:38658,tN:MainThread] Loaded tool id: metadata, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,364 [pN:main,p:38658,tN:MainThread] Loaded tool id: metadata_bam, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,365 [pN:main,p:38658,tN:MainThread] Loaded tool id: discover_metadata_files, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,365 [pN:main,p:38658,tN:MainThread] Loaded tool id: metadata_bcf, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,366 [pN:main,p:38658,tN:MainThread] Loaded tool id: metadata_bed, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,366 [pN:main,p:38658,tN:MainThread] Loaded tool id: metadata_biom1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,367 [pN:main,p:38658,tN:MainThread] Loaded tool id: metadata_check_eq, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,367 [pN:main,p:38658,tN:MainThread] Loaded tool id: metadata_columns, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,368 [pN:main,p:38658,tN:MainThread] Loaded tool id: strict_shell, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,368 [pN:main,p:38658,tN:MainThread] Loaded tool id: strict_shell_default_off, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,369 [pN:main,p:38658,tN:MainThread] Loaded tool id: strict_shell_profile, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,370 [pN:main,p:38658,tN:MainThread] Loaded tool id: detect_errors, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,370 [pN:main,p:38658,tN:MainThread] Loaded tool id: detect_errors_aggressive, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,371 [pN:main,p:38658,tN:MainThread] Loaded tool id: qc_stdout, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,371 [pN:main,p:38658,tN:MainThread] Loaded tool id: directory_uri, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,372 [pN:main,p:38658,tN:MainThread] Loaded tool id: md5sum, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,372 [pN:main,p:38658,tN:MainThread] Loaded tool id: checksum, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,373 [pN:main,p:38658,tN:MainThread] Loaded tool id: sim_size_delta, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,373 [pN:main,p:38658,tN:MainThread] Loaded tool id: shapefile_composite, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,374 [pN:main,p:38658,tN:MainThread] Loaded tool id: is_valid_xml, version: 0.001 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,375 [pN:main,p:38658,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,378 [pN:main,p:38658,tN:MainThread] Loaded tool id: pick_value, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,379 [pN:main,p:38658,tN:MainThread] Loaded tool id: job_properties, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,380 [pN:main,p:38658,tN:MainThread] Loaded tool id: job_environment_default, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,380 [pN:main,p:38658,tN:MainThread] Loaded tool id: job_environment_default_legacy, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,381 [pN:main,p:38658,tN:MainThread] Loaded tool id: job_environment_explicit_shared_home, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,381 [pN:main,p:38658,tN:MainThread] Loaded tool id: job_environment_explicit_isolated_home, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base ERROR 2024-02-21 12:20:46,381 [pN:main,p:38658,tN:MainThread] Error reading tool configuration file from path 'galaxy_slots_and_memory.xml': [Errno 2] No such file or directory
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,382 [pN:main,p:38658,tN:MainThread] Loaded tool id: version_command_plain, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,383 [pN:main,p:38658,tN:MainThread] Loaded tool id: version_command_interpreter, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,383 [pN:main,p:38658,tN:MainThread] Loaded tool id: version_command_tool_dir, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,387 [pN:main,p:38658,tN:MainThread] Loaded tool id: exit_code_oom, version: 0.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,388 [pN:main,p:38658,tN:MainThread] Loaded tool id: exit_code_from_file, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,389 [pN:main,p:38658,tN:MainThread] Loaded tool id: exit_code_from_env, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,390 [pN:main,p:38658,tN:MainThread] Loaded tool id: gzipped_inputs, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,390 [pN:main,p:38658,tN:MainThread] Loaded tool id: options_from_metadata_file, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,391 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_order, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,392 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_format, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,392 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_format_deprecated_when, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,392 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_format_collection, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,393 [pN:main,p:38658,tN:MainThread] Loaded tool id: format_source_in_conditional, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,394 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_filter, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,394 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_empty_work_dir, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,395 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_filter_with_input, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,395 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_filter_with_input_optional, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,396 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_filter_exception_1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,397 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_collection_filter, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,397 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_auto_format, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,398 [pN:main,p:38658,tN:MainThread] Loaded tool id: create_2, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,398 [pN:main,p:38658,tN:MainThread] Loaded tool id: create_10, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,399 [pN:main,p:38658,tN:MainThread] Loaded tool id: disambiguate_repeats, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,400 [pN:main,p:38658,tN:MainThread] Loaded tool id: min_repeat, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,401 [pN:main,p:38658,tN:MainThread] Loaded tool id: parallelism, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,401 [pN:main,p:38658,tN:MainThread] Loaded tool id: parallelism_optional, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,402 [pN:main,p:38658,tN:MainThread] Loaded tool id: implicit_default_conds, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,403 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_data_param, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,403 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_data_repeat, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,403 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_data_optional, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,403 [pN:main,p:38658,tN:MainThread] Loaded tool id: paths_as_file, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,403 [pN:main,p:38658,tN:MainThread] Loaded tool id: param_text_option, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,404 [pN:main,p:38658,tN:MainThread] Loaded tool id: column_param, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,404 [pN:main,p:38658,tN:MainThread] Loaded tool id: column_param_configfile, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,405 [pN:main,p:38658,tN:MainThread] Loaded tool id: column_param_list, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,407 [pN:main,p:38658,tN:MainThread] Loaded tool id: column_multi_param, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,410 [pN:main,p:38658,tN:MainThread] Loaded tool id: select_optional, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,411 [pN:main,p:38658,tN:MainThread] Loaded tool id: hidden_param, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,412 [pN:main,p:38658,tN:MainThread] Loaded tool id: special_params, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,412 [pN:main,p:38658,tN:MainThread] Loaded tool id: section, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,414 [pN:main,p:38658,tN:MainThread] Loaded tool id: test_sam_to_bam_conversions, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,415 [pN:main,p:38658,tN:MainThread] Loaded tool id: top_level_data, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,416 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_hdf5, version: 1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,416 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_zip, version: 1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,417 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_tar, version: 1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,418 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_tar_gz, version: 1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,418 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_default, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,419 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_sanitizer, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,419 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_repeat, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,420 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_metadata_in_range, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,421 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_metadata_in_datatable, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,422 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_dataset_metadata_in_file, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,422 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_value_in_datatable, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,423 [pN:main,p:38658,tN:MainThread] Loaded tool id: empty_output, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,423 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_empty_dataset, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,424 [pN:main,p:38658,tN:MainThread] Loaded tool id: implicit_conversion, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,424 [pN:main,p:38658,tN:MainThread] Loaded tool id: implicit_conversion_format_input, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,425 [pN:main,p:38658,tN:MainThread] Loaded tool id: implicit_conversion_optional_param, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,425 [pN:main,p:38658,tN:MainThread] Loaded tool id: implicit_collection_conversion, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,426 [pN:main,p:38658,tN:MainThread] Loaded tool id: implicit_nested_collection_conversion, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,426 [pN:main,p:38658,tN:MainThread] Loaded tool id: explicit_conversion, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,427 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_source, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,427 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_single, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,427 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_single_in_repeat, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,428 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_in_conditional, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,428 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_multiple, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,429 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_multiple_in_conditional, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,429 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_multiple_in_repeat, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,430 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_collection, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,430 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_all_collection_types, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,431 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_in_actions, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,431 [pN:main,p:38658,tN:MainThread] Loaded tool id: fail_identifier, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,431 [pN:main,p:38658,tN:MainThread] Loaded tool id: fail_writing_work_dir_file, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,432 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_directory, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,432 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_directory_docker, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,433 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_action_change_format, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,433 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_action_change_format_paired, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,434 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_paired_test, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,434 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_paired_default, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,434 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_paired_structured_like, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,435 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_paired_conditional_structured_like, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,435 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_nested_test, version: 0.1.0 into tool panel..
py.warnings WARNING 2024-02-21 12:20:46,436 [pN:main,p:38658,tN:MainThread] /Users/mvandenb/src/galaxy/lib/galaxy/tool_util/parser/xml.py:1310: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
if subcollection_elem:
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,437 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_nested_default, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,437 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_mixed_param, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,438 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_two_paired, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,439 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_pair, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,440 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_pair_format, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,440 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_pair_from_type, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,440 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_pair_from_work_dir, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,441 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_list, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,441 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_list_2, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,442 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_list_of_pairs, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,443 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_optional_param, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,443 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_split_on_column, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,444 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_dynamic_nested, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,445 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_dynamic_nested_from_json, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,445 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_dynamic_nested_from_json_elements, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,446 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_dynamic_list_of_pairs, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,447 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_type_source, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,447 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_type_source_map_over, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,447 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_list_fail, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,448 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_dynamic_nested_fail, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,448 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_cat_group_tag, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,448 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_cat_group_tag_multiple, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,449 [pN:main,p:38658,tN:MainThread] Loaded tool id: discover_sort_by, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,450 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_forty_two, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,450 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_pick_larger_file, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,450 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_parse_int, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,451 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_log_line_count, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,451 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_null_handling_boolean, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,451 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_null_handling_integer, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,452 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_null_handling_float, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,452 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_null_handling_text, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,453 [pN:main,p:38658,tN:MainThread] Loaded tool id: cheetah_casting, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,453 [pN:main,p:38658,tN:MainThread] Loaded tool id: cheetah_problem_unbound_var, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,454 [pN:main,p:38658,tN:MainThread] Loaded tool id: cheetah_problem_unbound_var_input, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,454 [pN:main,p:38658,tN:MainThread] Loaded tool id: cheetah_problem_syntax_error, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,454 [pN:main,p:38658,tN:MainThread] Loaded tool id: model_attributes, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,455 [pN:main,p:38658,tN:MainThread] Loaded tool id: python_environment_problem, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,455 [pN:main,p:38658,tN:MainThread] Loaded tool id: config_vars, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,458 [pN:main,p:38658,tN:MainThread] Loaded tool id: expect_num_outputs, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,458 [pN:main,p:38658,tN:MainThread] Loaded tool id: text_repeat, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,459 [pN:main,p:38658,tN:MainThread] Loaded tool id: integer_default, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,459 [pN:main,p:38658,tN:MainThread] Loaded tool id: multiple_versions, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,460 [pN:main,p:38658,tN:MainThread] Loaded tool id: multiple_versions_changes, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base ERROR 2024-02-21 12:20:46,461 [pN:main,p:38658,tN:MainThread] Error reading tool from path: interactivetool_simple.xml
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 873, in _load_tool_tag_set
tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 1100, in load_tool
tool = self.create_tool(
^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 547, in create_tool
return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 563, in _create_tool_from_source
return create_tool_from_source(self.app, tool_source, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 355, in create_tool_from_source
tool = ToolClass(config_file, tool_source, app, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 3070, in __init__
assert app.config.interactivetools_enable, ValueError(
AssertionError: Trying to load an InteractiveTool, but InteractiveTools are not enabled.
galaxy.tool_util.toolbox.base ERROR 2024-02-21 12:20:46,461 [pN:main,p:38658,tN:MainThread] Error reading tool from path: interactivetool_two_entry_points.xml
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 873, in _load_tool_tag_set
tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 1100, in load_tool
tool = self.create_tool(
^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 547, in create_tool
return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 563, in _create_tool_from_source
return create_tool_from_source(self.app, tool_source, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 355, in create_tool_from_source
tool = ToolClass(config_file, tool_source, app, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 3070, in __init__
assert app.config.interactivetools_enable, ValueError(
AssertionError: Trying to load an InteractiveTool, but InteractiveTools are not enabled.
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,462 [pN:main,p:38658,tN:MainThread] Loaded tool id: test_CONVERTER_biom, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,462 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,463 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat_list, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,463 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat_default, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,464 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat_collection, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,464 [pN:main,p:38658,tN:MainThread] Loaded tool id: head, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,464 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat_interleave, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,464 [pN:main,p:38658,tN:MainThread] Loaded tool id: pileup, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,465 [pN:main,p:38658,tN:MainThread] Loaded tool id: mapper, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,465 [pN:main,p:38658,tN:MainThread] Loaded tool id: mapper2, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,466 [pN:main,p:38658,tN:MainThread] Loaded tool id: mapper_two, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,466 [pN:main,p:38658,tN:MainThread] Loaded tool id: split, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,466 [pN:main,p:38658,tN:MainThread] Loaded tool id: empty_list, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,467 [pN:main,p:38658,tN:MainThread] Loaded tool id: count_list, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,467 [pN:main,p:38658,tN:MainThread] Loaded tool id: count_multi_file, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,468 [pN:main,p:38658,tN:MainThread] Loaded tool id: create_input_collection, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base ERROR 2024-02-21 12:20:46,468 [pN:main,p:38658,tN:MainThread] Error reading tool configuration file from path 'for_workflows/randomlines.xml': [Errno 2] No such file or directory
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,468 [pN:main,p:38658,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,469 [pN:main,p:38658,tN:MainThread] Loaded tool id: legacy_R, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,469 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_multi_1, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,470 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_multi_versionless, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,470 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_multi_incomplete, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,471 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_conflict, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,471 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_simple, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,472 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_explicit, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,472 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_invalid_case, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,472 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_broken_no_requirements, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,472 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_broken_no_requirements_fallback, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,473 [pN:main,p:38658,tN:MainThread] Loaded tool id: explicit_container, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,473 [pN:main,p:38658,tN:MainThread] Loaded tool id: explicit_singularity_container, version: 0.1.0 into tool panel..
galaxy.tool_util.parser.factory INFO 2024-02-21 12:20:46,473 [pN:main,p:38658,tN:MainThread] Loading tool from YAML - this is experimental - tool will not function in future.
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,474 [pN:main,p:38658,tN:MainThread] Loaded tool id: simple_constructs_y, version: 1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,475 [pN:main,p:38658,tN:MainThread] Loaded tool id: from_work_dir_glob, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,475 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat_data_and_sleep, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,475 [pN:main,p:38658,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,476 [pN:main,p:38658,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,476 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,476 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,476 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,476 [pN:main,p:38658,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,476 [pN:main,p:38658,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,476 [pN:main,p:38658,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,476 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,476 [pN:main,p:38658,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,476 [pN:main,p:38658,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,477 [pN:main,p:38658,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.2.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,477 [pN:main,p:38658,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,477 [pN:main,p:38658,tN:MainThread] Loaded tool id: __DUPLICATE_FILE_TO_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base INFO 2024-02-21 12:20:46,477 [pN:main,p:38658,tN:MainThread] Parsing the tool configuration /Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/shed_tool_conf.xml
galaxy.tool_util.toolbox.base INFO 2024-02-21 12:20:46,477 [pN:main,p:38658,tN:MainThread] Shed-enabled tool configuration file does not exist, but will be created on demand: /Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/shed_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,478 [pN:main,p:38658,tN:MainThread] Reading tools from config files finished (236.000 ms)
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,479 [pN:main,p:38658,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,479 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,479 [pN:main,p:38658,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,479 [pN:main,p:38658,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,480 [pN:main,p:38658,tN:MainThread] Loaded tool id: ncbi_datasets_source, version: 13.14.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,480 [pN:main,p:38658,tN:MainThread] Loaded tool id: sra_source, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: send_to_cloud, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,481 [pN:main,p:38658,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,482 [pN:main,p:38658,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,483 [pN:main,p:38658,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,483 [pN:main,p:38658,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,483 [pN:main,p:38658,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,483 [pN:main,p:38658,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,483 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,483 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,483 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,483 [pN:main,p:38658,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.views.edam DEBUG 2024-02-21 12:20:46,484 [pN:main,p:38658,tN:MainThread] Loading EDAM tool panel finished (6.394 ms)
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: ncbi_datasets_source, version: 13.14.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: sra_source, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,485 [pN:main,p:38658,tN:MainThread] Loaded tool id: send_to_cloud, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,486 [pN:main,p:38658,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:46,487 [pN:main,p:38658,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.views.edam DEBUG 2024-02-21 12:20:46,489 [pN:main,p:38658,tN:MainThread] Loading EDAM tool panel finished (4.269 ms)
galaxy.tool_util.deps WARNING 2024-02-21 12:20:46,489 [pN:main,p:38658,tN:MainThread] Path '/Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/tmpo1ompzky/database/dependencies' does not exist, ignoring
galaxy.tool_util.deps WARNING 2024-02-21 12:20:46,489 [pN:main,p:38658,tN:MainThread] Path '/Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/tmpo1ompzky/database/dependencies' is not directory, ignoring
galaxy.tool_util.deps.installable WARNING 2024-02-21 12:20:46,501 [pN:main,p:38658,tN:MainThread] Conda not installed and auto-installation disabled.
galaxy.tool_util.deps.installable WARNING 2024-02-21 12:20:46,502 [pN:main,p:38658,tN:MainThread] Conda not installed and auto-installation disabled.
galaxy.tool_util.deps.mulled.mulled_build ERROR 2024-02-21 12:20:46,553 [pN:main,p:38658,tN:MainThread] Failed to download involucro from url 'https://github.com/mvdbeek/involucro/releases/download/v1.1.2/involucro.darwin'
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 715, in urlopen
httplib_response = self._make_request(
^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 404, in _make_request
self._validate_conn(conn)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 1058, in _validate_conn
conn.connect()
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connection.py", line 419, in connect
self.sock = ssl_wrap_socket(
^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/util/ssl_.py", line 449, in ssl_wrap_socket
ssl_sock = _ssl_wrap_socket_impl(
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/util/ssl_.py", line 493, in _ssl_wrap_socket_impl
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 517, in wrap_socket
return self.sslsocket_class._create(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1108, in _create
self.do_handshake()
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1383, in do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/adapters.py", line 486, in send
resp = conn.urlopen(
^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 799, in urlopen
retries = retries.increment(
^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/util/retry.py", line 592, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /mvdbeek/involucro/releases/download/v1.1.2/involucro.darwin (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)')))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/deps/mulled/mulled_build.py", line 445, in install_involucro
download_to_file(involucro_link(), install_path)
File "/Users/mvandenb/src/galaxy/lib/galaxy/util/__init__.py", line 1842, in download_to_file
with requests.get(url, timeout=timeout, stream=True) as r, open(dest_file_path, "wb") as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, **send_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/adapters.py", line 517, in send
raise SSLError(e, request=request)
requests.exceptions.SSLError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /mvdbeek/involucro/releases/download/v1.1.2/involucro.darwin (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)')))
galaxy.tool_util.deps.installable WARNING 2024-02-21 12:20:46,559 [pN:main,p:38658,tN:MainThread] Involucro installation requested and failed.
galaxy.tool_util.deps.mulled.mulled_build ERROR 2024-02-21 12:20:46,603 [pN:main,p:38658,tN:MainThread] Failed to download involucro from url 'https://github.com/mvdbeek/involucro/releases/download/v1.1.2/involucro.darwin'
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 715, in urlopen
httplib_response = self._make_request(
^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 404, in _make_request
self._validate_conn(conn)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 1058, in _validate_conn
conn.connect()
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connection.py", line 419, in connect
self.sock = ssl_wrap_socket(
^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/util/ssl_.py", line 449, in ssl_wrap_socket
ssl_sock = _ssl_wrap_socket_impl(
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/util/ssl_.py", line 493, in _ssl_wrap_socket_impl
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 517, in wrap_socket
return self.sslsocket_class._create(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1108, in _create
self.do_handshake()
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1383, in do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/adapters.py", line 486, in send
resp = conn.urlopen(
^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 799, in urlopen
retries = retries.increment(
^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/util/retry.py", line 592, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /mvdbeek/involucro/releases/download/v1.1.2/involucro.darwin (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)')))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/deps/mulled/mulled_build.py", line 445, in install_involucro
download_to_file(involucro_link(), install_path)
File "/Users/mvandenb/src/galaxy/lib/galaxy/util/__init__.py", line 1842, in download_to_file
with requests.get(url, timeout=timeout, stream=True) as r, open(dest_file_path, "wb") as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, **send_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/adapters.py", line 517, in send
raise SSLError(e, request=request)
requests.exceptions.SSLError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /mvdbeek/involucro/releases/download/v1.1.2/involucro.darwin (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)')))
galaxy.tool_util.deps.installable WARNING 2024-02-21 12:20:46,604 [pN:main,p:38658,tN:MainThread] Involucro installation requested and failed.
galaxy.tools.search WARNING 2024-02-21 12:20:46,605 [pN:main,p:38658,tN:MainThread] Index at '/Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/tmpo1ompzky/database/tool_search_index/default' uses outdated schema, creating a new index
galaxy.tools.search WARNING 2024-02-21 12:20:46,606 [pN:main,p:38658,tN:MainThread] Index at '/Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/tmpo1ompzky/database/tool_search_index/ontology:edam_operations' uses outdated schema, creating a new index
galaxy.tools.search WARNING 2024-02-21 12:20:46,607 [pN:main,p:38658,tN:MainThread] Index at '/Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/tmpo1ompzky/database/tool_search_index/ontology:edam_topics' uses outdated schema, creating a new index
galaxy.tools.data_manager.manager DEBUG 2024-02-21 12:20:46,609 [pN:main,p:38658,tN:MainThread] Loaded Data Manager: test_data_manager
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,610 [pN:main,p:38658,tN:MainThread] Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,611 [pN:main,p:38658,tN:MainThread] Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,614 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,614 [pN:main,p:38658,tN:MainThread] Loaded display application 'igb_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,614 [pN:main,p:38658,tN:MainThread] Loaded display application 'iobio_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,614 [pN:main,p:38658,tN:MainThread] Loaded display application 'igb_bed' for datatype 'bed', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,615 [pN:main,p:38658,tN:MainThread] Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,615 [pN:main,p:38658,tN:MainThread] Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,615 [pN:main,p:38658,tN:MainThread] Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,616 [pN:main,p:38658,tN:MainThread] Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,616 [pN:main,p:38658,tN:MainThread] Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,616 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,616 [pN:main,p:38658,tN:MainThread] Loaded display application 'intermine_simple' for datatype 'intermine_tabular', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,618 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,619 [pN:main,p:38658,tN:MainThread] Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,620 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_gff' for datatype 'gff', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,620 [pN:main,p:38658,tN:MainThread] Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,621 [pN:main,p:38658,tN:MainThread] Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,621 [pN:main,p:38658,tN:MainThread] Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,621 [pN:main,p:38658,tN:MainThread] Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,625 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,625 [pN:main,p:38658,tN:MainThread] Loaded display application 'avivator' for datatype 'ome.tiff', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,625 [pN:main,p:38658,tN:MainThread] Loaded display application 'q2view' for datatype 'qza', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,625 [pN:main,p:38658,tN:MainThread] Loaded display application 'q2view' for datatype 'qzv', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,626 [pN:main,p:38658,tN:MainThread] Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,626 [pN:main,p:38658,tN:MainThread] Loaded display application 'minerva_tabular' for datatype 'tabular', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,627 [pN:main,p:38658,tN:MainThread] Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,631 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,632 [pN:main,p:38658,tN:MainThread] Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,632 [pN:main,p:38658,tN:MainThread] Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,632 [pN:main,p:38658,tN:MainThread] Loaded display application 'igb_wig' for datatype 'wig', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,637 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,639 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_genbank' for datatype 'genbank', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Loaded display application 'biom_simple' for datatype 'biom1', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'sdf', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'mol2', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'pdb', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,640 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,643 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,643 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,643 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,643 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,643 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,643 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,643 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,643 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,643 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,643 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,643 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'probed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,644 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'probed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,644 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'probed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,644 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'probed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,644 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,644 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,644 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,644 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,644 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'fasta.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,644 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'a3m'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,644 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,645 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,645 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,645 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,645 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.bz2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,645 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.bz2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,645 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,645 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,645 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'sequences'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'interval_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'interval_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'interval_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'interval_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'juicer_medium_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'juicer_medium_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'juicer_medium_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'juicer_medium_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'gff_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'gff_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'gff_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'gff_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,646 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'mothur.align'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,648 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,648 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,649 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,649 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,649 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,649 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,651 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_Bam_Bai_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,652 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,653 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,653 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,654 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,654 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,654 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_cram_to_bam_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,655 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_to_gff_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,656 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,657 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,657 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,657 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_to_fli_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,658 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bedgraph_to_bigwig
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,658 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_len_to_linecount
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,659 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_parquet_to_csv
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,660 [pN:main,p:38658,tN:MainThread] Loaded converter: bigwigtowig
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,661 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,661 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,662 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,662 [pN:main,p:38658,tN:MainThread] Loaded converter: csv_to_tabular
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,663 [pN:main,p:38658,tN:MainThread] Loaded converter: tabular_to_csv
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,663 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fasta_to_tabular
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,663 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_base_index
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,664 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_color_index
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,664 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fasta_to_2bit
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,664 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fasta_to_len
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,665 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fasta_to_fai
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,665 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,666 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,666 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,666 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,667 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,667 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,667 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,668 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,668 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,668 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,669 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,669 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,669 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,670 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,670 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,670 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,671 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,671 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,671 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,672 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,672 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,672 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,673 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gff_to_bed_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,673 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,673 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,674 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gff_to_fli_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,674 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,675 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,675 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,676 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,676 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,677 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,677 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,678 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,679 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bedstrict_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,679 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed6_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,680 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed12_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,680 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,681 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,682 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,682 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_picard_interval_list_to_bed6
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,682 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_tar_to_directory
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,683 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,683 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,684 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,684 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,684 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,685 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,685 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_maf_to_fasta_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,685 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_maf_to_interval_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,686 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,687 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,687 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,687 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,688 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,688 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_sam_to_unsorted_bam
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,689 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,689 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,689 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_sam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,690 [pN:main,p:38658,tN:MainThread] Loaded converter: tabular_to_dbnsfp
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,690 [pN:main,p:38658,tN:MainThread] Loaded converter: tabular_to_csv
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,690 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,691 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,692 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,692 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,693 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,693 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,694 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,694 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,694 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,695 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_wig_to_bigwig
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,695 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_wiggle_to_interval_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,696 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,696 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,696 [pN:main,p:38658,tN:MainThread] Loaded converter: lped2fpedconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,696 [pN:main,p:38658,tN:MainThread] Loaded converter: lped2pbedconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,697 [pN:main,p:38658,tN:MainThread] Loaded converter: pbed2lpedconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,697 [pN:main,p:38658,tN:MainThread] Loaded converter: pbed2ldindepconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,699 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,699 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,700 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_biom
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,700 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_biom
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,702 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,703 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,706 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,707 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_SMILES_to_MOL
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,709 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,710 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_smiles_to_smiles
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,712 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,715 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,717 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,718 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,720 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,721 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,722 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_inchi_to_mol
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,724 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,726 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,727 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,730 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,733 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,736 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,738 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,741 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,744 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,746 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,746 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_mol2_to_mol
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,749 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,750 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_cml_to_smiles
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,751 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,753 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,754 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,755 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_Pdb_to_Gro_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,755 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,756 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,756 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,757 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,758 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,758 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,758 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_Gro_to_Pdb_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,759 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_ref_to_seq_taxomony
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,759 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_neostorezip_to_neostore
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:46,762 [pN:main,p:38658,tN:MainThread] Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2024-02-21 12:20:46,764 [pN:main,p:38658,tN:MainThread] Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2024-02-21 12:20:46,765 [pN:main,p:38658,tN:MainThread] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__
galaxy.tools.special_tools DEBUG 2024-02-21 12:20:46,765 [pN:main,p:38658,tN:MainThread] Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2024-02-21 12:20:46,766 [pN:main,p:38658,tN:MainThread] Loaded data fetch tool: __DATA_FETCH__
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,767 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: PCA_3Dplot
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,768 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,768 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:46,769 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,769 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:46,784 [pN:main,p:38658,tN:MainThread] Visualizations plugin disabled: Circster. Skipping...
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:46,785 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,785 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: csg
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,786 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,787 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,788 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: editor
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,789 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: example
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:46,798 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,798 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: fits_image_viewer
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:46,820 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,820 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,821 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: h5web
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,825 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,826 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_default
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:46,826 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,826 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:46,826 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,827 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,830 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,831 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,832 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,833 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,834 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:46,834 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,834 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: audio_player
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:46,835 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,835 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: video_player
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,835 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: msa
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:46,837 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,837 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,839 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,840 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nora
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,843 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,846 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,847 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,848 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,848 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,849 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,850 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,850 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,851 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,852 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,852 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,853 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,854 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,854 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,857 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,858 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,861 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: phyloviz
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,862 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: pv
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,863 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:46,863 [pN:main,p:38658,tN:MainThread] Visualizations plugin disabled: Sweepster. Skipping...
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,864 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,864 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: ts_visjs
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:46,864 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,864 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:46,865 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: venn
galaxy.tours._impl INFO 2024-02-21 12:20:46,873 [pN:main,p:38658,tN:MainThread] Loaded tour 'core.galaxy_ui'
galaxy.tours._impl INFO 2024-02-21 12:20:46,878 [pN:main,p:38658,tN:MainThread] Loaded tour 'core.deferred'
galaxy.tours._impl INFO 2024-02-21 12:20:46,880 [pN:main,p:38658,tN:MainThread] Loaded tour 'core.windows'
galaxy.tours._impl INFO 2024-02-21 12:20:46,883 [pN:main,p:38658,tN:MainThread] Loaded tour 'core.history'
galaxy.jobs.manager DEBUG 2024-02-21 12:20:46,918 [pN:main,p:38658,tN:MainThread] Initializing job handler
galaxy.jobs INFO 2024-02-21 12:20:46,918 [pN:main,p:38658,tN:MainThread] Handler 'main' will load all configured runner plugins
galaxy.jobs.runners.state_handler_factory DEBUG 2024-02-21 12:20:46,928 [pN:main,p:38658,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs DEBUG 2024-02-21 12:20:46,928 [pN:main,p:38658,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
galaxy.jobs.runners.state_handler_factory DEBUG 2024-02-21 12:20:46,930 [pN:main,p:38658,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs.runners DEBUG 2024-02-21 12:20:46,930 [pN:main,p:38658,tN:MainThread] Starting 4 TaskRunner workers
galaxy.jobs DEBUG 2024-02-21 12:20:46,930 [pN:main,p:38658,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks'
galaxy.jobs.handler DEBUG 2024-02-21 12:20:46,930 [pN:main,p:38658,tN:MainThread] Loaded job runners plugins: local:tasks
galaxy.jobs.runners DEBUG 2024-02-21 12:20:46,943 [pN:main,p:38658,tN:MainThread] Starting 4 LocalRunner workers
galaxy.jobs.runners DEBUG 2024-02-21 12:20:46,944 [pN:main,p:38658,tN:MainThread] Starting 4 TaskRunner workers
galaxy.jobs.handler DEBUG 2024-02-21 12:20:46,944 [pN:main,p:38658,tN:MainThread] Handler queue starting for jobs assigned to handler: main
galaxy.jobs.handler INFO 2024-02-21 12:20:46,983 [pN:main,p:38658,tN:JobHandlerQueue.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method for handler 'main', tag(s):
galaxy.jobs.handler INFO 2024-02-21 12:20:46,983 [pN:main,p:38658,tN:MainThread] job handler queue started
galaxy.jobs.handler INFO 2024-02-21 12:20:46,984 [pN:main,p:38658,tN:MainThread] job handler stop queue started
galaxy.workflow.scheduling_manager INFO 2024-02-21 12:20:47,020 [pN:main,p:38658,tN:MainThread] No workflow schedulers plugin config file defined, using default scheduler.
galaxy.web_stack.handlers INFO 2024-02-21 12:20:47,020 [pN:main,p:38658,tN:MainThread] WorkflowSchedulingManager: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on <handlers> to override the default
galaxy.workflow.scheduling_manager DEBUG 2024-02-21 12:20:47,020 [pN:main,p:38658,tN:MainThread] Starting workflow schedulers
galaxy.jobs.handler INFO 2024-02-21 12:20:47,020 [pN:main,p:38658,tN:WorkflowRequestMonitor.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method for handler 'main', tag(s): _default_, None
galaxy.queue_worker INFO 2024-02-21 12:20:47,022 [pN:main,p:38658,tN:MainThread] Binding and starting galaxy control worker for main
galaxy.queue_worker INFO 2024-02-21 12:20:47,023 [pN:main,p:38658,tN:MainThread] Queuing async task rebuild_toolbox_search_index for main.
py.warnings WARNING 2024-02-21 12:20:47,057 [pN:main,p:38658,tN:MainThread] /Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/kombu/transport/sqlalchemy/models.py:63: RemovedIn20Warning: Deprecated API features detected! These feature(s) are not compatible with SQLAlchemy 2.0. To prevent incompatible upgrades prior to updating applications, ensure requirements files are pinned to "sqlalchemy<2.0". Set environment variable SQLALCHEMY_WARN_20=1 to show all deprecation warnings. Set environment variable SQLALCHEMY_SILENCE_UBER_WARNING=1 to silence this message. (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
self.queue = queue
galaxy.app INFO 2024-02-21 12:20:47,067 [pN:main,p:38658,tN:MainThread] Galaxy app startup finished (4178.153 ms)
test_driver INFO 2024-02-21 12:20:47,067 [pN:main,p:38658,tN:MainThread] Embedded Galaxy application started
galaxy.tools.search DEBUG 2024-02-21 12:20:47,067 [pN:main,p:38658,tN:MainThread] Starting to build toolbox index of panel default.
galaxy.queue_worker INFO 2024-02-21 12:20:47,088 [pN:main,p:38658,tN:Thread-3] Instance 'main' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.queue_worker DEBUG 2024-02-21 12:20:47,088 [pN:main,p:38658,tN:Thread-3] App is not a webapp, not building a search index
galaxy.model.database_heartbeat DEBUG 2024-02-21 12:20:47,098 [pN:main,p:38658,tN:database_heartbeart_main.thread] main is config watcher
galaxy.tools.search DEBUG 2024-02-21 12:20:47,685 [pN:main,p:38658,tN:MainThread] Toolbox index of panel default finished (617.352 ms)
galaxy.tools.search DEBUG 2024-02-21 12:20:47,689 [pN:main,p:38658,tN:MainThread] Starting to build toolbox index of panel ontology:edam_operations.
galaxy.tools.search DEBUG 2024-02-21 12:20:48,098 [pN:main,p:38658,tN:MainThread] Toolbox index of panel ontology:edam_operations finished (409.530 ms)
galaxy.tools.search DEBUG 2024-02-21 12:20:48,100 [pN:main,p:38658,tN:MainThread] Starting to build toolbox index of panel ontology:edam_topics.
galaxy.tools.search DEBUG 2024-02-21 12:20:48,433 [pN:main,p:38658,tN:MainThread] Toolbox index of panel ontology:edam_topics finished (332.911 ms)
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,439 [pN:main,p:38658,tN:MainThread] Enabling 'user' controller, class: User
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,440 [pN:main,p:38658,tN:MainThread] Enabling 'error' controller, class: Error
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,446 [pN:main,p:38658,tN:MainThread] Enabling 'page' controller, class: PageController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,449 [pN:main,p:38658,tN:MainThread] Enabling 'visualization' controller, class: VisualizationController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,499 [pN:main,p:38658,tN:MainThread] Enabling 'dataset' controller, class: DatasetInterface
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,502 [pN:main,p:38658,tN:MainThread] Enabling 'forms' controller, class: Forms
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,531 [pN:main,p:38658,tN:MainThread] Enabling 'admin' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,532 [pN:main,p:38658,tN:MainThread] Enabling 'shed_tool_static' controller, class: ShedToolStatic
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,534 [pN:main,p:38658,tN:MainThread] Enabling 'tool_runner' controller, class: ToolRunner
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,544 [pN:main,p:38658,tN:MainThread] Enabling 'admin_toolshed' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,544 [pN:main,p:38658,tN:MainThread] Enabling 'admin_toolshed' controller, class: AdminToolshed
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,554 [pN:main,p:38658,tN:MainThread] Enabling 'workflow' controller, class: WorkflowController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,556 [pN:main,p:38658,tN:MainThread] Enabling 'async' controller, class: ASync
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,558 [pN:main,p:38658,tN:MainThread] Enabling 'data_manager' controller, class: DataManager
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,559 [pN:main,p:38658,tN:MainThread] Enabling 'root' controller, class: RootController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,560 [pN:main,p:38658,tN:MainThread] Enabling 'tag' controller, class: TagsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,563 [pN:main,p:38658,tN:MainThread] Enabling 'authnz' controller, class: JSAppLauncher
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,563 [pN:main,p:38658,tN:MainThread] Enabling 'authnz' controller, class: OIDC
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,566 [pN:main,p:38658,tN:MainThread] Enabling 'history' controller, class: HistoryController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,719 [pN:main,p:38658,tN:MainThread] Enabling 'container_resolution' API controller, class: ContainerResolutionAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,728 [pN:main,p:38658,tN:MainThread] Enabling 'library_contents' API controller, class: LibraryContentsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:48,742 [pN:main,p:38658,tN:MainThread] Enabling 'plugins' API controller, class: PluginsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:49,183 [pN:main,p:38658,tN:MainThread] Enabling 'tool_entry_points' API controller, class: ToolEntryPointsAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:49,412 [pN:main,p:38658,tN:MainThread] Enabling 'users' API controller, class: UserAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:49,441 [pN:main,p:38658,tN:MainThread] Enabling 'toolshed' API controller, class: ToolShedController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:49,545 [pN:main,p:38658,tN:MainThread] Enabling 'tools' API controller, class: ToolsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:49,551 [pN:main,p:38658,tN:MainThread] Enabling 'library_datasets' API controller, class: LibraryDatasetsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:50,141 [pN:main,p:38658,tN:MainThread] Enabling 'page_revisions' API controller, class: PageRevisionsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:51,088 [pN:main,p:38658,tN:MainThread] Enabling 'forms' API controller, class: FormDefinitionAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:51,153 [pN:main,p:38658,tN:MainThread] Enabling 'visualizations' API controller, class: VisualizationsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:51,358 [pN:main,p:38658,tN:MainThread] Enabling 'jobs' API controller, class: JobController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:51,361 [pN:main,p:38658,tN:MainThread] Enabling 'job_ports' API controller, class: JobPortsAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:51,362 [pN:main,p:38658,tN:MainThread] Enabling 'trs_search' API controller, class: TrsSearchAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:51,468 [pN:main,p:38658,tN:MainThread] Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:51,504 [pN:main,p:38658,tN:MainThread] Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:51,504 [pN:main,p:38658,tN:MainThread] Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:51,505 [pN:main,p:38658,tN:MainThread] Enabling 'trs_consumer' API controller, class: TrsConsumeAPIController
py.warnings WARNING 2024-02-21 12:20:51,640 [pN:main,p:38658,tN:MainThread] /Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py:24: DeprecationWarning: Importing gxformat2._yaml is deprecated, use gxformat2.yaml instead
from gxformat2._yaml import ordered_dump
galaxy.web.framework.base DEBUG 2024-02-21 12:20:52,220 [pN:main,p:38658,tN:MainThread] Enabling 'workflows' API controller, class: WorkflowsAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:52,274 [pN:main,p:38658,tN:MainThread] Enabling 'cloudauthz' API controller, class: CloudAuthzController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:52,761 [pN:main,p:38658,tN:MainThread] Enabling 'sanitize_allow' API controller, class: SanitizeAllowController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:52,763 [pN:main,p:38658,tN:MainThread] Enabling 'job_files' API controller, class: JobFilesAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:52,768 [pN:main,p:38658,tN:MainThread] Enabling 'uploads' API controller, class: UploadsAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:52,785 [pN:main,p:38658,tN:MainThread] Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:52,786 [pN:main,p:38658,tN:MainThread] Enabling 'history_content_provenance' API controller, class: HDAProvenanceController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:52,786 [pN:main,p:38658,tN:MainThread] Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:52,786 [pN:main,p:38658,tN:MainThread] Enabling 'webhooks' API controller, class: WebhooksController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:52,796 [pN:main,p:38658,tN:MainThread] Enabling 'dynamic_tools' API controller, class: DynamicToolsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:52,850 [pN:main,p:38658,tN:MainThread] Enabling 'authenticate' API controller, class: AuthenticationController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:52,870 [pN:main,p:38658,tN:MainThread] Enabling 'history_annotations' API controller, class: HistoryAnnotationsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:52,870 [pN:main,p:38658,tN:MainThread] Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:52,870 [pN:main,p:38658,tN:MainThread] Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController
galaxy.webapps.util DEBUG 2024-02-21 12:20:53,549 [pN:main,p:38658,tN:MainThread] Enabling 'paste.httpexceptions' middleware
galaxy.webapps.util DEBUG 2024-02-21 12:20:53,549 [pN:main,p:38658,tN:MainThread] Enabling 'ErrorMiddleware' middleware
galaxy.webapps.util DEBUG 2024-02-21 12:20:53,549 [pN:main,p:38658,tN:MainThread] Enabling 'TusMiddleware' middleware
galaxy.webapps.util DEBUG 2024-02-21 12:20:53,549 [pN:main,p:38658,tN:MainThread] Enabling 'TusMiddleware' middleware
galaxy.webapps.util DEBUG 2024-02-21 12:20:53,549 [pN:main,p:38658,tN:MainThread] Enabling 'XForwardedHostMiddleware' middleware
galaxy.webapps.util DEBUG 2024-02-21 12:20:53,549 [pN:main,p:38658,tN:MainThread] Enabling 'RequestIDMiddleware' middleware
galaxy.webapps.util DEBUG 2024-02-21 12:20:53,549 [pN:main,p:38658,tN:MainThread] Enabling 'build_url_map' middleware
galaxy.web_stack INFO 2024-02-21 12:20:53,549 [pN:main,p:38658,tN:MainThread] Galaxy server instance 'main' is running
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,549 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 8003690176)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,549 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(Thread-2 (start), started daemon 6108590080)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,549 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-0, started daemon 11358203904)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,549 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-1, started daemon 11375030272)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,549 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-2, started daemon 11391856640)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,549 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-3, started daemon 11408683008)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-0, started daemon 11425509376)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-1, started daemon 11442335744)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-2, started daemon 11459162112)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-3, started daemon 11475988480)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-0, started daemon 11492814848)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-1, started daemon 11509641216)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-2, started daemon 11526467584)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-3, started daemon 11543293952)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(JobHandlerQueue.monitor_thread, started daemon 11560120320)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(JobHandlerStopQueue.monitor_thread, started daemon 11576946688)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(WorkflowRequestMonitor.monitor_thread, started daemon 11593773056)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(database_heartbeart_main.thread, started daemon 11610599424)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <GalaxyQueueWorker(Thread-3, started daemon 11627425792)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(Thread-5 (check), started daemon 11644252160)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:53,550 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(Thread-6 (check), started daemon 11661078528)> is alive.
asyncio DEBUG 2024-02-21 12:20:55,416 [pN:main,p:38658,tN:MainThread] Using selector: KqueueSelector
INFO: Started server process [38658]
INFO: Waiting for application startup.
INFO: Application startup complete.
INFO: Uvicorn running on http://127.0.0.1:9500 (Press CTRL+C to quit)
INFO: 127.0.0.1:52129 - "GET / HTTP/1.1" 200 OK
test_driver DEBUG 2024-02-21 12:20:55,997 [pN:main,p:38658,tN:MainThread] Embedded uvicorn web server for galaxy started at 127.0.0.1:9500/
test_driver INFO 2024-02-21 12:20:55,998 [pN:main,p:38658,tN:MainThread] 23 threads were active before stopping embedded server
test_driver INFO 2024-02-21 12:20:55,998 [pN:main,p:38658,tN:MainThread] Shutting down embedded galaxy uvicorn server
test_driver INFO 2024-02-21 12:20:55,998 [pN:main,p:38658,tN:MainThread] Embedded web server galaxy stopped
test_driver INFO 2024-02-21 12:20:55,998 [pN:main,p:38658,tN:MainThread] Stopping embedded server thread
INFO: Shutting down
INFO: Waiting for application shutdown.
INFO: Application shutdown complete.
INFO: Finished server process [38658]
test_driver INFO 2024-02-21 12:20:56,171 [pN:main,p:38658,tN:Thread-9 (run_in_loop)] Event loop for uvicorn closed
test_driver INFO 2024-02-21 12:20:56,171 [pN:main,p:38658,tN:MainThread] Embedded server thread stopped
test_driver INFO 2024-02-21 12:20:56,171 [pN:main,p:38658,tN:MainThread] Stopping application galaxy
galaxy.queue_worker INFO 2024-02-21 12:20:56,999 [pN:main,p:38658,tN:MainThread] Sending reconfigure_watcher control task.
galaxy.util.monitors DEBUG 2024-02-21 12:20:57,003 [pN:main,p:38658,tN:MainThread] Joining monitor thread
galaxy.jobs.handler INFO 2024-02-21 12:20:57,003 [pN:main,p:38658,tN:MainThread] sending stop signal to worker thread
galaxy.util.monitors DEBUG 2024-02-21 12:20:57,003 [pN:main,p:38658,tN:MainThread] Joining monitor thread
galaxy.jobs.handler INFO 2024-02-21 12:20:57,004 [pN:main,p:38658,tN:MainThread] job handler queue stopped
galaxy.jobs.runners INFO 2024-02-21 12:20:57,004 [pN:main,p:38658,tN:MainThread] LocalRunner: Sending stop signal to 4 job worker threads
galaxy.jobs.runners INFO 2024-02-21 12:20:57,004 [pN:main,p:38658,tN:MainThread] Waiting up to 5 seconds for job worker threads to shutdown...
galaxy.jobs.runners DEBUG 2024-02-21 12:20:57,004 [pN:main,p:38658,tN:MainThread] Job worker thread terminated: LocalRunner.work_thread-0
galaxy.jobs.runners INFO 2024-02-21 12:20:57,004 [pN:main,p:38658,tN:MainThread] All job worker threads shutdown cleanly
galaxy.jobs.runners INFO 2024-02-21 12:20:57,004 [pN:main,p:38658,tN:MainThread] TaskRunner: Sending stop signal to 4 job worker threads
galaxy.jobs.runners INFO 2024-02-21 12:20:57,004 [pN:main,p:38658,tN:MainThread] Waiting up to 5 seconds for job worker threads to shutdown...
galaxy.jobs.runners DEBUG 2024-02-21 12:20:57,004 [pN:main,p:38658,tN:MainThread] Job worker thread terminated: TaskRunner.work_thread-0
galaxy.jobs.runners DEBUG 2024-02-21 12:20:57,133 [pN:main,p:38658,tN:MainThread] Job worker thread terminated: TaskRunner.work_thread-2
galaxy.jobs.runners INFO 2024-02-21 12:20:57,134 [pN:main,p:38658,tN:MainThread] All job worker threads shutdown cleanly
galaxy.jobs.handler INFO 2024-02-21 12:20:57,134 [pN:main,p:38658,tN:MainThread] sending stop signal to worker thread
galaxy.util.monitors DEBUG 2024-02-21 12:20:57,134 [pN:main,p:38658,tN:MainThread] Joining monitor thread
galaxy.jobs.handler INFO 2024-02-21 12:20:57,134 [pN:main,p:38658,tN:MainThread] job handler stop queue stopped
test_driver INFO 2024-02-21 12:20:57,135 [pN:main,p:38658,tN:MainThread] Application galaxy stopped.
test_driver INFO 2024-02-21 12:20:57,135 [pN:main,p:38658,tN:MainThread] 2 active after stopping embedded server
test_driver DEBUG 2024-02-21 12:20:57,135 [pN:main,p:38658,tN:MainThread] After stopping all servers thread <_MainThread(MainThread, started 8003690176)> is alive.
test_driver DEBUG 2024-02-21 12:20:57,135 [pN:main,p:38658,tN:MainThread] After stopping all servers thread <Thread(Thread-2 (start), started daemon 6108590080)> is alive.
test_driver INFO 2024-02-21 12:20:57,135 [pN:main,p:38658,tN:MainThread] Galaxy database connection: postgresql://postgres:postgres@localhost:5555/gxtestYSQZLKSQPI?client_encoding=utf8
galaxy.app DEBUG 2024-02-21 12:20:57,136 [pN:main,p:38658,tN:MainThread] python path is: /Users/mvandenb/src/galaxy/test/integration/oidc, /Users/mvandenb/src/galaxy/test, /Users/mvandenb/src/galaxy/lib, /Users/mvandenb/src/galaxy/.venv/bin, /opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python311.zip, /opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11, /opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload, /Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages
galaxy.config DEBUG 2024-02-21 12:20:57,137 [pN:main,p:38658,tN:MainThread] Configuration directory is /Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq
galaxy.config DEBUG 2024-02-21 12:20:57,137 [pN:main,p:38658,tN:MainThread] Data directory is /Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/tmpo1ompzky/database
galaxy.config DEBUG 2024-02-21 12:20:57,137 [pN:main,p:38658,tN:MainThread] Managed config directory is /Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq
galaxy.config WARNING 2024-02-21 12:20:57,160 [pN:main,p:38658,tN:MainThread] Option master_api_key has been deprecated in favor of bootstrap_admin_api_key
galaxy.config DEBUG 2024-02-21 12:20:57,162 [pN:main,p:38658,tN:MainThread] No extra version JSON file detected at /Users/mvandenb/src/galaxy/version.json
galaxy.carbon_emissions WARNING 2024-02-21 12:20:57,163 [pN:main,p:38658,tN:MainThread] No corresponding location name exists for location code: .
galaxy.carbon_emissions INFO 2024-02-21 12:20:57,163 [pN:main,p:38658,tN:MainThread] Using global default values for location name and carbon intensity...
galaxy.config WARNING 2024-02-21 12:20:57,163 [pN:main,p:38658,tN:MainThread] The path '/Users/mvandenb/src/galaxy/config/sanitize_whitelist.txt' for the 'sanitize_allowlist_file' config option is deprecated and will be no longer checked in a future release. Please consult the latest version of the sample configuration file.
galaxy.app DEBUG 2024-02-21 12:20:57,349 [pN:main,p:38658,tN:MainThread] Using "galaxy.ini" config file: lib/galaxy/config/sample/galaxy.yml.sample
galaxy.app INFO 2024-02-21 12:20:57,350 [pN:main,p:38658,tN:MainThread] Install database targeting Galaxy's database configuration.
galaxy.web_stack DEBUG 2024-02-21 12:20:57,351 [pN:main,p:38658,tN:MainThread] WeblessApplicationStack initialized
galaxy.jobs WARNING 2024-02-21 12:20:57,355 [pN:main,p:38658,tN:MainThread] Job configuration "/Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq" does not exist, using default job configuration
galaxy.web_stack.handlers INFO 2024-02-21 12:20:57,380 [pN:main,p:38658,tN:MainThread] JobConfiguration: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on <handlers> to override the default
galaxy.jobs DEBUG 2024-02-21 12:20:57,380 [pN:main,p:38658,tN:MainThread] Done loading job configuration
galaxy.security.vault WARNING 2024-02-21 12:20:57,388 [pN:main,p:38658,tN:MainThread] No vault configured. We recommend defining the vault_config_file setting in galaxy.yml
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Loading datatypes from /Users/mvandenb/src/galaxy/lib/galaxy/config/sample/datatypes_conf.xml.sample
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.h.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.c.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cpp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.py.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.go.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.rs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hep.root.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:JP2 from the datatype registry for extension jp2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry for extension ab1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry for extension afg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.goldenpath:GoldenPath from the datatype registry for extension agp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_cog_profile.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_composite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension anvio_classifier.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioContigsDB from the datatype registry for extension anvio_contigs_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,409 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioDB from the datatype registry for extension anvio_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioGenomesDB from the datatype registry for extension anvio_genomes_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioPanDB from the datatype registry for extension anvio_pan_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_pfam_profile.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioProfileDB from the datatype registry for extension anvio_profile_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioSamplesDB from the datatype registry for extension anvio_samples_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension anvio_state.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioStructureDB from the datatype registry for extension anvio_structure_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension anvio_variability.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry for extension arff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Paf from the datatype registry for extension paf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa1 from the datatype registry for extension gfa1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa2 from the datatype registry for extension gfa2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension asn1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension asn1-binary.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry for extension axt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry for extension fli.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry for extension bam.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bai.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamInputSorted from the datatype registry for extension qname_input_sorted.bam.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamQuerynameSorted from the datatype registry for extension qname_sorted.bam.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamNative from the datatype registry for extension unsorted.bam.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ProBam from the datatype registry for extension probam.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry for extension cram.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry for extension bed.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry for extension bedgraph.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry for extension bedstrict.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry for extension bed6.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry for extension bed12.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ProBed from the datatype registry for extension probed.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry for extension len.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DAA from the datatype registry for extension daa.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,410 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RMA6 from the datatype registry for extension rma6.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DMND from the datatype registry for extension dmnd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Parquet from the datatype registry for extension parquet.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Idat from the datatype registry for extension idat.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry for extension bigbed.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry for extension bigwig.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cxb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry for extension chrint.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension csv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension tsv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension intermine_tabular.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry for extension customtrack.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry for extension bowtie_color_index.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry for extension bowtie_base_index.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry for extension csfasta.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension data.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension binary.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension d3_hierarchy.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:ImgtJson from the datatype registry for extension imgt.json.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:GeoJson from the datatype registry for extension geojson.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:DataManagerJson from the datatype registry for extension data_manager_json.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry for extension dbn.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension fai.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension fasta.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastg from the datatype registry for extension fastg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,411 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry for extension fastq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry for extension fastqsanger.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry for extension fastqsolexa.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry for extension fastqcssanger.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry for extension fastqillumina.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry for extension fqtoc.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry for extension eland.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry for extension elandmulti.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry for extension genetrack.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension a3m.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry for extension gff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry for extension gff3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry for extension gif.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry for extension gmaj.zip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension graph_dot.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry for extension gtf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension toolshed.gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hdf4.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension h5.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension scool.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Grib from the datatype registry for extension grib.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Loom from the datatype registry for extension loom.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Anndata from the datatype registry for extension h5ad.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Visium from the datatype registry for extension visium.tar.gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mz5.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hyphy_results.json.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hivtrace.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Cool from the datatype registry for extension cool.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,412 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MCool from the datatype registry for extension mcool.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5MLM from the datatype registry for extension h5mlm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:LudwigModel from the datatype registry for extension ludwig_model.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension html.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension ludwig_report.html.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry for extension interval.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension jellyfish.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension ktab.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension prof.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaTab from the datatype registry for extension isa-tab.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaJson from the datatype registry for extension isa-json.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension picard_interval_list.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_interval.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_report.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_dbsnp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_tranche.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_recal.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cnn.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cns.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cnr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hhr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry for extension jpg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tiff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf8.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension btf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tif.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension svs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension scn.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension bif.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:OMETiff from the datatype registry for extension ome.tiff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vms.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,413 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vmu.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension ndpi.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry for extension mrxs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry for extension svslide.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry for extension bmp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry for extension im.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry for extension pcd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry for extension pcx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry for extension ppm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry for extension psd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry for extension xbm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry for extension xpm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry for extension rgb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry for extension pbm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry for extension pgm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nrrd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nhdr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry for extension rna_eps.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Artifact from the datatype registry for extension qza.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Visualization from the datatype registry for extension qzv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Metadata from the datatype registry for extension qiime2.tabular.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension zip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension ncbi_genome_dataset.zip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension directory.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension yaml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mrm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Dta from the datatype registry for extension dta.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Dta2d from the datatype registry for extension dta2d.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Edta from the datatype registry for extension edta.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension pepxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension raw_pepxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension peptideprophet_pepxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension interprophet_pepxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry for extension protxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ParamXml from the datatype registry for extension paramxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Kroenik from the datatype registry for extension kroenik.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepList from the datatype registry for extension peplist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PSMS from the datatype registry for extension psms.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry for extension pepxml.tsv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry for extension protxml.tsv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry for extension mascotdat.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,414 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry for extension mzid.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry for extension idxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry for extension tandem.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sirius.ms.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry for extension thermo.raw.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BafTar from the datatype registry for extension brukerbaf.d.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:YepTar from the datatype registry for extension agilentbrukeryep.d.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:TdfTar from the datatype registry for extension brukertdf.d.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MassHunterTar from the datatype registry for extension agilentmasshunter.d.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MassLynxTar from the datatype registry for extension watersmasslynx.raw.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:WiffTar from the datatype registry for extension wiff.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Wiff2Tar from the datatype registry for extension wiff2.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotXML from the datatype registry for extension mascotxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzTab from the datatype registry for extension mztab.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzTab2 from the datatype registry for extension mztab2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry for extension mzml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:NmrML from the datatype registry for extension nmrml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Meryldb from the datatype registry for extension meryldb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bref3 from the datatype registry for extension bref3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry for extension mgf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry for extension wiff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff2 from the datatype registry for extension wiff2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry for extension mzxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry for extension mzdata.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry for extension ms2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry for extension mzq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry for extension sqlite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry for extension mz.sqlite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OSW from the datatype registry for extension osw.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:PQP from the datatype registry for extension pqp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry for extension traml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TrafoXML from the datatype registry for extension trafoxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry for extension featurexml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry for extension consensusxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry for extension uniprotxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XquestXML from the datatype registry for extension xquest.xml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XquestSpecXML from the datatype registry for extension spec.xml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:QCML from the datatype registry for extension qcml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension mzqc.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry for extension msp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry for extension splib_noindex.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,415 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry for extension splib.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BlibSQlite from the datatype registry for extension blib.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DlibSQlite from the datatype registry for extension dlib.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ElibSQlite from the datatype registry for extension elib.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry for extension hlf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry for extension idpdb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry for extension sf3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cps.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry for extension ct.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:PostgresqlArchive from the datatype registry for extension postgresql.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MongoDBArchive from the datatype registry for extension mongodb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GeneNoteBook from the datatype registry for extension genenotebook.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry for extension searchgui_archive.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry for extension fast5.tar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry for extension fast5.tar.gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry for extension fast5.tar.bz2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension peptideshaker_archive.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension percin.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension percout.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hardklor.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension kronik.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry for extension imzml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Analyze75 from the datatype registry for extension analyze75.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nifti1 from the datatype registry for extension nii1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nifti2 from the datatype registry for extension nii2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gifti from the datatype registry for extension gii.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tck from the datatype registry for extension tck.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Trk from the datatype registry for extension trk.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Mrc2014 from the datatype registry for extension mrc.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Star from the datatype registry for extension star.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PEFF from the datatype registry for extension peff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension toml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.flow:FCS from the datatype registry for extension fcs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowtext.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowclr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowmfi.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,416 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowscore.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowframe.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension fsom.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowset.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension metacyto_clr.txt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.metacyto:mSummary from the datatype registry for extension metacyto_summary.txt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.metacyto:mStats from the datatype registry for extension metacyto_stats.txt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_compute_matrix_archive.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_coverage_matrix.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry for extension netcdf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry for extension eps.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry for extension rast.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry for extension laj.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry for extension lav.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry for extension maf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry for extension mafcustomtrack.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:MatrixMarket from the datatype registry for extension mtx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CMAP from the datatype registry for extension cmap.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry for extension encodepeak.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry for extension pdf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry for extension pileup.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Psl from the datatype registry for extension psl.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry for extension obo.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry for extension owl.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry for extension png.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry for extension qual.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry for extension qualsolexa.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,417 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry for extension qualillumina.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,422 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry for extension qualsolid.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,422 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry for extension qual454.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,422 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry for extension roadmaps.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,422 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry for extension sam.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,422 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry for extension scf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,422 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry for extension sequences.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,422 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry for extension snpeffdb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,422 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry for extension snpsiftdbnsfp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dbnsfp.tabular.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry for extension sff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry for extension sra.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:SraManifest from the datatype registry for extension sra_manifest.tabular.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension svg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry for extension taxonomy.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension tabular.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry for extension twobit.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SQmass from the datatype registry for extension sqmass.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry for extension gemini.sqlite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ChiraSQLite from the datatype registry for extension chira.sqlite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CuffDiffSQlite from the datatype registry for extension cuffdiff.sqlite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GAFASQLite from the datatype registry for extension gafa.sqlite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:NcbiTaxonomySQlite from the datatype registry for extension ncbitaxonomy.sqlite.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension txt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry for extension linecount.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry for extension memepsp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry for extension memexml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry for extension cisml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xsd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Dzi from the datatype registry for extension dzi.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry for extension vcf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf_bgzip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry for extension bcf_uncompressed.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry for extension velvet.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry for extension wig.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension interval_index.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension odgi.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,423 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension vg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension xg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension onnx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tabix.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:IntervalTabix from the datatype registry for extension interval_tabix.gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:JuicerMediumTabix from the datatype registry for extension juicer_medium_tabix.gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedTabix from the datatype registry for extension bed_tabix.gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:GffTabix from the datatype registry for extension gff_tabix.gz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bgzip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry for extension vcf_bgzip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bus.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension kallisto.idx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry for extension phyloxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension newick.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension nhx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry for extension nex.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:IQTree from the datatype registry for extension iqtree.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mldist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry for extension affybatch.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry for extension eigenstratgeno.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry for extension eigenstratpca.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry for extension eset.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry for extension fped.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry for extension fphe.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry for extension gg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry for extension ldindep.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry for extension malist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry for extension lped.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry for extension pbed.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry for extension pheno.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry for extension pphe.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry for extension rexpbase.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry for extension rgenetics.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry for extension snptest.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry for extension snpmatrix.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension xls.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,424 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry for extension ipynb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension json.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:ExpressionJson from the datatype registry for extension expression.json.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry for extension xgmml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry for extension sif.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry for extension triples.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry for extension hdt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry for extension nt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry for extension n3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry for extension ttl.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry for extension rdf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry for extension jsonld.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension excel.xls.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry for extension xlsx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension docx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension btwisted.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cai.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cat_db.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension charge.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension checktrans.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension chips.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codcmp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension coderet.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension compseq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgplot.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgreport.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cusp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cut.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dan.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension digest.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dreg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension einverted.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension epestfind.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension equicktandem.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension est2genome.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension etandem.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension freak.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzznuc.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,425 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzzpro.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzztran.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension garnier.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension geecee.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension helixturnhelix.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hmoment.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension isochore.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension match.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nametable.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension needle.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgreport.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgseek.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension noreturn.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension palindrome.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepcoil.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepinfo.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepstats.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension polydot.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension preg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prettyseq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension primersearch.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showfeat.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showorf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sixpack.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension strider.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension supermatcher.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension syco.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension textsearch.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension vectorstrip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wobble.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wordcount.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dbmotif.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension diffseq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension excel.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feattable.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension motif.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension regions.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension seqtable.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,426 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension simple.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension table.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension tagseq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension acedb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension clustal.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codata.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension embl.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fitch.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gcg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry for extension genbank.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hennig86.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ig.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifer.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifernon.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mega.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension meganon.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ncbi.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexus.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexusnon.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.phylip:Phylip from the datatype registry for extension phylip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension phylipnon.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pir.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension staden.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension swiss.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Msf from the datatype registry for extension msf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx0.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx10.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pair.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension score.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srspair.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry for extension snaphmm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry for extension augustus.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ICM from the datatype registry for extension icm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:InfernalCM from the datatype registry for extension cm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry for extension hmm2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry for extension hmm3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry for extension stockholm.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,427 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry for extension xmfa.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Cel from the datatype registry for extension cel.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gpr from the datatype registry for extension gpr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gal from the datatype registry for extension gal.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension rds.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension phyloseq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.sce.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.raw.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.msnbase.raw.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.findchrompeaks.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.group.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.retcor.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.fillpeaks.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.positive.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.negative.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.quick.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.hdf5:HDF5SummarizedExperiment from the datatype registry for extension rdata.se.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rdock_as.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry for extension oxlicg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry for extension oxling.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry for extension oxlits.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry for extension oxlist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry for extension oxliss.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry for extension oxligl.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry for extension stl.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry for extension plyascii.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry for extension plybinary.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry for extension vtkascii.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry for extension vtkbinary.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry for extension biom1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry for extension biom2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MashSketch from the datatype registry for extension msh.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry for extension scidx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry for extension smi.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry for extension sdf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry for extension inchi.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry for extension mol.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,428 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry for extension mol2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry for extension cml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry for extension fps.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry for extension obfs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry for extension drf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry for extension phar.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry for extension pdb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry for extension pdbqt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PQR from the datatype registry for extension pqr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:Cell from the datatype registry for extension cell.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:CIF from the datatype registry for extension cif.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:XYZ from the datatype registry for extension xyz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:ExtendedXYZ from the datatype registry for extension extxyz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:Magres from the datatype registry for extension magres.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Trr from the datatype registry for extension trr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Dcd from the datatype registry for extension dcd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension top.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prmtop.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension itp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mdp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ndx.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension xvg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Xtc from the datatype registry for extension xtc.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Cpt from the datatype registry for extension cpt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Edr from the datatype registry for extension edr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tpr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:GRO from the datatype registry for extension gro.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension inpcrd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Vel from the datatype registry for extension vel.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry for extension grd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry for extension grd.tgz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.otu.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.list.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.sabund.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.rabund.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.shared.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.relabund.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry for extension mothur.names.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.design.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,429 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry for extension mothur.summary.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.groups.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry for extension mothur.oligos.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension mothur.align.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.accnos.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.otulabels.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mothur.otu.corr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry for extension mothur.map.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry for extension mothur.align.check.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry for extension mothur.align.report.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry for extension mothur.filter.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry for extension mothur.dist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mothur.tre.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry for extension mothur.pair.dist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mothur.square.dist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry for extension mothur.lower.dist.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.ref.taxonomy.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.seq.taxonomy.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.rdp.taxonomy.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry for extension mothur.cons.taxonomy.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry for extension mothur.tax.summary.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry for extension mothur.freq.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.quan.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.quan.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.masked.quan.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.masked.quan.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry for extension mothur.axes.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry for extension mothur.sff.flow.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry for extension mothur.count_table.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry for extension neostore.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDBzip from the datatype registry for extension neostore.zip.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry for extension trackhub.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry for extension blastxml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry for extension blastdbn.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry for extension blastdbp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry for extension blastdbd.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,430 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:LastDb from the datatype registry for extension lastdb.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb5 from the datatype registry for extension blastdbn5.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb5 from the datatype registry for extension blastdbp5.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb5 from the datatype registry for extension blastdbd5.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension maskinfo-asn1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension maskinfo-asn1-binary.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension pssm-asn1.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry for extension ptkscmp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry for extension smat.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenotypeMatrix from the datatype registry for extension alohomora_gts.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_map.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_maf.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_ped.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension linkage_pedin.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:DataIn from the datatype registry for extension linkage_datain.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:MarkerMap from the datatype registry for extension linkage_map.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_ihaplo.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_descent.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:AllegroLOD from the datatype registry for extension allegro_fparam.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:IdeasPre from the datatype registry for extension ideaspre.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Sbml from the datatype registry for extension sbml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnNuclDb from the datatype registry for extension spalndbnp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnProtDb from the datatype registry for extension spalndba.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_dada.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_errorrates.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_mergepairs.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_sequencetable.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_uniques.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension ampvis2.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension ckpt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tgz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Wav from the datatype registry for extension wav.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mp3 from the datatype registry for extension mp3.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mkv from the datatype registry for extension mkv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mp4 from the datatype registry for extension mp4.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,431 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Flv from the datatype registry for extension flv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mpg from the datatype registry for extension mpg.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.speech:TextGrid from the datatype registry for extension textgrid.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.speech:BPF from the datatype registry for extension par.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension ffindex.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension ffdata.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Pretext from the datatype registry for extension pretext.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension immuneml_receptors.html.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdMaterials from the datatype registry for extension hexrd.materials.h5.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension npz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdImagesNpz from the datatype registry for extension hexrd.images.npz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdEtaOmeNpz from the datatype registry for extension hexrd.eta_ome.npz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension hexrd.scored_orientations.npz.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hexrd.accepted_orientations.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension hexrd.yml.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTess from the datatype registry for extension neper.tess.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTesr from the datatype registry for extension neper.tesr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPoints from the datatype registry for extension neper.points.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPointsTabular from the datatype registry for extension neper.points.tsv.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperMultiScaleCell from the datatype registry for extension neper.mscell.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshMsh from the datatype registry for extension gmsh.msh.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshGeo from the datatype registry for extension gmsh.geo.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:ZsetGeof from the datatype registry for extension zset.geof.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension stl.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Overriding conflicting datatype with extension 'stl', using datatype from /Users/mvandenb/src/galaxy/lib/galaxy/config/sample/datatypes_conf.xml.sample.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Text from the datatype registry for extension pov.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaResult from the datatype registry for extension pithya.result.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaProperty from the datatype registry for extension pithya.property.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaModel from the datatype registry for extension pithya.model.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:BCSLts from the datatype registry for extension bcsl.ts.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:BCSLmodel from the datatype registry for extension bcsl.model.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:StormSample from the datatype registry for extension storm.sample.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:StormCheck from the datatype registry for extension storm.check.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,432 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:CTLresult from the datatype registry for extension ctl.result.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Castep from the datatype registry for extension castep.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Param from the datatype registry for extension param.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:FormattedDensity from the datatype registry for extension den_fmt.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.larch:AthenaProject from the datatype registry for extension prj.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.larch:FEFFInput from the datatype registry for extension inp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension sp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension gds.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension feff.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feffit.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bil.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hdr.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.gis:Shapefile from the datatype registry for extension shp.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:FITS from the datatype registry for extension fits.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Retrieved datatype module galaxy.datatypes.chain:Chain from the datatype registry for extension chain.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTess'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTesr'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:GmshMsh'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.goldenpath:GoldenPath'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:JP2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,433 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQmass'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OSW'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PQP'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ElibSQlite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DlibSQlite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BlibSQlite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ChiraSQLite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CuffDiffSQlite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GAFASQLite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NcbiTaxonomySQlite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5MLM'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cool'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MCool'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Loom'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Anndata'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdMaterials'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Grib'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdImagesNpz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdEtaOmeNpz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Npz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamQuerynameSorted'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamNative'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DAA'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RMA6'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Parquet'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BafTar'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TdfTar'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassHunterTar'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassLynxTar'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:YepTar'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:WiffTar'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Meryldb'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bref3'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PostgresqlArchive'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ICM'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Idat'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Trr'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Dcd'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xtc'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cpt'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Edr'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Vel'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xlsx'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Metadata'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,434 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Artifact'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Visualization'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedZipArchive'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pretext'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.chain:Chain'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gifti'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Dzi'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Sbml'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Dta2d'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Edta'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ConsensusXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:IdXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:FeatureXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MascotXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Ms2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ParamXml'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:NmrML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Kroenik'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepList'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PSMS'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TrafoXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestSpecXML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:QCML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Wiff'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PEFF'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,435 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastg'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Cell'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CIF'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:ExtendedXYZ'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:XYZ'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Magres'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PQR'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:GRO'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.phylip:Phylip'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqCSSanger'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Html'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Psl'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Paf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Newick'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:IQTree'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,436 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Obo'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Arff'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:ImgtJson'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:GeoJson'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaResult'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLts'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Json'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:GenotypeMatrix'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:DataIn'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:MarkerMap'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:AllegroLOD'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CMAP'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mSummary'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mStats'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:MatrixMarket'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:InfernalCM'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Cel'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gpr'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gal'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RData'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RDS'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Mrc2014'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Png'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:OMETiff'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,437 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gif'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Im'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Psd'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Eps'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rast'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tck'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Trk'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti1'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Star'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Wav'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mkv'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp3'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp4'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Flv'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mpg'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:TextGrid'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:BPF'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.larch:FEFFInput'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.larch:AthenaProject'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Castep'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:CTLresult'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:FormattedDensity'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Param'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Yaml'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:FITS'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,438 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.neo4j:Neo4jDBzip'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,439 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaProperty'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,439 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaModel'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,439 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLmodel'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,439 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormSample'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,439 [pN:main,p:38658,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormCheck'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,440 [pN:main,p:38658,tN:MainThread] Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample].
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,440 [pN:main,p:38658,tN:MainThread] Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla']
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,441 [pN:main,p:38658,tN:MainThread] 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']
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,441 [pN:main,p:38658,tN:MainThread] Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,441 [pN:main,p:38658,tN:MainThread] Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,441 [pN:main,p:38658,tN:MainThread] Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample].
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,441 [pN:main,p:38658,tN:MainThread] Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,441 [pN:main,p:38658,tN:MainThread] Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample].
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:57,441 [pN:main,p:38658,tN:MainThread] Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample
galaxy.util.tool_shed.tool_shed_registry DEBUG 2024-02-21 12:20:57,441 [pN:main,p:38658,tN:MainThread] Loading references to tool sheds from internal default config
galaxy.util.tool_shed.tool_shed_registry DEBUG 2024-02-21 12:20:57,441 [pN:main,p:38658,tN:MainThread] Loaded reference to tool shed: Galaxy Main Tool Shed
galaxy.web_stack DEBUG 2024-02-21 12:20:57,443 [pN:main,p:38658,tN:MainThread] server_name set to: main
galaxy.queue_worker INFO 2024-02-21 12:20:57,443 [pN:main,p:38658,tN:MainThread] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/tmpo1ompzky/database/control.sqlite?isolation_level=IMMEDIATE
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,483 [pN:main,p:38658,tN:MainThread] Loaded 11 lines from 'all_fasta.loc' for 'all_fasta'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,483 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'all_fasta' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,484 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/bfast_indexes.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,484 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/bfast_indexes.loc.sample' for 'bfast_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,484 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'bfast_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,484 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/blastdb.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,484 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/blastdb.loc.sample' for 'blastdb'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,484 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'blastdb' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,484 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/blastdb_p.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,484 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/blastdb_p.loc.sample' for 'blastdb_p'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,484 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'blastdb_p' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,484 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/blastdb_d.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,485 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/blastdb_d.loc.sample' for 'blastdb_d'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,485 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'blastdb_d' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data WARNING 2024-02-21 12:20:57,485 [pN:main,p:38658,tN:MainThread] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,485 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'bwa_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data WARNING 2024-02-21 12:20:57,485 [pN:main,p:38658,tN:MainThread] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,485 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'bwa_indexes_color' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,487 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/maf_index.loc' for 'indexed_maf_files'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,487 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'indexed_maf_files' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,487 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/ngs_sim_fasta.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,487 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,487 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'ngs_sim_fasta' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,487 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/perm_base_index.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,487 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/perm_base_index.loc.sample' for 'perm_base_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,487 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'perm_base_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,488 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/perm_color_index.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,488 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/perm_color_index.loc.sample' for 'perm_color_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,488 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'perm_color_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,488 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/picard_index.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,488 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/picard_index.loc.sample' for 'picard_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,488 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'picard_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,488 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/picard_index.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,488 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/picard_index.loc.sample' for 'srma_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,488 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'srma_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,488 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/mosaik_index.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,488 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/mosaik_index.loc.sample' for 'mosaik_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,488 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'mosaik_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,488 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/twobit.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,489 [pN:main,p:38658,tN:MainThread] Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/twobit.loc.sample' for 'twobit'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,489 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'twobit' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,793 [pN:main,p:38658,tN:MainThread] Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/Users/mvandenb/tmp/TTDT_URL_igv_broad_genomes-abqppn9b".
galaxy.tool_util.data WARNING 2024-02-21 12:20:57,794 [pN:main,p:38658,tN:MainThread] Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields):
<Server-Side Genome List>
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,794 [pN:main,p:38658,tN:MainThread] Loaded 156 lines from '/Users/mvandenb/tmp/TTDT_URL_igv_broad_genomes-abqppn9b' for 'igv_broad_genomes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,795 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'igv_broad_genomes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,795 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/tool-data/liftOver.loc' for 'liftOver'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,795 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'liftOver' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,795 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/bam_iobio.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,795 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/tool-data/bam_iobio.loc.sample' for 'bam_iobio'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,795 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'bam_iobio' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,796 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/vcf_iobio.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,796 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/tool-data/vcf_iobio.loc.sample' for 'vcf_iobio'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,796 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'vcf_iobio' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,796 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/biom_simple_display.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,796 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/tool-data/biom_simple_display.loc.sample' for 'biom_simple_display'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,796 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'biom_simple_display' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,796 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/intermine_simple_display.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,797 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/tool-data/intermine_simple_display.loc.sample' for 'intermine_simple_display'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,797 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'intermine_simple_display' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,797 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/icn3d_simple_display.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,797 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/tool-data/icn3d_simple_display.loc.sample' for 'icn3d_simple_display'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,797 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'icn3d_simple_display' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,798 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table '__dbkeys__'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,798 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table '__dbkeys__'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,798 [pN:main,p:38658,tN:MainThread] Loaded tool data table '__dbkeys__' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,798 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'all_fasta'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,798 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'all_fasta'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,798 [pN:main,p:38658,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample', attempting to merge content.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,798 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'fasta_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,798 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'fasta_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,798 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'fasta_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,799 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'bowtie2_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,799 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'bowtie2_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,799 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'bowtie2_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,799 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'bwa_mem_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,799 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'bwa_mem_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,799 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'bwa_mem_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,799 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'hisat2_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,799 [pN:main,p:38658,tN:MainThread] Encountered a file element (<file from_config="refgenie_config_file"/>) that does not contain a path value when loading tool data table 'hisat2_indexes'.
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,799 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'hisat2_indexes' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data INFO 2024-02-21 12:20:57,799 [pN:main,p:38658,tN:MainThread] Could not find tool data /Users/mvandenb/src/galaxy/tool-data/q2view_display.loc, reading sample
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,799 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/tool-data/q2view_display.loc.sample' for 'q2view_display'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,800 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'q2view_display' from file '/Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_data_table_conf.xml.sample'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,800 [pN:main,p:38658,tN:MainThread] Loaded 2 lines from '/Users/mvandenb/src/galaxy/test/functional/tool-data/testalpha.loc' for 'testalpha'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,800 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'testalpha' from file '/Users/mvandenb/src/galaxy/test/functional/tool-data/sample_tool_data_tables.xml'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,800 [pN:main,p:38658,tN:MainThread] Loaded 1 lines from '/Users/mvandenb/src/galaxy/test/functional/tool-data/testbeta.loc' for 'testbeta'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,800 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'testbeta' from file '/Users/mvandenb/src/galaxy/test/functional/tool-data/sample_tool_data_tables.xml'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,801 [pN:main,p:38658,tN:MainThread] Loaded 3 lines from '/Users/mvandenb/src/galaxy/test/functional/tool-data/fasta_indexes.loc' for 'test_fasta_indexes'
galaxy.tool_util.data DEBUG 2024-02-21 12:20:57,801 [pN:main,p:38658,tN:MainThread] Loaded tool data table 'test_fasta_indexes' from file '/Users/mvandenb/src/galaxy/test/functional/tool-data/sample_tool_data_tables.xml'
galaxy.util WARNING 2024-02-21 12:20:57,820 [pN:main,p:38658,tN:MainThread] directory not found: /Users/mvandenb/src/galaxy/lib/galaxy/util/../../../config/plugins/activities
galaxy.tools WARNING 2024-02-21 12:20:57,821 [pN:main,p:38658,tN:MainThread] The default shed tool config file (/Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/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 2024-02-21 12:20:57,821 [pN:main,p:38658,tN:MainThread] Parsing the tool configuration /Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_conf.xml.sample
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,821 [pN:main,p:38658,tN:MainThread] Tool path for tool configuration /Users/mvandenb/src/galaxy/lib/galaxy/config/sample/tool_conf.xml.sample is None
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,824 [pN:main,p:38658,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,825 [pN:main,p:38658,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,825 [pN:main,p:38658,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,826 [pN:main,p:38658,tN:MainThread] Loaded tool id: ncbi_datasets_source, version: 13.14.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,827 [pN:main,p:38658,tN:MainThread] Loaded tool id: sra_source, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,827 [pN:main,p:38658,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,828 [pN:main,p:38658,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,828 [pN:main,p:38658,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,829 [pN:main,p:38658,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,829 [pN:main,p:38658,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,830 [pN:main,p:38658,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,830 [pN:main,p:38658,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,831 [pN:main,p:38658,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,831 [pN:main,p:38658,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,831 [pN:main,p:38658,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,832 [pN:main,p:38658,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,832 [pN:main,p:38658,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,833 [pN:main,p:38658,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,833 [pN:main,p:38658,tN:MainThread] Loaded tool id: send_to_cloud, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,834 [pN:main,p:38658,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,835 [pN:main,p:38658,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,835 [pN:main,p:38658,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,836 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,837 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,837 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,840 [pN:main,p:38658,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,841 [pN:main,p:38658,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,842 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,843 [pN:main,p:38658,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,844 [pN:main,p:38658,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,845 [pN:main,p:38658,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,845 [pN:main,p:38658,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,846 [pN:main,p:38658,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.2.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,847 [pN:main,p:38658,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,848 [pN:main,p:38658,tN:MainThread] Loaded tool id: __DUPLICATE_FILE_TO_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,849 [pN:main,p:38658,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,850 [pN:main,p:38658,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,851 [pN:main,p:38658,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,851 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,852 [pN:main,p:38658,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,853 [pN:main,p:38658,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,854 [pN:main,p:38658,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,854 [pN:main,p:38658,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,854 [pN:main,p:38658,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,855 [pN:main,p:38658,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,855 [pN:main,p:38658,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,856 [pN:main,p:38658,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,856 [pN:main,p:38658,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,857 [pN:main,p:38658,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,857 [pN:main,p:38658,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,858 [pN:main,p:38658,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,858 [pN:main,p:38658,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,859 [pN:main,p:38658,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,859 [pN:main,p:38658,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,859 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,860 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,861 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,861 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,862 [pN:main,p:38658,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,863 [pN:main,p:38658,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,863 [pN:main,p:38658,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,864 [pN:main,p:38658,tN:MainThread] Loaded tool id: Filter1, version: 1.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,865 [pN:main,p:38658,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,866 [pN:main,p:38658,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,867 [pN:main,p:38658,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,867 [pN:main,p:38658,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,867 [pN:main,p:38658,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,868 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,868 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,869 [pN:main,p:38658,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,870 [pN:main,p:38658,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,870 [pN:main,p:38658,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,872 [pN:main,p:38658,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,873 [pN:main,p:38658,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,873 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,875 [pN:main,p:38658,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,875 [pN:main,p:38658,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,876 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,876 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,877 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,877 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,878 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,878 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,879 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,879 [pN:main,p:38658,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,880 [pN:main,p:38658,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,880 [pN:main,p:38658,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,881 [pN:main,p:38658,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,881 [pN:main,p:38658,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,882 [pN:main,p:38658,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base ERROR 2024-02-21 12:20:57,882 [pN:main,p:38658,tN:MainThread] Error reading tool from path: phenotype_association/sift.xml
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 873, in _load_tool_tag_set
tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 1100, in load_tool
tool = self.create_tool(
^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 547, in create_tool
return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 563, in _create_tool_from_source
return create_tool_from_source(self.app, tool_source, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 355, in create_tool_from_source
tool = ToolClass(config_file, tool_source, app, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 820, in __init__
raise e
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 817, in __init__
self.parse(tool_source, guid=guid, dynamic=dynamic)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 1142, in parse
self.parse_inputs(self.tool_source)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 1427, in parse_inputs
inputs = self.parse_input_elem(page_source, enctypes)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 1622, in parse_input_elem
param = self.parse_param_elem(input_source, enctypes, context)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 1635, in parse_param_elem
param = ToolParameter.build(self, input_source)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/basic.py", line 329, in build
return parameter_types[param_type](tool, input_source)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/basic.py", line 2054, in __init__
super().__init__(tool, input_source, trans)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/basic.py", line 1845, in __init__
super().__init__(tool, input_source)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/basic.py", line 185, in __init__
self.validators.append(validation.Validator.from_element(self, elem))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/validation.py", line 45, in from_element
return validator_types[_type].from_element(param, elem)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/validation.py", line 397, in from_element
assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found"
AssertionError: File /Users/mvandenb/src/galaxy/tool-data/sift_db.loc specified by the 'filename' attribute not found
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,884 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,884 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,885 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,885 [pN:main,p:38658,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel..
galaxy.tools WARNING 2024-02-21 12:20:57,885 [pN:main,p:38658,tN:MainThread] The default shed tool config file (/Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/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 2024-02-21 12:20:57,885 [pN:main,p:38658,tN:MainThread] Parsing the tool configuration /Users/mvandenb/src/galaxy/test/functional/tools/sample_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,885 [pN:main,p:38658,tN:MainThread] Tool path for tool configuration /Users/mvandenb/src/galaxy/test/functional/tools/sample_tool_conf.xml is ${tool_conf_dir}
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,888 [pN:main,p:38658,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,888 [pN:main,p:38658,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,889 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_data_optional, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,889 [pN:main,p:38658,tN:MainThread] Loaded tool id: paths_as_file, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,890 [pN:main,p:38658,tN:MainThread] Loaded tool id: param_text_option, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,890 [pN:main,p:38658,tN:MainThread] Loaded tool id: column_param, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,891 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_format_input, version: 1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,891 [pN:main,p:38658,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,891 [pN:main,p:38658,tN:MainThread] Loaded tool id: test_data_source, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,892 [pN:main,p:38658,tN:MainThread] Loaded tool id: simple_constructs, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,892 [pN:main,p:38658,tN:MainThread] Loaded tool id: color_param, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,893 [pN:main,p:38658,tN:MainThread] Loaded tool id: inheritance_simple, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,894 [pN:main,p:38658,tN:MainThread] Loaded tool id: boolean_conditional, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,894 [pN:main,p:38658,tN:MainThread] Loaded tool id: composite, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,894 [pN:main,p:38658,tN:MainThread] Loaded tool id: environment_variables, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,895 [pN:main,p:38658,tN:MainThread] Loaded tool id: environment_variables_inject, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,895 [pN:main,p:38658,tN:MainThread] Loaded tool id: code_file, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,896 [pN:main,p:38658,tN:MainThread] Loaded tool id: disambiguate_cond, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,896 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_repeats, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,897 [pN:main,p:38658,tN:MainThread] Loaded tool id: remove_value, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,897 [pN:main,p:38658,tN:MainThread] Loaded tool id: bibtex, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,898 [pN:main,p:38658,tN:MainThread] Loaded tool id: select_from_url, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,898 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_select, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,898 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_output, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,899 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_output_configured, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,899 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_output_assign_primary, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,899 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_output_assign_primary_ext_dbkey, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,900 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_output_recurse, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,901 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_output_recurse_collection, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,901 [pN:main,p:38658,tN:MainThread] Loaded tool id: galaxy_json_sleep, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,901 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,902 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_2, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,902 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_3, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,902 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_4, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,902 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_5, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,903 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_6, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,903 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_7, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,903 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_8, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,904 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_9, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,904 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_10, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,904 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_11, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,905 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_provided_metadata_12, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,905 [pN:main,p:38658,tN:MainThread] Loaded tool id: empty_datasets, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,905 [pN:main,p:38658,tN:MainThread] Loaded tool id: is_of_type, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,905 [pN:main,p:38658,tN:MainThread] Loaded tool id: data_optional, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,906 [pN:main,p:38658,tN:MainThread] Loaded tool id: inputs_as_json, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,907 [pN:main,p:38658,tN:MainThread] Loaded tool id: inputs_as_json_profile, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,907 [pN:main,p:38658,tN:MainThread] Loaded tool id: inputs_as_json_with_paths, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,908 [pN:main,p:38658,tN:MainThread] Loaded tool id: inputs_as_json_with_staging_paths, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,908 [pN:main,p:38658,tN:MainThread] Loaded tool id: filter_multiple_splitter, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,909 [pN:main,p:38658,tN:MainThread] Loaded tool id: filter_param_value, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,909 [pN:main,p:38658,tN:MainThread] Loaded tool id: filter_param_value_ref_attribute, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,910 [pN:main,p:38658,tN:MainThread] Loaded tool id: filter_static_regexp, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,910 [pN:main,p:38658,tN:MainThread] Loaded tool id: select_from_dataset, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,911 [pN:main,p:38658,tN:MainThread] Loaded tool id: select_from_csvdataset, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,911 [pN:main,p:38658,tN:MainThread] Loaded tool id: select_from_dataset_optional, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,912 [pN:main,p:38658,tN:MainThread] Loaded tool id: drill_down, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,912 [pN:main,p:38658,tN:MainThread] Loaded tool id: dbkey_filter_input, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,913 [pN:main,p:38658,tN:MainThread] Loaded tool id: dbkey_filter_multi_input, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,913 [pN:main,p:38658,tN:MainThread] Loaded tool id: dbkey_filter_collection_input, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,914 [pN:main,p:38658,tN:MainThread] Loaded tool id: dbkey_output_action, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,914 [pN:main,p:38658,tN:MainThread] Loaded tool id: composite_output, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,915 [pN:main,p:38658,tN:MainThread] Loaded tool id: composite_output_tests, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,915 [pN:main,p:38658,tN:MainThread] Loaded tool id: unicode_stream, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,916 [pN:main,p:38658,tN:MainThread] Loaded tool id: vcf_bgzip_test, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,916 [pN:main,p:38658,tN:MainThread] Loaded tool id: metadata, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,916 [pN:main,p:38658,tN:MainThread] Loaded tool id: metadata_bam, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,917 [pN:main,p:38658,tN:MainThread] Loaded tool id: discover_metadata_files, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,917 [pN:main,p:38658,tN:MainThread] Loaded tool id: metadata_bcf, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,917 [pN:main,p:38658,tN:MainThread] Loaded tool id: metadata_bed, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,918 [pN:main,p:38658,tN:MainThread] Loaded tool id: metadata_biom1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,918 [pN:main,p:38658,tN:MainThread] Loaded tool id: metadata_check_eq, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,918 [pN:main,p:38658,tN:MainThread] Loaded tool id: metadata_columns, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,919 [pN:main,p:38658,tN:MainThread] Loaded tool id: strict_shell, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,919 [pN:main,p:38658,tN:MainThread] Loaded tool id: strict_shell_default_off, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,919 [pN:main,p:38658,tN:MainThread] Loaded tool id: strict_shell_profile, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,920 [pN:main,p:38658,tN:MainThread] Loaded tool id: detect_errors, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,920 [pN:main,p:38658,tN:MainThread] Loaded tool id: detect_errors_aggressive, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,921 [pN:main,p:38658,tN:MainThread] Loaded tool id: qc_stdout, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,921 [pN:main,p:38658,tN:MainThread] Loaded tool id: directory_uri, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,922 [pN:main,p:38658,tN:MainThread] Loaded tool id: md5sum, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,922 [pN:main,p:38658,tN:MainThread] Loaded tool id: checksum, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,922 [pN:main,p:38658,tN:MainThread] Loaded tool id: sim_size_delta, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,923 [pN:main,p:38658,tN:MainThread] Loaded tool id: shapefile_composite, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,923 [pN:main,p:38658,tN:MainThread] Loaded tool id: is_valid_xml, version: 0.001 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,923 [pN:main,p:38658,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,926 [pN:main,p:38658,tN:MainThread] Loaded tool id: pick_value, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,927 [pN:main,p:38658,tN:MainThread] Loaded tool id: job_properties, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,927 [pN:main,p:38658,tN:MainThread] Loaded tool id: job_environment_default, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,928 [pN:main,p:38658,tN:MainThread] Loaded tool id: job_environment_default_legacy, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,928 [pN:main,p:38658,tN:MainThread] Loaded tool id: job_environment_explicit_shared_home, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,928 [pN:main,p:38658,tN:MainThread] Loaded tool id: job_environment_explicit_isolated_home, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base ERROR 2024-02-21 12:20:57,928 [pN:main,p:38658,tN:MainThread] Error reading tool configuration file from path 'galaxy_slots_and_memory.xml': [Errno 2] No such file or directory
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,928 [pN:main,p:38658,tN:MainThread] Loaded tool id: version_command_plain, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,929 [pN:main,p:38658,tN:MainThread] Loaded tool id: version_command_interpreter, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,929 [pN:main,p:38658,tN:MainThread] Loaded tool id: version_command_tool_dir, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,930 [pN:main,p:38658,tN:MainThread] Loaded tool id: exit_code_oom, version: 0.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,930 [pN:main,p:38658,tN:MainThread] Loaded tool id: exit_code_from_file, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,930 [pN:main,p:38658,tN:MainThread] Loaded tool id: exit_code_from_env, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,931 [pN:main,p:38658,tN:MainThread] Loaded tool id: gzipped_inputs, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,931 [pN:main,p:38658,tN:MainThread] Loaded tool id: options_from_metadata_file, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,931 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_order, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,932 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_format, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,932 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_format_deprecated_when, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,932 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_format_collection, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,933 [pN:main,p:38658,tN:MainThread] Loaded tool id: format_source_in_conditional, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,934 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_filter, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,934 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_empty_work_dir, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,934 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_filter_with_input, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,934 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_filter_with_input_optional, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,935 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_filter_exception_1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,935 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_collection_filter, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,935 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_auto_format, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,936 [pN:main,p:38658,tN:MainThread] Loaded tool id: create_2, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,936 [pN:main,p:38658,tN:MainThread] Loaded tool id: create_10, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,937 [pN:main,p:38658,tN:MainThread] Loaded tool id: disambiguate_repeats, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,937 [pN:main,p:38658,tN:MainThread] Loaded tool id: min_repeat, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,937 [pN:main,p:38658,tN:MainThread] Loaded tool id: parallelism, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,938 [pN:main,p:38658,tN:MainThread] Loaded tool id: parallelism_optional, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,938 [pN:main,p:38658,tN:MainThread] Loaded tool id: implicit_default_conds, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,938 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_data_param, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,939 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_data_repeat, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,939 [pN:main,p:38658,tN:MainThread] Loaded tool id: multi_data_optional, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,939 [pN:main,p:38658,tN:MainThread] Loaded tool id: paths_as_file, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,939 [pN:main,p:38658,tN:MainThread] Loaded tool id: param_text_option, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,939 [pN:main,p:38658,tN:MainThread] Loaded tool id: column_param, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,939 [pN:main,p:38658,tN:MainThread] Loaded tool id: column_param_configfile, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,940 [pN:main,p:38658,tN:MainThread] Loaded tool id: column_param_list, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,940 [pN:main,p:38658,tN:MainThread] Loaded tool id: column_multi_param, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,941 [pN:main,p:38658,tN:MainThread] Loaded tool id: select_optional, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,941 [pN:main,p:38658,tN:MainThread] Loaded tool id: hidden_param, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,941 [pN:main,p:38658,tN:MainThread] Loaded tool id: special_params, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,942 [pN:main,p:38658,tN:MainThread] Loaded tool id: section, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,942 [pN:main,p:38658,tN:MainThread] Loaded tool id: test_sam_to_bam_conversions, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,943 [pN:main,p:38658,tN:MainThread] Loaded tool id: top_level_data, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,943 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_hdf5, version: 1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,943 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_zip, version: 1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,944 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_tar, version: 1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,944 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_tar_gz, version: 1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,945 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_default, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,945 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_sanitizer, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,945 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_repeat, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,945 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_metadata_in_range, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,946 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_metadata_in_datatable, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,947 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_dataset_metadata_in_file, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,947 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_value_in_datatable, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,947 [pN:main,p:38658,tN:MainThread] Loaded tool id: empty_output, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,948 [pN:main,p:38658,tN:MainThread] Loaded tool id: validation_empty_dataset, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,948 [pN:main,p:38658,tN:MainThread] Loaded tool id: implicit_conversion, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,948 [pN:main,p:38658,tN:MainThread] Loaded tool id: implicit_conversion_format_input, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,949 [pN:main,p:38658,tN:MainThread] Loaded tool id: implicit_conversion_optional_param, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,949 [pN:main,p:38658,tN:MainThread] Loaded tool id: implicit_collection_conversion, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,949 [pN:main,p:38658,tN:MainThread] Loaded tool id: implicit_nested_collection_conversion, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,950 [pN:main,p:38658,tN:MainThread] Loaded tool id: explicit_conversion, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,950 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_source, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,950 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_single, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,950 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_single_in_repeat, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,951 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_in_conditional, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,951 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_multiple, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,951 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_multiple_in_conditional, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,951 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_multiple_in_repeat, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,952 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_collection, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,952 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_all_collection_types, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,953 [pN:main,p:38658,tN:MainThread] Loaded tool id: identifier_in_actions, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,953 [pN:main,p:38658,tN:MainThread] Loaded tool id: fail_identifier, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,953 [pN:main,p:38658,tN:MainThread] Loaded tool id: fail_writing_work_dir_file, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,953 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_directory, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,953 [pN:main,p:38658,tN:MainThread] Loaded tool id: tool_directory_docker, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,954 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_action_change_format, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,954 [pN:main,p:38658,tN:MainThread] Loaded tool id: output_action_change_format_paired, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,955 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_paired_test, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,955 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_paired_default, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,955 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_paired_structured_like, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,956 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_paired_conditional_structured_like, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,956 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_nested_test, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,957 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_nested_default, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,957 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_mixed_param, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,957 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_two_paired, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,958 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_pair, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,958 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_pair_format, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,958 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_pair_from_type, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,959 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_pair_from_work_dir, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,959 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_list, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,959 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_list_2, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,959 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_list_of_pairs, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,960 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_optional_param, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,960 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_split_on_column, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,960 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_dynamic_nested, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,961 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_dynamic_nested_from_json, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,961 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_dynamic_nested_from_json_elements, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,962 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_dynamic_list_of_pairs, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,962 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_type_source, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,962 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_type_source_map_over, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,963 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_list_fail, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,963 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_creates_dynamic_nested_fail, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,963 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_cat_group_tag, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,963 [pN:main,p:38658,tN:MainThread] Loaded tool id: collection_cat_group_tag_multiple, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,964 [pN:main,p:38658,tN:MainThread] Loaded tool id: discover_sort_by, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,964 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_forty_two, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,965 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_pick_larger_file, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,965 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_parse_int, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,965 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_log_line_count, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,965 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_null_handling_boolean, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,966 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_null_handling_integer, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,966 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_null_handling_float, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,966 [pN:main,p:38658,tN:MainThread] Loaded tool id: expression_null_handling_text, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,967 [pN:main,p:38658,tN:MainThread] Loaded tool id: cheetah_casting, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,967 [pN:main,p:38658,tN:MainThread] Loaded tool id: cheetah_problem_unbound_var, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,967 [pN:main,p:38658,tN:MainThread] Loaded tool id: cheetah_problem_unbound_var_input, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,968 [pN:main,p:38658,tN:MainThread] Loaded tool id: cheetah_problem_syntax_error, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,968 [pN:main,p:38658,tN:MainThread] Loaded tool id: model_attributes, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,968 [pN:main,p:38658,tN:MainThread] Loaded tool id: python_environment_problem, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,968 [pN:main,p:38658,tN:MainThread] Loaded tool id: config_vars, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,971 [pN:main,p:38658,tN:MainThread] Loaded tool id: expect_num_outputs, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,971 [pN:main,p:38658,tN:MainThread] Loaded tool id: text_repeat, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,971 [pN:main,p:38658,tN:MainThread] Loaded tool id: integer_default, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,972 [pN:main,p:38658,tN:MainThread] Loaded tool id: multiple_versions, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,972 [pN:main,p:38658,tN:MainThread] Loaded tool id: multiple_versions_changes, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base ERROR 2024-02-21 12:20:57,973 [pN:main,p:38658,tN:MainThread] Error reading tool from path: interactivetool_simple.xml
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 873, in _load_tool_tag_set
tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 1100, in load_tool
tool = self.create_tool(
^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 547, in create_tool
return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 563, in _create_tool_from_source
return create_tool_from_source(self.app, tool_source, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 355, in create_tool_from_source
tool = ToolClass(config_file, tool_source, app, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 3070, in __init__
assert app.config.interactivetools_enable, ValueError(
AssertionError: Trying to load an InteractiveTool, but InteractiveTools are not enabled.
galaxy.tool_util.toolbox.base ERROR 2024-02-21 12:20:57,973 [pN:main,p:38658,tN:MainThread] Error reading tool from path: interactivetool_two_entry_points.xml
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 873, in _load_tool_tag_set
tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 1100, in load_tool
tool = self.create_tool(
^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 547, in create_tool
return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 563, in _create_tool_from_source
return create_tool_from_source(self.app, tool_source, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 355, in create_tool_from_source
tool = ToolClass(config_file, tool_source, app, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 3070, in __init__
assert app.config.interactivetools_enable, ValueError(
AssertionError: Trying to load an InteractiveTool, but InteractiveTools are not enabled.
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,974 [pN:main,p:38658,tN:MainThread] Loaded tool id: test_CONVERTER_biom, version: 0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,974 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,974 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat_list, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,975 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat_default, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,975 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat_collection, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,975 [pN:main,p:38658,tN:MainThread] Loaded tool id: head, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,975 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat_interleave, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,976 [pN:main,p:38658,tN:MainThread] Loaded tool id: pileup, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,976 [pN:main,p:38658,tN:MainThread] Loaded tool id: mapper, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,976 [pN:main,p:38658,tN:MainThread] Loaded tool id: mapper2, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,977 [pN:main,p:38658,tN:MainThread] Loaded tool id: mapper_two, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,977 [pN:main,p:38658,tN:MainThread] Loaded tool id: split, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,977 [pN:main,p:38658,tN:MainThread] Loaded tool id: empty_list, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,977 [pN:main,p:38658,tN:MainThread] Loaded tool id: count_list, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,978 [pN:main,p:38658,tN:MainThread] Loaded tool id: count_multi_file, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,978 [pN:main,p:38658,tN:MainThread] Loaded tool id: create_input_collection, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base ERROR 2024-02-21 12:20:57,978 [pN:main,p:38658,tN:MainThread] Error reading tool configuration file from path 'for_workflows/randomlines.xml': [Errno 2] No such file or directory
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,978 [pN:main,p:38658,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,979 [pN:main,p:38658,tN:MainThread] Loaded tool id: legacy_R, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,979 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_multi_1, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,979 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_multi_versionless, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,980 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_multi_incomplete, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,980 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_conflict, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,980 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_simple, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,981 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_explicit, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,981 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_invalid_case, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,981 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_broken_no_requirements, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,981 [pN:main,p:38658,tN:MainThread] Loaded tool id: mulled_example_broken_no_requirements_fallback, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,981 [pN:main,p:38658,tN:MainThread] Loaded tool id: explicit_container, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,982 [pN:main,p:38658,tN:MainThread] Loaded tool id: explicit_singularity_container, version: 0.1.0 into tool panel..
galaxy.tool_util.parser.factory INFO 2024-02-21 12:20:57,982 [pN:main,p:38658,tN:MainThread] Loading tool from YAML - this is experimental - tool will not function in future.
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,983 [pN:main,p:38658,tN:MainThread] Loaded tool id: simple_constructs_y, version: 1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,983 [pN:main,p:38658,tN:MainThread] Loaded tool id: from_work_dir_glob, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,983 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat_data_and_sleep, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,983 [pN:main,p:38658,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,983 [pN:main,p:38658,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,983 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,984 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,984 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,984 [pN:main,p:38658,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,984 [pN:main,p:38658,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,984 [pN:main,p:38658,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,984 [pN:main,p:38658,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,984 [pN:main,p:38658,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,984 [pN:main,p:38658,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,984 [pN:main,p:38658,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.2.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,984 [pN:main,p:38658,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,984 [pN:main,p:38658,tN:MainThread] Loaded tool id: __DUPLICATE_FILE_TO_COLLECTION__, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base INFO 2024-02-21 12:20:57,984 [pN:main,p:38658,tN:MainThread] Parsing the tool configuration /Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/shed_tool_conf.xml
galaxy.tool_util.toolbox.base INFO 2024-02-21 12:20:57,984 [pN:main,p:38658,tN:MainThread] Shed-enabled tool configuration file does not exist, but will be created on demand: /Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/shed_tool_conf.xml
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,984 [pN:main,p:38658,tN:MainThread] Reading tools from config files finished (163.624 ms)
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: ncbi_datasets_source, version: 13.14.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: sra_source, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: send_to_cloud, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,986 [pN:main,p:38658,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,987 [pN:main,p:38658,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.views.edam DEBUG 2024-02-21 12:20:57,989 [pN:main,p:38658,tN:MainThread] Loading EDAM tool panel finished (4.506 ms)
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: ncbi_datasets_source, version: 13.14.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: sra_source, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: send_to_cloud, version: 0.1.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,990 [pN:main,p:38658,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.base DEBUG 2024-02-21 12:20:57,991 [pN:main,p:38658,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel..
galaxy.tool_util.toolbox.views.edam DEBUG 2024-02-21 12:20:57,993 [pN:main,p:38658,tN:MainThread] Loading EDAM tool panel finished (3.983 ms)
galaxy.tool_util.deps.installable WARNING 2024-02-21 12:20:57,995 [pN:main,p:38658,tN:MainThread] Conda not installed and auto-installation disabled.
galaxy.tool_util.deps.installable WARNING 2024-02-21 12:20:57,996 [pN:main,p:38658,tN:MainThread] Conda not installed and auto-installation disabled.
galaxy.tool_util.deps.mulled.mulled_build ERROR 2024-02-21 12:20:58,032 [pN:main,p:38658,tN:MainThread] Failed to download involucro from url 'https://github.com/mvdbeek/involucro/releases/download/v1.1.2/involucro.darwin'
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 715, in urlopen
httplib_response = self._make_request(
^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 404, in _make_request
self._validate_conn(conn)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 1058, in _validate_conn
conn.connect()
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connection.py", line 419, in connect
self.sock = ssl_wrap_socket(
^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/util/ssl_.py", line 449, in ssl_wrap_socket
ssl_sock = _ssl_wrap_socket_impl(
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/util/ssl_.py", line 493, in _ssl_wrap_socket_impl
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 517, in wrap_socket
return self.sslsocket_class._create(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1108, in _create
self.do_handshake()
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1383, in do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/adapters.py", line 486, in send
resp = conn.urlopen(
^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 799, in urlopen
retries = retries.increment(
^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/util/retry.py", line 592, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /mvdbeek/involucro/releases/download/v1.1.2/involucro.darwin (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)')))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/deps/mulled/mulled_build.py", line 445, in install_involucro
download_to_file(involucro_link(), install_path)
File "/Users/mvandenb/src/galaxy/lib/galaxy/util/__init__.py", line 1842, in download_to_file
with requests.get(url, timeout=timeout, stream=True) as r, open(dest_file_path, "wb") as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, **send_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/adapters.py", line 517, in send
raise SSLError(e, request=request)
requests.exceptions.SSLError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /mvdbeek/involucro/releases/download/v1.1.2/involucro.darwin (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)')))
galaxy.tool_util.deps.installable WARNING 2024-02-21 12:20:58,033 [pN:main,p:38658,tN:MainThread] Involucro installation requested and failed.
galaxy.tool_util.deps.mulled.mulled_build ERROR 2024-02-21 12:20:58,069 [pN:main,p:38658,tN:MainThread] Failed to download involucro from url 'https://github.com/mvdbeek/involucro/releases/download/v1.1.2/involucro.darwin'
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 715, in urlopen
httplib_response = self._make_request(
^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 404, in _make_request
self._validate_conn(conn)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 1058, in _validate_conn
conn.connect()
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connection.py", line 419, in connect
self.sock = ssl_wrap_socket(
^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/util/ssl_.py", line 449, in ssl_wrap_socket
ssl_sock = _ssl_wrap_socket_impl(
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/util/ssl_.py", line 493, in _ssl_wrap_socket_impl
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 517, in wrap_socket
return self.sslsocket_class._create(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1108, in _create
self.do_handshake()
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1383, in do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/adapters.py", line 486, in send
resp = conn.urlopen(
^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py", line 799, in urlopen
retries = retries.increment(
^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/util/retry.py", line 592, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /mvdbeek/involucro/releases/download/v1.1.2/involucro.darwin (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)')))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/deps/mulled/mulled_build.py", line 445, in install_involucro
download_to_file(involucro_link(), install_path)
File "/Users/mvandenb/src/galaxy/lib/galaxy/util/__init__.py", line 1842, in download_to_file
with requests.get(url, timeout=timeout, stream=True) as r, open(dest_file_path, "wb") as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, **send_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/requests/adapters.py", line 517, in send
raise SSLError(e, request=request)
requests.exceptions.SSLError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /mvdbeek/involucro/releases/download/v1.1.2/involucro.darwin (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1006)')))
galaxy.tool_util.deps.installable WARNING 2024-02-21 12:20:58,070 [pN:main,p:38658,tN:MainThread] Involucro installation requested and failed.
galaxy.tools.data_manager.manager DEBUG 2024-02-21 12:20:58,075 [pN:main,p:38658,tN:MainThread] Loaded Data Manager: test_data_manager
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,076 [pN:main,p:38658,tN:MainThread] Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,077 [pN:main,p:38658,tN:MainThread] Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,080 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,080 [pN:main,p:38658,tN:MainThread] Loaded display application 'igb_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,080 [pN:main,p:38658,tN:MainThread] Loaded display application 'iobio_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,080 [pN:main,p:38658,tN:MainThread] Loaded display application 'igb_bed' for datatype 'bed', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,080 [pN:main,p:38658,tN:MainThread] Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,081 [pN:main,p:38658,tN:MainThread] Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,081 [pN:main,p:38658,tN:MainThread] Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,081 [pN:main,p:38658,tN:MainThread] Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,081 [pN:main,p:38658,tN:MainThread] Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,081 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,081 [pN:main,p:38658,tN:MainThread] Loaded display application 'intermine_simple' for datatype 'intermine_tabular', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,083 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,084 [pN:main,p:38658,tN:MainThread] Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,086 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_gff' for datatype 'gff', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,086 [pN:main,p:38658,tN:MainThread] Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,086 [pN:main,p:38658,tN:MainThread] Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,087 [pN:main,p:38658,tN:MainThread] Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,087 [pN:main,p:38658,tN:MainThread] Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,089 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,089 [pN:main,p:38658,tN:MainThread] Loaded display application 'avivator' for datatype 'ome.tiff', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,089 [pN:main,p:38658,tN:MainThread] Loaded display application 'q2view' for datatype 'qza', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,089 [pN:main,p:38658,tN:MainThread] Loaded display application 'q2view' for datatype 'qzv', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,090 [pN:main,p:38658,tN:MainThread] Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,090 [pN:main,p:38658,tN:MainThread] Loaded display application 'minerva_tabular' for datatype 'tabular', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,090 [pN:main,p:38658,tN:MainThread] Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,093 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,093 [pN:main,p:38658,tN:MainThread] Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,093 [pN:main,p:38658,tN:MainThread] Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,093 [pN:main,p:38658,tN:MainThread] Loaded display application 'igb_wig' for datatype 'wig', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,096 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Loaded display application 'igv_genbank' for datatype 'genbank', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Loaded display application 'biom_simple' for datatype 'biom1', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'sdf', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'mol2', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'pdb', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False.
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'probed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'probed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'probed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'probed'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,098 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'fasta.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'a3m'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.bz2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.bz2'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'sequences'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'interval_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'interval_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'interval_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'interval_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'juicer_medium_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'juicer_medium_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'juicer_medium_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'juicer_medium_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'gff_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'gff_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'gff_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,099 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'gff_tabix.gz'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,100 [pN:main,p:38658,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'mothur.align'
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,101 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,101 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,102 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,102 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,103 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,103 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,103 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_Bam_Bai_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,104 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,104 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,104 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,105 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,105 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,105 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_cram_to_bam_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,106 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_to_gff_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,106 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,107 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,107 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,108 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_to_fli_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,108 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bedgraph_to_bigwig
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,108 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_len_to_linecount
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,109 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_parquet_to_csv
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,109 [pN:main,p:38658,tN:MainThread] Loaded converter: bigwigtowig
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,110 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,111 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,111 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,111 [pN:main,p:38658,tN:MainThread] Loaded converter: csv_to_tabular
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,111 [pN:main,p:38658,tN:MainThread] Loaded converter: tabular_to_csv
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,112 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fasta_to_tabular
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,112 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_base_index
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,112 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_color_index
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,112 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fasta_to_2bit
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,113 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fasta_to_len
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,113 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fasta_to_fai
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,114 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,114 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,114 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,114 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,115 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,116 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,116 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,116 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,116 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,117 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,117 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,117 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,118 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,118 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,118 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,118 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,119 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,119 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,119 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,119 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,120 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,120 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,120 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gff_to_bed_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,121 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,121 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,121 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gff_to_fli_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,122 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,122 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,123 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,123 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,123 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,123 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,123 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,124 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,124 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bedstrict_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,124 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed6_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,124 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed12_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,125 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,126 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,126 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,126 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_picard_interval_list_to_bed6
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,127 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_tar_to_directory
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,127 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,127 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,128 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,128 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,128 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,128 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,129 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_maf_to_fasta_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,129 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_maf_to_interval_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,129 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,130 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,130 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,131 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,131 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,132 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_sam_to_unsorted_bam
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,132 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,132 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,132 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_sam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,133 [pN:main,p:38658,tN:MainThread] Loaded converter: tabular_to_dbnsfp
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,133 [pN:main,p:38658,tN:MainThread] Loaded converter: tabular_to_csv
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,133 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,133 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,134 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,134 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,135 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,135 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,136 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,136 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,136 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,137 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_wig_to_bigwig
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,137 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_wiggle_to_interval_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,137 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,138 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,138 [pN:main,p:38658,tN:MainThread] Loaded converter: lped2fpedconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,138 [pN:main,p:38658,tN:MainThread] Loaded converter: lped2pbedconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,138 [pN:main,p:38658,tN:MainThread] Loaded converter: pbed2lpedconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,138 [pN:main,p:38658,tN:MainThread] Loaded converter: pbed2ldindepconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,139 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,139 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,139 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_biom
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,140 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_biom
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,141 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,143 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,144 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,144 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_SMILES_to_MOL
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,145 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,146 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_smiles_to_smiles
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,147 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,149 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,150 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,151 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,153 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,154 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,154 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_inchi_to_mol
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,155 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,157 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,158 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,159 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,161 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,162 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,163 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,165 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,166 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,167 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,167 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_mol2_to_mol
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,169 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,169 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_cml_to_smiles
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,170 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,172 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,173 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_molecules
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,173 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_Pdb_to_Gro_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,174 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,174 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,175 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,175 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,175 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,176 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_mdconvert
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,176 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_Gro_to_Pdb_0
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,176 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_ref_to_seq_taxomony
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,177 [pN:main,p:38658,tN:MainThread] Loaded converter: CONVERTER_neostorezip_to_neostore
galaxy.datatypes.registry DEBUG 2024-02-21 12:20:58,177 [pN:main,p:38658,tN:MainThread] Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2024-02-21 12:20:58,177 [pN:main,p:38658,tN:MainThread] Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2024-02-21 12:20:58,178 [pN:main,p:38658,tN:MainThread] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__
galaxy.tools.special_tools DEBUG 2024-02-21 12:20:58,178 [pN:main,p:38658,tN:MainThread] Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2024-02-21 12:20:58,178 [pN:main,p:38658,tN:MainThread] Loaded data fetch tool: __DATA_FETCH__
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,179 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: PCA_3Dplot
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,180 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,180 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:58,180 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,180 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:58,181 [pN:main,p:38658,tN:MainThread] Visualizations plugin disabled: Circster. Skipping...
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:58,181 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,182 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: csg
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,182 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,182 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,183 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: editor
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,183 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: example
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:58,184 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,184 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: fits_image_viewer
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:58,185 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,185 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,185 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: h5web
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,187 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,188 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_default
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:58,188 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,188 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:58,188 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,188 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,190 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,190 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,191 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,191 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,192 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:58,192 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,192 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: audio_player
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:58,192 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,192 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: video_player
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,193 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: msa
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:58,193 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,193 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,194 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,195 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nora
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,196 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,197 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,198 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,198 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,199 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,199 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,200 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,200 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,201 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,201 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,202 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,202 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,203 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,203 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,204 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,205 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,205 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: phyloviz
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,206 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: pv
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,206 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:58,206 [pN:main,p:38658,tN:MainThread] Visualizations plugin disabled: Sweepster. Skipping...
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,207 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,207 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: ts_visjs
galaxy.visualization.plugins.config_parser INFO 2024-02-21 12:20:58,207 [pN:main,p:38658,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,207 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept
galaxy.visualization.plugins.registry INFO 2024-02-21 12:20:58,207 [pN:main,p:38658,tN:MainThread] VisualizationsRegistry, loaded plugin: venn
galaxy.tours._impl INFO 2024-02-21 12:20:58,213 [pN:main,p:38658,tN:MainThread] Loaded tour 'core.galaxy_ui'
galaxy.tours._impl INFO 2024-02-21 12:20:58,217 [pN:main,p:38658,tN:MainThread] Loaded tour 'core.deferred'
galaxy.tours._impl INFO 2024-02-21 12:20:58,219 [pN:main,p:38658,tN:MainThread] Loaded tour 'core.windows'
galaxy.tours._impl INFO 2024-02-21 12:20:58,222 [pN:main,p:38658,tN:MainThread] Loaded tour 'core.history'
galaxy.jobs.manager DEBUG 2024-02-21 12:20:58,240 [pN:main,p:38658,tN:MainThread] Initializing job handler
galaxy.jobs INFO 2024-02-21 12:20:58,240 [pN:main,p:38658,tN:MainThread] Handler 'main' will load all configured runner plugins
galaxy.jobs.runners.state_handler_factory DEBUG 2024-02-21 12:20:58,240 [pN:main,p:38658,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs DEBUG 2024-02-21 12:20:58,240 [pN:main,p:38658,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
galaxy.jobs.runners.state_handler_factory DEBUG 2024-02-21 12:20:58,240 [pN:main,p:38658,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs.runners DEBUG 2024-02-21 12:20:58,240 [pN:main,p:38658,tN:MainThread] Starting 4 TaskRunner workers
galaxy.jobs DEBUG 2024-02-21 12:20:58,240 [pN:main,p:38658,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks'
galaxy.jobs.handler DEBUG 2024-02-21 12:20:58,240 [pN:main,p:38658,tN:MainThread] Loaded job runners plugins: local:tasks
galaxy.jobs.runners DEBUG 2024-02-21 12:20:58,245 [pN:main,p:38658,tN:MainThread] Starting 4 LocalRunner workers
galaxy.jobs.runners DEBUG 2024-02-21 12:20:58,245 [pN:main,p:38658,tN:MainThread] Starting 4 TaskRunner workers
galaxy.jobs.handler DEBUG 2024-02-21 12:20:58,245 [pN:main,p:38658,tN:MainThread] Handler queue starting for jobs assigned to handler: main
galaxy.jobs.handler INFO 2024-02-21 12:20:58,252 [pN:main,p:38658,tN:JobHandlerQueue.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method for handler 'main', tag(s):
galaxy.jobs.handler INFO 2024-02-21 12:20:58,252 [pN:main,p:38658,tN:MainThread] job handler queue started
galaxy.jobs.handler INFO 2024-02-21 12:20:58,253 [pN:main,p:38658,tN:MainThread] job handler stop queue started
galaxy.workflow.scheduling_manager INFO 2024-02-21 12:20:58,253 [pN:main,p:38658,tN:MainThread] No workflow schedulers plugin config file defined, using default scheduler.
galaxy.web_stack.handlers INFO 2024-02-21 12:20:58,253 [pN:main,p:38658,tN:MainThread] WorkflowSchedulingManager: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on <handlers> to override the default
galaxy.workflow.scheduling_manager DEBUG 2024-02-21 12:20:58,253 [pN:main,p:38658,tN:MainThread] Starting workflow schedulers
galaxy.jobs.handler INFO 2024-02-21 12:20:58,253 [pN:main,p:38658,tN:WorkflowRequestMonitor.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method for handler 'main', tag(s): _default_, None
galaxy.queue_worker INFO 2024-02-21 12:20:58,253 [pN:main,p:38658,tN:MainThread] Binding and starting galaxy control worker for main
galaxy.queue_worker INFO 2024-02-21 12:20:58,254 [pN:main,p:38658,tN:MainThread] Queuing async task rebuild_toolbox_search_index for main.
galaxy.app INFO 2024-02-21 12:20:58,260 [pN:main,p:38658,tN:MainThread] Galaxy app startup finished (1124.773 ms)
test_driver INFO 2024-02-21 12:20:58,260 [pN:main,p:38658,tN:MainThread] Embedded Galaxy application started
galaxy.tools.search DEBUG 2024-02-21 12:20:58,260 [pN:main,p:38658,tN:MainThread] Starting to build toolbox index of panel default.
galaxy.model.database_heartbeat DEBUG 2024-02-21 12:20:58,284 [pN:main,p:38658,tN:database_heartbeart_main.thread] main is config watcher
galaxy.queue_worker INFO 2024-02-21 12:20:58,290 [pN:main,p:38658,tN:Thread-10] Instance 'main' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2024-02-21 12:20:58,293 [pN:main,p:38658,tN:MainThread] Toolbox index of panel default finished (32.457 ms)
galaxy.tools.search DEBUG 2024-02-21 12:20:58,293 [pN:main,p:38658,tN:MainThread] Starting to build toolbox index of panel ontology:edam_operations.
galaxy.tools.search DEBUG 2024-02-21 12:20:58,313 [pN:main,p:38658,tN:MainThread] Toolbox index of panel ontology:edam_operations finished (20.478 ms)
galaxy.tools.search DEBUG 2024-02-21 12:20:58,313 [pN:main,p:38658,tN:MainThread] Starting to build toolbox index of panel ontology:edam_topics.
galaxy.tools.search DEBUG 2024-02-21 12:20:58,331 [pN:main,p:38658,tN:MainThread] Toolbox index of panel ontology:edam_topics finished (17.797 ms)
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,332 [pN:main,p:38658,tN:MainThread] Enabling 'user' controller, class: User
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,332 [pN:main,p:38658,tN:MainThread] Enabling 'error' controller, class: Error
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,332 [pN:main,p:38658,tN:MainThread] Enabling 'page' controller, class: PageController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,332 [pN:main,p:38658,tN:MainThread] Enabling 'visualization' controller, class: VisualizationController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,333 [pN:main,p:38658,tN:MainThread] Enabling 'dataset' controller, class: DatasetInterface
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,333 [pN:main,p:38658,tN:MainThread] Enabling 'forms' controller, class: Forms
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,333 [pN:main,p:38658,tN:MainThread] Enabling 'admin' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,333 [pN:main,p:38658,tN:MainThread] Enabling 'shed_tool_static' controller, class: ShedToolStatic
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,333 [pN:main,p:38658,tN:MainThread] Enabling 'tool_runner' controller, class: ToolRunner
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,333 [pN:main,p:38658,tN:MainThread] Enabling 'admin_toolshed' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,334 [pN:main,p:38658,tN:MainThread] Enabling 'admin_toolshed' controller, class: AdminToolshed
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,334 [pN:main,p:38658,tN:MainThread] Enabling 'workflow' controller, class: WorkflowController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,334 [pN:main,p:38658,tN:MainThread] Enabling 'async' controller, class: ASync
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,334 [pN:main,p:38658,tN:MainThread] Enabling 'data_manager' controller, class: DataManager
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,334 [pN:main,p:38658,tN:MainThread] Enabling 'root' controller, class: RootController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,334 [pN:main,p:38658,tN:MainThread] Enabling 'tag' controller, class: TagsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,334 [pN:main,p:38658,tN:MainThread] Enabling 'authnz' controller, class: JSAppLauncher
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,334 [pN:main,p:38658,tN:MainThread] Enabling 'authnz' controller, class: OIDC
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,334 [pN:main,p:38658,tN:MainThread] Enabling 'history' controller, class: HistoryController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,335 [pN:main,p:38658,tN:MainThread] Enabling 'container_resolution' API controller, class: ContainerResolutionAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,335 [pN:main,p:38658,tN:MainThread] Enabling 'library_contents' API controller, class: LibraryContentsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,335 [pN:main,p:38658,tN:MainThread] Enabling 'plugins' API controller, class: PluginsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,335 [pN:main,p:38658,tN:MainThread] Enabling 'tool_entry_points' API controller, class: ToolEntryPointsAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,336 [pN:main,p:38658,tN:MainThread] Enabling 'users' API controller, class: UserAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,336 [pN:main,p:38658,tN:MainThread] Enabling 'toolshed' API controller, class: ToolShedController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,336 [pN:main,p:38658,tN:MainThread] Enabling 'tools' API controller, class: ToolsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,336 [pN:main,p:38658,tN:MainThread] Enabling 'library_datasets' API controller, class: LibraryDatasetsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,336 [pN:main,p:38658,tN:MainThread] Enabling 'page_revisions' API controller, class: PageRevisionsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,337 [pN:main,p:38658,tN:MainThread] Enabling 'forms' API controller, class: FormDefinitionAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,337 [pN:main,p:38658,tN:MainThread] Enabling 'visualizations' API controller, class: VisualizationsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,337 [pN:main,p:38658,tN:MainThread] Enabling 'jobs' API controller, class: JobController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,337 [pN:main,p:38658,tN:MainThread] Enabling 'job_ports' API controller, class: JobPortsAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,337 [pN:main,p:38658,tN:MainThread] Enabling 'trs_search' API controller, class: TrsSearchAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,337 [pN:main,p:38658,tN:MainThread] Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,337 [pN:main,p:38658,tN:MainThread] Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,337 [pN:main,p:38658,tN:MainThread] Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,337 [pN:main,p:38658,tN:MainThread] Enabling 'trs_consumer' API controller, class: TrsConsumeAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,338 [pN:main,p:38658,tN:MainThread] Enabling 'workflows' API controller, class: WorkflowsAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,338 [pN:main,p:38658,tN:MainThread] Enabling 'cloudauthz' API controller, class: CloudAuthzController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,338 [pN:main,p:38658,tN:MainThread] Enabling 'sanitize_allow' API controller, class: SanitizeAllowController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,338 [pN:main,p:38658,tN:MainThread] Enabling 'job_files' API controller, class: JobFilesAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,338 [pN:main,p:38658,tN:MainThread] Enabling 'uploads' API controller, class: UploadsAPIController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,338 [pN:main,p:38658,tN:MainThread] Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,338 [pN:main,p:38658,tN:MainThread] Enabling 'history_content_provenance' API controller, class: HDAProvenanceController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,339 [pN:main,p:38658,tN:MainThread] Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,339 [pN:main,p:38658,tN:MainThread] Enabling 'webhooks' API controller, class: WebhooksController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,339 [pN:main,p:38658,tN:MainThread] Enabling 'dynamic_tools' API controller, class: DynamicToolsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,339 [pN:main,p:38658,tN:MainThread] Enabling 'authenticate' API controller, class: AuthenticationController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,339 [pN:main,p:38658,tN:MainThread] Enabling 'history_annotations' API controller, class: HistoryAnnotationsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,339 [pN:main,p:38658,tN:MainThread] Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController
galaxy.web.framework.base DEBUG 2024-02-21 12:20:58,339 [pN:main,p:38658,tN:MainThread] Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController
galaxy.webapps.util DEBUG 2024-02-21 12:20:58,376 [pN:main,p:38658,tN:MainThread] Enabling 'paste.httpexceptions' middleware
galaxy.webapps.util DEBUG 2024-02-21 12:20:58,376 [pN:main,p:38658,tN:MainThread] Enabling 'ErrorMiddleware' middleware
galaxy.webapps.util DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Enabling 'TusMiddleware' middleware
galaxy.webapps.util DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Enabling 'TusMiddleware' middleware
galaxy.webapps.util DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Enabling 'XForwardedHostMiddleware' middleware
galaxy.webapps.util DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Enabling 'RequestIDMiddleware' middleware
galaxy.webapps.util DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Enabling 'build_url_map' middleware
galaxy.web_stack INFO 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Galaxy server instance 'main' is running
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 8003690176)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(Thread-2 (start), started daemon 6108590080)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-0, started daemon 11377078272)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-1, started daemon 11393904640)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-2, started daemon 11410731008)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-3, started daemon 11427557376)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-0, started daemon 11444383744)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-1, started daemon 11461210112)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-2, started daemon 11478036480)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-3, started daemon 11494862848)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-0, started daemon 11511689216)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-1, started daemon 11528515584)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-2, started daemon 11545341952)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-3, started daemon 11562168320)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(JobHandlerQueue.monitor_thread, started daemon 11578994688)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(JobHandlerStopQueue.monitor_thread, started daemon 11595821056)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(WorkflowRequestMonitor.monitor_thread, started daemon 11612647424)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(database_heartbeart_main.thread, started daemon 11629473792)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <GalaxyQueueWorker(Thread-10, started daemon 11646300160)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(Thread-12 (check), started daemon 11854245888)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2024-02-21 12:20:58,377 [pN:main,p:38658,tN:MainThread] Prior to webapp return, Galaxy thread <Thread(Thread-13 (check), started daemon 11871072256)> is alive.
asyncio DEBUG 2024-02-21 12:21:00,316 [pN:main,p:38658,tN:MainThread] Using selector: KqueueSelector
INFO: Started server process [38658]
INFO: Waiting for application startup.
INFO: Application startup complete.
INFO: Uvicorn running on http://127.0.0.1:9500 (Press CTRL+C to quit)
INFO: 127.0.0.1:52158 - "GET / HTTP/1.1" 200 OK
test_driver DEBUG 2024-02-21 12:21:00,436 [pN:main,p:38658,tN:MainThread] Embedded uvicorn web server for galaxy started at 127.0.0.1:9500/
py.warnings WARNING 2024-02-21 12:21:00,683 [pN:main,p:38658,tN:WSGI_0] /Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py:1061: InsecureRequestWarning: Unverified HTTPS request is being made to host 'localhost'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#ssl-warnings
warnings.warn(
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:00,820 [pN:main,p:38658,tN:WSGI_0] Generated new state 029k0ORcRyeHu0vGGhShJ6bIwbAPS2.
INFO: 127.0.0.1:52159 - "GET /authnz/keycloak/login HTTP/1.1" 200 OK
py.warnings WARNING 2024-02-21 12:21:00,833 [pN:main,p:38658,tN:MainThread] /Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py:1061: InsecureRequestWarning: Unverified HTTPS request is being made to host 'localhost'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#ssl-warnings
warnings.warn(
py.warnings WARNING 2024-02-21 12:21:01,046 [pN:main,p:38658,tN:MainThread] /Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py:1061: InsecureRequestWarning: Unverified HTTPS request is being made to host 'localhost'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#ssl-warnings
warnings.warn(
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,234 [pN:main,p:38658,tN:WSGI_0] Encoding `client_id` "gxyclient" with `client_secret` as Basic auth credentials.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,235 [pN:main,p:38658,tN:WSGI_0] Requesting url https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token using method POST.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,235 [pN:main,p:38658,tN:WSGI_0] Supplying headers {'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0'} and data {'grant_type': 'authorization_code', 'code': 'ff436d5b-5635-45cc-805a-0f8369b2c1d2.9e7f24a4-79c5-40c8-9809-365aea187c49.52e25e17-fdb7-423a-83ab-90c27711d391', 'redirect_uri': 'http://127.0.0.1:9500/authnz/keycloak/callback'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,235 [pN:main,p:38658,tN:WSGI_0] Passing through key word arguments {'timeout': None, 'auth': <requests.auth.HTTPBasicAuth object at 0x2c5b0b4d0>, 'verify': False, 'proxies': None, 'cert': None}.
py.warnings WARNING 2024-02-21 12:21:01,242 [pN:main,p:38658,tN:WSGI_0] /Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/urllib3/connectionpool.py:1061: InsecureRequestWarning: Unverified HTTPS request is being made to host 'localhost'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#ssl-warnings
warnings.warn(
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,279 [pN:main,p:38658,tN:WSGI_0] Request to fetch token completed with status 200.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,279 [pN:main,p:38658,tN:WSGI_0] Request url was https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,279 [pN:main,p:38658,tN:WSGI_0] Request headers were {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0', 'Content-Length': '219', 'Content-Type': 'application/x-www-form-urlencoded'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,279 [pN:main,p:38658,tN:WSGI_0] Request body was grant_type=authorization_code&code=ff436d5b-5635-45cc-805a-0f8369b2c1d2.9e7f24a4-79c5-40c8-9809-365aea187c49.52e25e17-fdb7-423a-83ab-90c27711d391&redirect_uri=http%3A%2F%2F127.0.0.1%3A9500%2Fauthnz%2Fkeycloak%2Fcallback
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,279 [pN:main,p:38658,tN:WSGI_0] Response headers were {'Referrer-Policy': 'no-referrer', 'X-Frame-Options': 'SAMEORIGIN', 'Strict-Transport-Security': 'max-age=31536000; includeSubDomains', 'Cache-Control': 'no-store', 'X-Content-Type-Options': 'nosniff', 'Pragma': 'no-cache', 'X-XSS-Protection': '1; mode=block', 'Content-Type': 'application/json', 'content-length': '3824'} and content {"access_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.qeRbXiMKDFqBl51s91sYD066fOd2FPR9vb1RkLZh-m5p2N9DAfIVlUlKkZY9j2xliSSgy5uuxB-4VsVYPWzMxxA7IQR3U0C2Rn7AKG4b_GknxT9M8qp5lZF8559UYD9bKkV0lXP1DrIuFMvOmKcU6-XGHeS_kFazMnEnu8z02Nn7z3W2S1318wTcmX-nYTth3isjO8-5Xl1v0b-u23doXoBl0jji9dmraHJUhBmIW3bdUGFn-hELtXo-Do4vUCYiOzeqVwwGAlDxXzaisuHCU7P6HN6dKk6rLsMLrxRHsUm84gmP9gyqypcMTR-qNoGRrHFslXZYdh7pJ5kex6_E-Q","expires_in":6,"refresh_expires_in":1800,"refresh_token":"eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.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.eIk-sDV7hPcbYQmXQd2D3Aat0nzq70g6P12m5ePhIe4","token_type":"Bearer","id_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.I1ZSq74V-uwTfSR79KbzkmLbZsJ7ZwQ8t3zSXJCTAxpRtGBpuw1hhShQHP1DB8NjUsuBLQUNKEriIFEFx4SV-3mc2XjaYw4zkXENDhNGkn3U-jWHYjVNyN5wJhx2IYLhP0_e5ltiiCd31vZrp_-XzkPk4iRC1l_iKai31Z72LpZV4vasjmGTd99OcownFw9ehzjnyY4EboprwEtLFrWblToBuN0TkXIDkwoVc9GCS7BOXdK6Y5e1_4O7KJuuQkEcOer010OOiBeNLfe1mA--0YbiqkQb4ctsh_328weYdLUNgLSDwnjxhYkXG4QszXO06oYwIRYXciUwBlYPXdQO7g","not-before-policy":0,"session_state":"9e7f24a4-79c5-40c8-9809-365aea187c49","scope":"openid profile email https://galaxyproject.org/api:*"}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,280 [pN:main,p:38658,tN:WSGI_0] Invoking 0 token response hooks.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,280 [pN:main,p:38658,tN:WSGI_0] Obtained token {'access_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.qeRbXiMKDFqBl51s91sYD066fOd2FPR9vb1RkLZh-m5p2N9DAfIVlUlKkZY9j2xliSSgy5uuxB-4VsVYPWzMxxA7IQR3U0C2Rn7AKG4b_GknxT9M8qp5lZF8559UYD9bKkV0lXP1DrIuFMvOmKcU6-XGHeS_kFazMnEnu8z02Nn7z3W2S1318wTcmX-nYTth3isjO8-5Xl1v0b-u23doXoBl0jji9dmraHJUhBmIW3bdUGFn-hELtXo-Do4vUCYiOzeqVwwGAlDxXzaisuHCU7P6HN6dKk6rLsMLrxRHsUm84gmP9gyqypcMTR-qNoGRrHFslXZYdh7pJ5kex6_E-Q', 'expires_in': 6, 'refresh_expires_in': 1800, 'refresh_token': 'eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.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.eIk-sDV7hPcbYQmXQd2D3Aat0nzq70g6P12m5ePhIe4', 'token_type': 'Bearer', 'id_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.I1ZSq74V-uwTfSR79KbzkmLbZsJ7ZwQ8t3zSXJCTAxpRtGBpuw1hhShQHP1DB8NjUsuBLQUNKEriIFEFx4SV-3mc2XjaYw4zkXENDhNGkn3U-jWHYjVNyN5wJhx2IYLhP0_e5ltiiCd31vZrp_-XzkPk4iRC1l_iKai31Z72LpZV4vasjmGTd99OcownFw9ehzjnyY4EboprwEtLFrWblToBuN0TkXIDkwoVc9GCS7BOXdK6Y5e1_4O7KJuuQkEcOer010OOiBeNLfe1mA--0YbiqkQb4ctsh_328weYdLUNgLSDwnjxhYkXG4QszXO06oYwIRYXciUwBlYPXdQO7g', 'not-before-policy': 0, 'session_state': '9e7f24a4-79c5-40c8-9809-365aea187c49', 'scope': ['openid', 'profile', 'email', 'https://galaxyproject.org/api:*'], 'expires_at': 1708514467.280378}.
INFO: 127.0.0.1:52159 - "GET /authnz/keycloak/callback?state=029k0ORcRyeHu0vGGhShJ6bIwbAPS2&session_state=9e7f24a4-79c5-40c8-9809-365aea187c49&code=ff436d5b-5635-45cc-805a-0f8369b2c1d2.9e7f24a4-79c5-40c8-9809-365aea187c49.52e25e17-fdb7-423a-83ab-90c27711d391 HTTP/1.1" 302 Found
INFO: 127.0.0.1:52159 - "GET /user/external_ids?notification=Your%20Keycloak%20identity%20has%20been%20linked%20to%20your%20Galaxy%20account. HTTP/1.1" 200 OK
INFO: 127.0.0.1:52169 - "GET /api/users/current HTTP/1.1" 200 OK
PASSEDINFO: 127.0.0.1:52170 - "GET /api/jobs?state=running HTTP/1.1" 200 OK
test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_oidc_login_existing_user requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,446 [pN:main,p:38658,tN:WSGI_0] Generated new state 7l6Fo47IYTarfdWLDb4WXCGFqFYUxa.
INFO: 127.0.0.1:52171 - "GET /authnz/keycloak/login HTTP/1.1" 200 OK
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,497 [pN:main,p:38658,tN:WSGI_0] Encoding `client_id` "gxyclient" with `client_secret` as Basic auth credentials.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,498 [pN:main,p:38658,tN:WSGI_0] Requesting url https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token using method POST.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,498 [pN:main,p:38658,tN:WSGI_0] Supplying headers {'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0'} and data {'grant_type': 'authorization_code', 'code': '1633679b-60d1-49bf-84af-06b046cbaa0b.af4cbfb9-2239-4d99-bc6f-3fa05aafbfd3.52e25e17-fdb7-423a-83ab-90c27711d391', 'redirect_uri': 'http://127.0.0.1:9500/authnz/keycloak/callback'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,498 [pN:main,p:38658,tN:WSGI_0] Passing through key word arguments {'timeout': None, 'auth': <requests.auth.HTTPBasicAuth object at 0x2c82fd150>, 'verify': False, 'proxies': None, 'cert': None}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,515 [pN:main,p:38658,tN:WSGI_0] Request to fetch token completed with status 200.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,515 [pN:main,p:38658,tN:WSGI_0] Request url was https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,515 [pN:main,p:38658,tN:WSGI_0] Request headers were {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0', 'Content-Length': '219', 'Content-Type': 'application/x-www-form-urlencoded'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,515 [pN:main,p:38658,tN:WSGI_0] Request body was grant_type=authorization_code&code=1633679b-60d1-49bf-84af-06b046cbaa0b.af4cbfb9-2239-4d99-bc6f-3fa05aafbfd3.52e25e17-fdb7-423a-83ab-90c27711d391&redirect_uri=http%3A%2F%2F127.0.0.1%3A9500%2Fauthnz%2Fkeycloak%2Fcallback
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,515 [pN:main,p:38658,tN:WSGI_0] Response headers were {'Referrer-Policy': 'no-referrer', 'X-Frame-Options': 'SAMEORIGIN', 'Strict-Transport-Security': 'max-age=31536000; includeSubDomains', 'Cache-Control': 'no-store', 'X-Content-Type-Options': 'nosniff', 'Pragma': 'no-cache', 'X-XSS-Protection': '1; mode=block', 'Content-Type': 'application/json', 'content-length': '3848'} and content {"access_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.CFV5BrA0mGtyp5zqOoBpj7GiMdYDIhGKbXrBLxhKojGA5WeelDFEE5Pqu6GujndBeWPXdNZpPSO9Esc2h2nwlBOMe2giWcoU9AqVjYHk_oxPmB0jK4HK_B_Iagqa7QzZDxGFfNCGWUCAWv7RHzrzh6Ohe9bbhejiknFNOh2FyVGyDxzNi9VR4N0bHCTnd_yHMILQU3SWv-67rCriWgJuRD31NiINWcVHC6yMvhFfT4zI8eTUIkFFtWGCaiaBQL4lV78Hvevcy4E14ORFtde6qGNQy0eHJRvfD0ufxvy6N68yGSYd_rprLvypFAiUCUYO1NEhd11ORPCVqdlUixTtkQ","expires_in":6,"refresh_expires_in":1800,"refresh_token":"eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.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.XhrQZFHxSXdDPysrE8YrkegxuSsP19NEaISms2FHysk","token_type":"Bearer","id_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.hOQR9QVAF3Go-CVwksEv6-RuHiCfUOeTpn-ITHitbM-tqrMDuf3efjwI3We-aP1vWQOD1hN84ZSiobahrphg1tOuUJNo_wxFqHtNdD7azjr8ThtdFLCvELNRHf-aFkksVybKMMdkhnZpGPALDvDPOW5n9jrd0rAS0dJuDzCkgZ49mV8gXWPO5SWXwEfmAvfinlW7tHlau0L0nZHPfDOCNV9-Qr7mkkTeXBLQs5q9i5kblIFioL0f2bjnzXpfi5Zv1Nuh3SJtw4iDaeO_OL6i6neDFAq4gfquztTUrcY6jdc7yn8sLeWmf2RRregP2ctT8Y1AX3nBdPDlm-OZkMPm5Q","not-before-policy":0,"session_state":"af4cbfb9-2239-4d99-bc6f-3fa05aafbfd3","scope":"openid profile email https://galaxyproject.org/api:*"}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,515 [pN:main,p:38658,tN:WSGI_0] Invoking 0 token response hooks.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,516 [pN:main,p:38658,tN:WSGI_0] Obtained token {'access_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.CFV5BrA0mGtyp5zqOoBpj7GiMdYDIhGKbXrBLxhKojGA5WeelDFEE5Pqu6GujndBeWPXdNZpPSO9Esc2h2nwlBOMe2giWcoU9AqVjYHk_oxPmB0jK4HK_B_Iagqa7QzZDxGFfNCGWUCAWv7RHzrzh6Ohe9bbhejiknFNOh2FyVGyDxzNi9VR4N0bHCTnd_yHMILQU3SWv-67rCriWgJuRD31NiINWcVHC6yMvhFfT4zI8eTUIkFFtWGCaiaBQL4lV78Hvevcy4E14ORFtde6qGNQy0eHJRvfD0ufxvy6N68yGSYd_rprLvypFAiUCUYO1NEhd11ORPCVqdlUixTtkQ', 'expires_in': 6, 'refresh_expires_in': 1800, 'refresh_token': 'eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.eyJleHAiOjE3MDg1MTYyNjEsImlhdCI6MTcwODUxNDQ2MSwianRpIjoiZDczNGVlNWItN2QzYy00NGNkLTk0YzYtOGRkYjc2Y2Y1MDkyIiwiaXNzIjoiaHR0cHM6Ly9sb2NhbGhvc3Q6OTQ0My9yZWFsbXMvZ3h5cmVhbG0iLCJhdWQiOiJodHRwczovL2xvY2FsaG9zdDo5NDQzL3JlYWxtcy9neHlyZWFsbSIsInN1YiI6IjI0ZmZhM2ZmLWQzNTEtNGQ1ZS1iMTBiLThkNjE1MDgyZWM5YiIsInR5cCI6IlJlZnJlc2giLCJhenAiOiJneHljbGllbnQiLCJub25jZSI6ImUzMTMzNzYzZDRiNWQyM2ZmMTFiMzRhMmQzMTU2NDNiODRlNTA0NDViNTZjZTU0ODAzYzYyZTEzZjdkMjA2YWQiLCJzZXNzaW9uX3N0YXRlIjoiYWY0Y2JmYjktMjIzOS00ZDk5LWJjNmYtM2ZhMDVhYWZiZmQzIiwic2NvcGUiOiJvcGVuaWQgcHJvZmlsZSBlbWFpbCBodHRwczovL2dhbGF4eXByb2plY3Qub3JnL2FwaToqIiwic2lkIjoiYWY0Y2JmYjktMjIzOS00ZDk5LWJjNmYtM2ZhMDVhYWZiZmQzIn0.XhrQZFHxSXdDPysrE8YrkegxuSsP19NEaISms2FHysk', 'token_type': 'Bearer', 'id_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.hOQR9QVAF3Go-CVwksEv6-RuHiCfUOeTpn-ITHitbM-tqrMDuf3efjwI3We-aP1vWQOD1hN84ZSiobahrphg1tOuUJNo_wxFqHtNdD7azjr8ThtdFLCvELNRHf-aFkksVybKMMdkhnZpGPALDvDPOW5n9jrd0rAS0dJuDzCkgZ49mV8gXWPO5SWXwEfmAvfinlW7tHlau0L0nZHPfDOCNV9-Qr7mkkTeXBLQs5q9i5kblIFioL0f2bjnzXpfi5Zv1Nuh3SJtw4iDaeO_OL6i6neDFAq4gfquztTUrcY6jdc7yn8sLeWmf2RRregP2ctT8Y1AX3nBdPDlm-OZkMPm5Q', 'not-before-policy': 0, 'session_state': 'af4cbfb9-2239-4d99-bc6f-3fa05aafbfd3', 'scope': ['openid', 'profile', 'email', 'https://galaxyproject.org/api:*'], 'expires_at': 1708514467.516018}.
galaxy.authnz.custos_authnz INFO 2024-02-21 12:21:01,517 [pN:main,p:38658,tN:WSGI_0] There already exists a user with email gxyuser_existing@galaxy.org. To associate this external login, you must first be logged in as that existing account.
INFO: 127.0.0.1:52171 - "GET /authnz/keycloak/callback?state=7l6Fo47IYTarfdWLDb4WXCGFqFYUxa&session_state=af4cbfb9-2239-4d99-bc6f-3fa05aafbfd3&code=1633679b-60d1-49bf-84af-06b046cbaa0b.af4cbfb9-2239-4d99-bc6f-3fa05aafbfd3.52e25e17-fdb7-423a-83ab-90c27711d391 HTTP/1.1" 302 Found
INFO: 127.0.0.1:52171 - "GET /login/start?connect_external_provider=keycloak&connect_external_email=gxyuser_existing@galaxy.org&connect_external_label=Keycloak HTTP/1.1" 200 OK
INFO: 127.0.0.1:52174 - "GET /api/users/current HTTP/1.1" 400 Bad Request
PASSEDINFO: 127.0.0.1:52175 - "GET /api/jobs?state=running HTTP/1.1" 500 Internal Server Error
test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_oidc_login_account_linkup ERROR: Exception in ASGI application
+ Exception Group Traceback (most recent call last):
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 87, in collapse_excgroups
| yield
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 190, in __call__
| async with anyio.create_task_group() as task_group:
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 678, in __aexit__
| raise BaseExceptionGroup(
| ExceptionGroup: unhandled errors in a TaskGroup (1 sub-exception)
+-+---------------- 1 ----------------
| Traceback (most recent call last):
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/protocols/http/h11_impl.py", line 412, in run_asgi
| result = await app( # type: ignore[func-returns-value]
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 84, in __call__
| return await self.app(scope, receive, send)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/applications.py", line 1054, in __call__
| await super().__call__(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/applications.py", line 123, in __call__
| await self.middleware_stack(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 186, in __call__
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 164, in __call__
| await self.app(scope, receive, _send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette_context/middleware/raw_middleware.py", line 92, in __call__
| await self.app(scope, receive, send_wrapper)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 189, in __call__
| with collapse_excgroups():
| File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 158, in __exit__
| self.gen.throw(typ, value, traceback)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 93, in collapse_excgroups
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 191, in __call__
| response = await self.dispatch_func(request, call_next)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
| response = await call_next(request)
| ^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 165, in call_next
| raise app_exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 151, in coro
| await self.app(scope, receive_or_disconnect, send_no_error)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 62, in __call__
| await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
| await app(scope, receive, sender)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 758, in __call__
| await self.middleware_stack(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 778, in app
| await route.handle(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 299, in handle
| await self.app(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 79, in app
| await wrap_app_handling_exceptions(app, request)(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
| await app(scope, receive, sender)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 74, in app
| response = await func(request)
| ^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 299, in app
| raise e
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 294, in app
| raw_response = await run_endpoint_function(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 193, in run_endpoint_function
| return await run_in_threadpool(dependant.call, **values)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/concurrency.py", line 42, in run_in_threadpool
| return await anyio.to_thread.run_sync(func, *args)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/to_thread.py", line 56, in run_sync
| return await get_async_backend().run_sync_in_worker_thread(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 2134, in run_sync_in_worker_thread
| return await future
| ^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 851, in run
| result = context.run(func, *args)
| ^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/jobs.py", line 248, in index
| return self.service.index(trans, payload)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/services/jobs.py", line 83, in index
| jobs = self.job_manager.index_query(trans, payload)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/managers/jobs.py", line 211, in index_query
| stmt = stmt.where(Job.user_id == trans.user.id)
| ^^^^^^^^^^^^^
| AttributeError: 'NoneType' object has no attribute 'id'
+------------------------------------
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/protocols/http/h11_impl.py", line 412, in run_asgi
result = await app( # type: ignore[func-returns-value]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 84, in __call__
return await self.app(scope, receive, send)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/applications.py", line 1054, in __call__
await super().__call__(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/applications.py", line 123, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 186, in __call__
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 164, in __call__
await self.app(scope, receive, _send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette_context/middleware/raw_middleware.py", line 92, in __call__
await self.app(scope, receive, send_wrapper)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 189, in __call__
with collapse_excgroups():
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 158, in __exit__
self.gen.throw(typ, value, traceback)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 93, in collapse_excgroups
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 191, in __call__
response = await self.dispatch_func(request, call_next)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
response = await call_next(request)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 165, in call_next
raise app_exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 151, in coro
await self.app(scope, receive_or_disconnect, send_no_error)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 62, in __call__
await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
await app(scope, receive, sender)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 758, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 778, in app
await route.handle(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 299, in handle
await self.app(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 79, in app
await wrap_app_handling_exceptions(app, request)(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
await app(scope, receive, sender)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 74, in app
response = await func(request)
^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 299, in app
raise e
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 294, in app
raw_response = await run_endpoint_function(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 193, in run_endpoint_function
return await run_in_threadpool(dependant.call, **values)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/concurrency.py", line 42, in run_in_threadpool
return await anyio.to_thread.run_sync(func, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/to_thread.py", line 56, in run_sync
return await get_async_backend().run_sync_in_worker_thread(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 2134, in run_sync_in_worker_thread
return await future
^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 851, in run
result = context.run(func, *args)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/jobs.py", line 248, in index
return self.service.index(trans, payload)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/services/jobs.py", line 83, in index
jobs = self.job_manager.index_query(trans, payload)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/managers/jobs.py", line 211, in index_query
stmt = stmt.where(Job.user_id == trans.user.id)
^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'id'
INFO: 127.0.0.1:52180 - "GET /login/start HTTP/1.1" 200 OK
galaxy.webapps.galaxy.controllers.user DEBUG 2024-02-21 12:21:01,573 [pN:main,p:38658,tN:WSGI_0] trans.app.config.auth_config_file: /Users/mvandenb/tmp/tmpw5j9tgad/tmp7wom9gbq/auth_conf.xml
galaxy.auth.providers.localdb DEBUG 2024-02-21 12:21:01,599 [pN:main,p:38658,tN:WSGI_0] User: gxyuser_existing@galaxy.org, LOCALDB: True
INFO: 127.0.0.1:52180 - "POST /user/login HTTP/1.1" 200 OK
INFO: 127.0.0.1:52180 - "GET /api/users/current HTTP/1.1" 200 OK
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,634 [pN:main,p:38658,tN:WSGI_0] Generated new state r1whDy04PgPKt6Lj6Eg9AoVUEtxttt.
INFO: 127.0.0.1:52180 - "GET /authnz/keycloak/login HTTP/1.1" 200 OK
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,681 [pN:main,p:38658,tN:WSGI_0] Encoding `client_id` "gxyclient" with `client_secret` as Basic auth credentials.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,681 [pN:main,p:38658,tN:WSGI_0] Requesting url https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token using method POST.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,681 [pN:main,p:38658,tN:WSGI_0] Supplying headers {'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0'} and data {'grant_type': 'authorization_code', 'code': '4f7dc104-9e7c-4bf7-9444-45b6c649968c.44baa069-4351-4360-a0f8-08c145c87ebc.52e25e17-fdb7-423a-83ab-90c27711d391', 'redirect_uri': 'http://127.0.0.1:9500/authnz/keycloak/callback'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,681 [pN:main,p:38658,tN:WSGI_0] Passing through key word arguments {'timeout': None, 'auth': <requests.auth.HTTPBasicAuth object at 0x144ff06d0>, 'verify': False, 'proxies': None, 'cert': None}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,694 [pN:main,p:38658,tN:WSGI_0] Request to fetch token completed with status 200.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,694 [pN:main,p:38658,tN:WSGI_0] Request url was https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,694 [pN:main,p:38658,tN:WSGI_0] Request headers were {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0', 'Content-Length': '219', 'Content-Type': 'application/x-www-form-urlencoded'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,694 [pN:main,p:38658,tN:WSGI_0] Request body was grant_type=authorization_code&code=4f7dc104-9e7c-4bf7-9444-45b6c649968c.44baa069-4351-4360-a0f8-08c145c87ebc.52e25e17-fdb7-423a-83ab-90c27711d391&redirect_uri=http%3A%2F%2F127.0.0.1%3A9500%2Fauthnz%2Fkeycloak%2Fcallback
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,694 [pN:main,p:38658,tN:WSGI_0] Response headers were {'Referrer-Policy': 'no-referrer', 'X-Frame-Options': 'SAMEORIGIN', 'Strict-Transport-Security': 'max-age=31536000; includeSubDomains', 'Cache-Control': 'no-store', 'X-Content-Type-Options': 'nosniff', 'Pragma': 'no-cache', 'X-XSS-Protection': '1; mode=block', 'Content-Type': 'application/json', 'content-length': '3848'} and content {"access_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.QSKjLsYff1vq6ii-KnLMYC_uKHLQBc9xR1V89zcN4haVc0KW-Um32RVudt8dau26jTgIQkk4KrFjqaW9uv3Vk_XcQAK3vOEe5mjKuMFl124XDqT8geYeQupiawQsAUyP3shixE1eX8ufuwXDFgy1xecxmTXmjBbE6DmjaGY7wuZ_tfUjlaH7lv9S4X19zWlHzUMeWLzV9J5Bw3S7mDHNgAoPcaPDPFbcZM4kjKyichPcQ74JspOUrhbyDZruDZTGbZehg_jMO-9msGxBfjL0oZHy8T9Iuc6RP9wuDKbjzUWRnHuFi-ZMtZ4b954afoYbidNp_uLHb5PNbmUOT_fZrg","expires_in":6,"refresh_expires_in":1800,"refresh_token":"eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.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.XcEjoiKl79ahzMjXYF2XOIvRFNUvhjk5rOQoex3hwQo","token_type":"Bearer","id_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.QM8xXuvM7j_-RTfV16VM6r3Yj8opzSMtOHTXPl4_xOGT9Twz-tBZAeISG_0sNlZr8dF1g97x-qhq8YMC_LAedJ3aAdH1tsoEvFShq6-fI2cB2dpDmTKf839VPlACuG26FRcpiO7r1RCHogbkRtgnlrrHyw_TTVdFoyuQTV_14hf1cipG_9D5fw8b607brITvgazwys4qQDxy41qxa5CGGKHB0Iah0stJV0TiaVP5uY2x64PHAgngbFkHc8w4MRrqGTew3FS_ofNInEMEATI9J5n9v3tJkCV0VAnoQkvBt3eLeBAT97Jm4_nwe_231tXYeFcyghOD9YvKcGyLvutXtg","not-before-policy":0,"session_state":"44baa069-4351-4360-a0f8-08c145c87ebc","scope":"openid profile email https://galaxyproject.org/api:*"}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,695 [pN:main,p:38658,tN:WSGI_0] Invoking 0 token response hooks.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,695 [pN:main,p:38658,tN:WSGI_0] Obtained token {'access_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.QSKjLsYff1vq6ii-KnLMYC_uKHLQBc9xR1V89zcN4haVc0KW-Um32RVudt8dau26jTgIQkk4KrFjqaW9uv3Vk_XcQAK3vOEe5mjKuMFl124XDqT8geYeQupiawQsAUyP3shixE1eX8ufuwXDFgy1xecxmTXmjBbE6DmjaGY7wuZ_tfUjlaH7lv9S4X19zWlHzUMeWLzV9J5Bw3S7mDHNgAoPcaPDPFbcZM4kjKyichPcQ74JspOUrhbyDZruDZTGbZehg_jMO-9msGxBfjL0oZHy8T9Iuc6RP9wuDKbjzUWRnHuFi-ZMtZ4b954afoYbidNp_uLHb5PNbmUOT_fZrg', 'expires_in': 6, 'refresh_expires_in': 1800, 'refresh_token': 'eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.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.XcEjoiKl79ahzMjXYF2XOIvRFNUvhjk5rOQoex3hwQo', 'token_type': 'Bearer', 'id_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.QM8xXuvM7j_-RTfV16VM6r3Yj8opzSMtOHTXPl4_xOGT9Twz-tBZAeISG_0sNlZr8dF1g97x-qhq8YMC_LAedJ3aAdH1tsoEvFShq6-fI2cB2dpDmTKf839VPlACuG26FRcpiO7r1RCHogbkRtgnlrrHyw_TTVdFoyuQTV_14hf1cipG_9D5fw8b607brITvgazwys4qQDxy41qxa5CGGKHB0Iah0stJV0TiaVP5uY2x64PHAgngbFkHc8w4MRrqGTew3FS_ofNInEMEATI9J5n9v3tJkCV0VAnoQkvBt3eLeBAT97Jm4_nwe_231tXYeFcyghOD9YvKcGyLvutXtg', 'not-before-policy': 0, 'session_state': '44baa069-4351-4360-a0f8-08c145c87ebc', 'scope': ['openid', 'profile', 'email', 'https://galaxyproject.org/api:*'], 'expires_at': 1708514467.6951628}.
INFO: 127.0.0.1:52180 - "GET /authnz/keycloak/callback?state=r1whDy04PgPKt6Lj6Eg9AoVUEtxttt&session_state=44baa069-4351-4360-a0f8-08c145c87ebc&code=4f7dc104-9e7c-4bf7-9444-45b6c649968c.44baa069-4351-4360-a0f8-08c145c87ebc.52e25e17-fdb7-423a-83ab-90c27711d391 HTTP/1.1" 302 Found
INFO: 127.0.0.1:52180 - "GET /user/external_ids?notification=Your%20Keycloak%20identity%20has%20been%20linked%20to%20your%20Galaxy%20account. HTTP/1.1" 200 OK
INFO: 127.0.0.1:52180 - "GET /api/users/current HTTP/1.1" 200 OK
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,731 [pN:main,p:38658,tN:WSGI_0] Generated new state NYL5xfBlvKSyOkJ6zgkCYvYCjUScVC.
INFO: 127.0.0.1:52183 - "GET /authnz/keycloak/login HTTP/1.1" 200 OK
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,772 [pN:main,p:38658,tN:WSGI_0] Encoding `client_id` "gxyclient" with `client_secret` as Basic auth credentials.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,772 [pN:main,p:38658,tN:WSGI_0] Requesting url https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token using method POST.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,773 [pN:main,p:38658,tN:WSGI_0] Supplying headers {'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0'} and data {'grant_type': 'authorization_code', 'code': '55f2e4e4-9f66-419d-ace3-aad95962f7e2.a2f446ed-9e4c-40eb-89ea-424d14eb97b3.52e25e17-fdb7-423a-83ab-90c27711d391', 'redirect_uri': 'http://127.0.0.1:9500/authnz/keycloak/callback'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,773 [pN:main,p:38658,tN:WSGI_0] Passing through key word arguments {'timeout': None, 'auth': <requests.auth.HTTPBasicAuth object at 0x2c7307c10>, 'verify': False, 'proxies': None, 'cert': None}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,786 [pN:main,p:38658,tN:WSGI_0] Request to fetch token completed with status 200.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,786 [pN:main,p:38658,tN:WSGI_0] Request url was https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,786 [pN:main,p:38658,tN:WSGI_0] Request headers were {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0', 'Content-Length': '219', 'Content-Type': 'application/x-www-form-urlencoded'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,787 [pN:main,p:38658,tN:WSGI_0] Request body was grant_type=authorization_code&code=55f2e4e4-9f66-419d-ace3-aad95962f7e2.a2f446ed-9e4c-40eb-89ea-424d14eb97b3.52e25e17-fdb7-423a-83ab-90c27711d391&redirect_uri=http%3A%2F%2F127.0.0.1%3A9500%2Fauthnz%2Fkeycloak%2Fcallback
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,787 [pN:main,p:38658,tN:WSGI_0] Response headers were {'Referrer-Policy': 'no-referrer', 'X-Frame-Options': 'SAMEORIGIN', 'Strict-Transport-Security': 'max-age=31536000; includeSubDomains', 'Cache-Control': 'no-store', 'X-Content-Type-Options': 'nosniff', 'Pragma': 'no-cache', 'X-XSS-Protection': '1; mode=block', 'Content-Type': 'application/json', 'content-length': '3848'} and content {"access_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.cy91IojX14aXZ3w-H6ZeUiMWYrgEzbOfs7CwxbYw7vceN-w1MG3eMmWTXnGwy9nPWDFi-0XcNS3ES-dN9wfESnvrYH9FnFmYgRKWkpAf3c0HExCNEiCpE10d7smcOdACIVyVGq7QqtjSoC3nr8iSXKcE04hgaLNcHpWXlupDU5BZwwu4lJRkeoQroPlXbUEhcmt7y4u-VvfI3FH7HTpOsMJz7bqqSSWC3uo6QkASJxAQBBoGwd3SxhCAKj4rNIC05l3bMLZvi1GZHrwBMBcLYhEY7PyKtn0EzeGtsdRLrBVnmsQ7prh8oje35oodaCcIt0TwRFp9uFf-GiRGBni-Zg","expires_in":6,"refresh_expires_in":1800,"refresh_token":"eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.eyJleHAiOjE3MDg1MTYyNjEsImlhdCI6MTcwODUxNDQ2MSwianRpIjoiNTU2NDhkM2UtOTk2Mi00M2ZhLWJlMGUtNjBmYTg2OGFmODE2IiwiaXNzIjoiaHR0cHM6Ly9sb2NhbGhvc3Q6OTQ0My9yZWFsbXMvZ3h5cmVhbG0iLCJhdWQiOiJodHRwczovL2xvY2FsaG9zdDo5NDQzL3JlYWxtcy9neHlyZWFsbSIsInN1YiI6IjI0ZmZhM2ZmLWQzNTEtNGQ1ZS1iMTBiLThkNjE1MDgyZWM5YiIsInR5cCI6IlJlZnJlc2giLCJhenAiOiJneHljbGllbnQiLCJub25jZSI6Ijc0YWQyYTY3ODYxNmZmOTFlMDBjNDEwNTZmM2U2NGU5NmVjZmMzODA4ODNlNjk0M2IwYTczZWM0YzRiMTFjMmIiLCJzZXNzaW9uX3N0YXRlIjoiYTJmNDQ2ZWQtOWU0Yy00MGViLTg5ZWEtNDI0ZDE0ZWI5N2IzIiwic2NvcGUiOiJvcGVuaWQgcHJvZmlsZSBlbWFpbCBodHRwczovL2dhbGF4eXByb2plY3Qub3JnL2FwaToqIiwic2lkIjoiYTJmNDQ2ZWQtOWU0Yy00MGViLTg5ZWEtNDI0ZDE0ZWI5N2IzIn0.Kd8nBLxyZLzzR2DL9_e74yrUK3NhOoggAOC_KBmmgu4","token_type":"Bearer","id_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.dTbh9v3Umsnk2aKCKze-rvTPpDBUJ_gYTpy4CwY9gBRM8wePNE8nQUYHcyB1nYZ4nff2zaSipbjAw68CXOBz6dWeq1W51SHAKDl5cuiWqA1KhJubX0xPpfvTUnkvvI_qQ9axtr_2Mbtj9lcG-xHYHGlCTqUi3Lnp_UOGheKWAzSKefTnHMuCB6HzGPo5KguvZwdnw8uwkdRd-jqni7V2hNuaD4GnP8cCCUAgrpHuvOsCFw2wR2QutV1iXNkN2qqnVFbQJ2o1kXRWyrkVIcpjy2uKlBrTHrklJhD2xlUSpdhFPKF00DJXaSdih9wg2PNerRp-9d2Wy5ew5TZFdKBP1w","not-before-policy":0,"session_state":"a2f446ed-9e4c-40eb-89ea-424d14eb97b3","scope":"openid profile email https://galaxyproject.org/api:*"}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,787 [pN:main,p:38658,tN:WSGI_0] Invoking 0 token response hooks.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,787 [pN:main,p:38658,tN:WSGI_0] Obtained token {'access_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.cy91IojX14aXZ3w-H6ZeUiMWYrgEzbOfs7CwxbYw7vceN-w1MG3eMmWTXnGwy9nPWDFi-0XcNS3ES-dN9wfESnvrYH9FnFmYgRKWkpAf3c0HExCNEiCpE10d7smcOdACIVyVGq7QqtjSoC3nr8iSXKcE04hgaLNcHpWXlupDU5BZwwu4lJRkeoQroPlXbUEhcmt7y4u-VvfI3FH7HTpOsMJz7bqqSSWC3uo6QkASJxAQBBoGwd3SxhCAKj4rNIC05l3bMLZvi1GZHrwBMBcLYhEY7PyKtn0EzeGtsdRLrBVnmsQ7prh8oje35oodaCcIt0TwRFp9uFf-GiRGBni-Zg', 'expires_in': 6, 'refresh_expires_in': 1800, 'refresh_token': 'eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.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.Kd8nBLxyZLzzR2DL9_e74yrUK3NhOoggAOC_KBmmgu4', 'token_type': 'Bearer', 'id_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.dTbh9v3Umsnk2aKCKze-rvTPpDBUJ_gYTpy4CwY9gBRM8wePNE8nQUYHcyB1nYZ4nff2zaSipbjAw68CXOBz6dWeq1W51SHAKDl5cuiWqA1KhJubX0xPpfvTUnkvvI_qQ9axtr_2Mbtj9lcG-xHYHGlCTqUi3Lnp_UOGheKWAzSKefTnHMuCB6HzGPo5KguvZwdnw8uwkdRd-jqni7V2hNuaD4GnP8cCCUAgrpHuvOsCFw2wR2QutV1iXNkN2qqnVFbQJ2o1kXRWyrkVIcpjy2uKlBrTHrklJhD2xlUSpdhFPKF00DJXaSdih9wg2PNerRp-9d2Wy5ew5TZFdKBP1w', 'not-before-policy': 0, 'session_state': 'a2f446ed-9e4c-40eb-89ea-424d14eb97b3', 'scope': ['openid', 'profile', 'email', 'https://galaxyproject.org/api:*'], 'expires_at': 1708514467.7871628}.
INFO: 127.0.0.1:52183 - "GET /authnz/keycloak/callback?state=NYL5xfBlvKSyOkJ6zgkCYvYCjUScVC&session_state=a2f446ed-9e4c-40eb-89ea-424d14eb97b3&code=55f2e4e4-9f66-419d-ace3-aad95962f7e2.a2f446ed-9e4c-40eb-89ea-424d14eb97b3.52e25e17-fdb7-423a-83ab-90c27711d391 HTTP/1.1" 302 Found
INFO: 127.0.0.1:52183 - "GET / HTTP/1.1" 200 OK
INFO: 127.0.0.1:52183 - "GET /api/users/current HTTP/1.1" 200 OK
PASSEDINFO: 127.0.0.1:52186 - "GET /api/jobs?state=running HTTP/1.1" 200 OK
test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_oidc_logout requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,826 [pN:main,p:38658,tN:WSGI_0] Generated new state mKU7N0W30D3bgyNJwsU00MPdtJDbnj.
INFO: 127.0.0.1:52187 - "GET /authnz/keycloak/login HTTP/1.1" 200 OK
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,868 [pN:main,p:38658,tN:WSGI_0] Encoding `client_id` "gxyclient" with `client_secret` as Basic auth credentials.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,868 [pN:main,p:38658,tN:WSGI_0] Requesting url https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token using method POST.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,868 [pN:main,p:38658,tN:WSGI_0] Supplying headers {'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0'} and data {'grant_type': 'authorization_code', 'code': '375e06ef-7970-474e-a20a-4fbbc952c507.f613da29-cc32-463b-b8fc-97495d607602.52e25e17-fdb7-423a-83ab-90c27711d391', 'redirect_uri': 'http://127.0.0.1:9500/authnz/keycloak/callback'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,868 [pN:main,p:38658,tN:WSGI_0] Passing through key word arguments {'timeout': None, 'auth': <requests.auth.HTTPBasicAuth object at 0x2c72744d0>, 'verify': False, 'proxies': None, 'cert': None}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,880 [pN:main,p:38658,tN:WSGI_0] Request to fetch token completed with status 200.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,880 [pN:main,p:38658,tN:WSGI_0] Request url was https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,880 [pN:main,p:38658,tN:WSGI_0] Request headers were {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0', 'Content-Length': '219', 'Content-Type': 'application/x-www-form-urlencoded'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,880 [pN:main,p:38658,tN:WSGI_0] Request body was grant_type=authorization_code&code=375e06ef-7970-474e-a20a-4fbbc952c507.f613da29-cc32-463b-b8fc-97495d607602.52e25e17-fdb7-423a-83ab-90c27711d391&redirect_uri=http%3A%2F%2F127.0.0.1%3A9500%2Fauthnz%2Fkeycloak%2Fcallback
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,880 [pN:main,p:38658,tN:WSGI_0] Response headers were {'Referrer-Policy': 'no-referrer', 'X-Frame-Options': 'SAMEORIGIN', 'Strict-Transport-Security': 'max-age=31536000; includeSubDomains', 'Cache-Control': 'no-store', 'X-Content-Type-Options': 'nosniff', 'Pragma': 'no-cache', 'X-XSS-Protection': '1; mode=block', 'Content-Type': 'application/json', 'content-length': '3824'} and content {"access_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.fyHGmM5LOvLez5tlB0SmAKVp0A8KN0DctjkJk4EAPAoI2fhFub0z4ziopwL5CM7l3-hhlhd4yKJqKuEY0kKdpG3Pct4YolCc-K8M_u4H7a7fUuF615HhPpxcY3pzJp1uBWplR4fIa1d9YuFoi7HAKg5WkDqosT00iW_8qyPWXAzfJmfQudEmrCD3xXKyclwhthLY5VWi3k_t6QGK7SxQVIvKOPkAZKyLOYhn9iww0igmNQImrprFFHCp_jJSxmTxVVydNQGlDjMgQ3it3WePkxYtbpxqJjmXwdwUkwOkPemtLyHZiTWZmdRFQtYHK2ZFWyrXhUBfK55FShnFpixL_w","expires_in":6,"refresh_expires_in":1800,"refresh_token":"eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.eyJleHAiOjE3MDg1MTYyNjEsImlhdCI6MTcwODUxNDQ2MSwianRpIjoiNTRmOTM5MzYtN2Q4ZC00NjcxLWFjNmMtY2E1OGUxM2JlMjg2IiwiaXNzIjoiaHR0cHM6Ly9sb2NhbGhvc3Q6OTQ0My9yZWFsbXMvZ3h5cmVhbG0iLCJhdWQiOiJodHRwczovL2xvY2FsaG9zdDo5NDQzL3JlYWxtcy9neHlyZWFsbSIsInN1YiI6IjI0ZmZhM2ZmLWQzNTEtNGQ1ZS1iMTBiLThkNjE1MDgyZWM5YyIsInR5cCI6IlJlZnJlc2giLCJhenAiOiJneHljbGllbnQiLCJub25jZSI6Ijg4NjYzNjhkMGZkYmUyMjI4NGY0YmE3YTQ0YTdjODIxYzJiYWU5Y2Q5ZmRhNmE2ZjdkZTkzNWMyMTRmNzkzODYiLCJzZXNzaW9uX3N0YXRlIjoiZjYxM2RhMjktY2MzMi00NjNiLWI4ZmMtOTc0OTVkNjA3NjAyIiwic2NvcGUiOiJvcGVuaWQgcHJvZmlsZSBlbWFpbCBodHRwczovL2dhbGF4eXByb2plY3Qub3JnL2FwaToqIiwic2lkIjoiZjYxM2RhMjktY2MzMi00NjNiLWI4ZmMtOTc0OTVkNjA3NjAyIn0.KAoKMNeIZNEp8wgWs9qkryhc4W1RtvBpCjgu_UgtQsQ","token_type":"Bearer","id_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.qanzALBzbAdk6DHpHUA9S5U6xaDZS_AHA98ZjbRlNBkoxEziQpBn7O_dYCTNhh2mBpOpV_x9DgZp2zd7xLFZC9xd5Y7-3fy2gAyM10Jua3ZJNjUrv_eRdf2YXKCS0RBX8cVIREKvdv6Y82fLo-XxdeuPmEs9p_pKdA9Hhrs-b6-SgHSvFrcQolOEavenCAjMczndzN50JACfHro9VZxHAFNcCh7wieTP1nqeNxSSJH-gTyEi0GW-jWQS4hUxtwA_xOl1Vft4ATUMpU1VsFAsjeQ_kTABCrZv3lU02Yob1Gmkk80Ow7LnlQJKTBlXZNu4XZE9z77iZx9fRLo-FBIIrA","not-before-policy":0,"session_state":"f613da29-cc32-463b-b8fc-97495d607602","scope":"openid profile email https://galaxyproject.org/api:*"}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,880 [pN:main,p:38658,tN:WSGI_0] Invoking 0 token response hooks.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,880 [pN:main,p:38658,tN:WSGI_0] Obtained token {'access_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.fyHGmM5LOvLez5tlB0SmAKVp0A8KN0DctjkJk4EAPAoI2fhFub0z4ziopwL5CM7l3-hhlhd4yKJqKuEY0kKdpG3Pct4YolCc-K8M_u4H7a7fUuF615HhPpxcY3pzJp1uBWplR4fIa1d9YuFoi7HAKg5WkDqosT00iW_8qyPWXAzfJmfQudEmrCD3xXKyclwhthLY5VWi3k_t6QGK7SxQVIvKOPkAZKyLOYhn9iww0igmNQImrprFFHCp_jJSxmTxVVydNQGlDjMgQ3it3WePkxYtbpxqJjmXwdwUkwOkPemtLyHZiTWZmdRFQtYHK2ZFWyrXhUBfK55FShnFpixL_w', 'expires_in': 6, 'refresh_expires_in': 1800, 'refresh_token': 'eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.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.KAoKMNeIZNEp8wgWs9qkryhc4W1RtvBpCjgu_UgtQsQ', 'token_type': 'Bearer', 'id_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.qanzALBzbAdk6DHpHUA9S5U6xaDZS_AHA98ZjbRlNBkoxEziQpBn7O_dYCTNhh2mBpOpV_x9DgZp2zd7xLFZC9xd5Y7-3fy2gAyM10Jua3ZJNjUrv_eRdf2YXKCS0RBX8cVIREKvdv6Y82fLo-XxdeuPmEs9p_pKdA9Hhrs-b6-SgHSvFrcQolOEavenCAjMczndzN50JACfHro9VZxHAFNcCh7wieTP1nqeNxSSJH-gTyEi0GW-jWQS4hUxtwA_xOl1Vft4ATUMpU1VsFAsjeQ_kTABCrZv3lU02Yob1Gmkk80Ow7LnlQJKTBlXZNu4XZE9z77iZx9fRLo-FBIIrA', 'not-before-policy': 0, 'session_state': 'f613da29-cc32-463b-b8fc-97495d607602', 'scope': ['openid', 'profile', 'email', 'https://galaxyproject.org/api:*'], 'expires_at': 1708514467.880577}.
INFO: 127.0.0.1:52187 - "GET /authnz/keycloak/callback?state=mKU7N0W30D3bgyNJwsU00MPdtJDbnj&session_state=f613da29-cc32-463b-b8fc-97495d607602&code=375e06ef-7970-474e-a20a-4fbbc952c507.f613da29-cc32-463b-b8fc-97495d607602.52e25e17-fdb7-423a-83ab-90c27711d391 HTTP/1.1" 302 Found
INFO: 127.0.0.1:52187 - "GET / HTTP/1.1" 200 OK
INFO: 127.0.0.1:52187 - "GET /api/users/current HTTP/1.1" 200 OK
INFO: 127.0.0.1:52187 - "GET /authnz/logout HTTP/1.1" 302 Found
INFO: 127.0.0.1:52187 - "GET /authnz/keycloak/logout HTTP/1.1" 200 OK
INFO: 127.0.0.1:52187 - "GET /api/users/current HTTP/1.1" 400 Bad Request
PASSEDINFO: 127.0.0.1:52190 - "GET /api/jobs?state=running HTTP/1.1" 500 Internal Server Error
test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_auth_by_access_token_logged_in_once ERROR: Exception in ASGI application
+ Exception Group Traceback (most recent call last):
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 87, in collapse_excgroups
| yield
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 190, in __call__
| async with anyio.create_task_group() as task_group:
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 678, in __aexit__
| raise BaseExceptionGroup(
| ExceptionGroup: unhandled errors in a TaskGroup (1 sub-exception)
+-+---------------- 1 ----------------
| Traceback (most recent call last):
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/protocols/http/h11_impl.py", line 412, in run_asgi
| result = await app( # type: ignore[func-returns-value]
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 84, in __call__
| return await self.app(scope, receive, send)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/applications.py", line 1054, in __call__
| await super().__call__(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/applications.py", line 123, in __call__
| await self.middleware_stack(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 186, in __call__
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 164, in __call__
| await self.app(scope, receive, _send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette_context/middleware/raw_middleware.py", line 92, in __call__
| await self.app(scope, receive, send_wrapper)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 189, in __call__
| with collapse_excgroups():
| File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 158, in __exit__
| self.gen.throw(typ, value, traceback)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 93, in collapse_excgroups
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 191, in __call__
| response = await self.dispatch_func(request, call_next)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
| response = await call_next(request)
| ^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 165, in call_next
| raise app_exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 151, in coro
| await self.app(scope, receive_or_disconnect, send_no_error)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 62, in __call__
| await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
| await app(scope, receive, sender)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 758, in __call__
| await self.middleware_stack(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 778, in app
| await route.handle(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 299, in handle
| await self.app(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 79, in app
| await wrap_app_handling_exceptions(app, request)(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
| await app(scope, receive, sender)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 74, in app
| response = await func(request)
| ^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 299, in app
| raise e
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 294, in app
| raw_response = await run_endpoint_function(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 193, in run_endpoint_function
| return await run_in_threadpool(dependant.call, **values)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/concurrency.py", line 42, in run_in_threadpool
| return await anyio.to_thread.run_sync(func, *args)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/to_thread.py", line 56, in run_sync
| return await get_async_backend().run_sync_in_worker_thread(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 2134, in run_sync_in_worker_thread
| return await future
| ^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 851, in run
| result = context.run(func, *args)
| ^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/jobs.py", line 248, in index
| return self.service.index(trans, payload)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/services/jobs.py", line 83, in index
| jobs = self.job_manager.index_query(trans, payload)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/managers/jobs.py", line 211, in index_query
| stmt = stmt.where(Job.user_id == trans.user.id)
| ^^^^^^^^^^^^^
| AttributeError: 'NoneType' object has no attribute 'id'
+------------------------------------
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/protocols/http/h11_impl.py", line 412, in run_asgi
result = await app( # type: ignore[func-returns-value]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 84, in __call__
return await self.app(scope, receive, send)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/applications.py", line 1054, in __call__
await super().__call__(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/applications.py", line 123, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 186, in __call__
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 164, in __call__
await self.app(scope, receive, _send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette_context/middleware/raw_middleware.py", line 92, in __call__
await self.app(scope, receive, send_wrapper)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 189, in __call__
with collapse_excgroups():
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 158, in __exit__
self.gen.throw(typ, value, traceback)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 93, in collapse_excgroups
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 191, in __call__
response = await self.dispatch_func(request, call_next)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
response = await call_next(request)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 165, in call_next
raise app_exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 151, in coro
await self.app(scope, receive_or_disconnect, send_no_error)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 62, in __call__
await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
await app(scope, receive, sender)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 758, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 778, in app
await route.handle(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 299, in handle
await self.app(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 79, in app
await wrap_app_handling_exceptions(app, request)(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
await app(scope, receive, sender)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 74, in app
response = await func(request)
^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 299, in app
raise e
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 294, in app
raw_response = await run_endpoint_function(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 193, in run_endpoint_function
return await run_in_threadpool(dependant.call, **values)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/concurrency.py", line 42, in run_in_threadpool
return await anyio.to_thread.run_sync(func, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/to_thread.py", line 56, in run_sync
return await get_async_backend().run_sync_in_worker_thread(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 2134, in run_sync_in_worker_thread
return await future
^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 851, in run
result = context.run(func, *args)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/jobs.py", line 248, in index
return self.service.index(trans, payload)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/services/jobs.py", line 83, in index
jobs = self.job_manager.index_query(trans, payload)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/managers/jobs.py", line 211, in index_query
stmt = stmt.where(Job.user_id == trans.user.id)
^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'id'
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,954 [pN:main,p:38658,tN:WSGI_0] Generated new state 7nV8LoTnnpuen5nLRYKRCF3CScmJZ1.
INFO: 127.0.0.1:52191 - "GET /authnz/keycloak/login HTTP/1.1" 200 OK
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,996 [pN:main,p:38658,tN:WSGI_0] Encoding `client_id` "gxyclient" with `client_secret` as Basic auth credentials.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,996 [pN:main,p:38658,tN:WSGI_0] Requesting url https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token using method POST.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,997 [pN:main,p:38658,tN:WSGI_0] Supplying headers {'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0'} and data {'grant_type': 'authorization_code', 'code': 'ebbdd785-25fe-42d7-9a4e-f0c7e01988b7.4e446df1-37b1-4391-bf1d-8561ccbbb012.52e25e17-fdb7-423a-83ab-90c27711d391', 'redirect_uri': 'http://127.0.0.1:9500/authnz/keycloak/callback'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:01,997 [pN:main,p:38658,tN:WSGI_0] Passing through key word arguments {'timeout': None, 'auth': <requests.auth.HTTPBasicAuth object at 0x2c723e850>, 'verify': False, 'proxies': None, 'cert': None}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,010 [pN:main,p:38658,tN:WSGI_0] Request to fetch token completed with status 200.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,010 [pN:main,p:38658,tN:WSGI_0] Request url was https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,010 [pN:main,p:38658,tN:WSGI_0] Request headers were {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0', 'Content-Length': '219', 'Content-Type': 'application/x-www-form-urlencoded'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,010 [pN:main,p:38658,tN:WSGI_0] Request body was grant_type=authorization_code&code=ebbdd785-25fe-42d7-9a4e-f0c7e01988b7.4e446df1-37b1-4391-bf1d-8561ccbbb012.52e25e17-fdb7-423a-83ab-90c27711d391&redirect_uri=http%3A%2F%2F127.0.0.1%3A9500%2Fauthnz%2Fkeycloak%2Fcallback
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,010 [pN:main,p:38658,tN:WSGI_0] Response headers were {'Referrer-Policy': 'no-referrer', 'X-Frame-Options': 'SAMEORIGIN', 'Strict-Transport-Security': 'max-age=31536000; includeSubDomains', 'Cache-Control': 'no-store', 'X-Content-Type-Options': 'nosniff', 'Pragma': 'no-cache', 'X-XSS-Protection': '1; mode=block', 'Content-Type': 'application/json', 'content-length': '3880'} and content {"access_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.eyJleHAiOjE3MDg1MTQ0NjgsImlhdCI6MTcwODUxNDQ2MiwiYXV0aF90aW1lIjoxNzA4NTE0NDYxLCJqdGkiOiI0M2RiMjYxMy0wZDdkLTQ2ZWUtYmNhNS04MzMzNTBiOTY5ODciLCJpc3MiOiJodHRwczovL2xvY2FsaG9zdDo5NDQzL3JlYWxtcy9neHlyZWFsbSIsImF1ZCI6Imd4eWNsaWVudCIsInN1YiI6IjI0ZmZhM2ZmLWQzNTEtNGQ1ZS1iMTBiLThkNjE1MDgyZWM5ZCIsInR5cCI6IkJlYXJlciIsImF6cCI6Imd4eWNsaWVudCIsIm5vbmNlIjoiMDVlZWEwMmYwNmZmMWVjYzhjNDhhNGQ5ZTgxMTg4Zjk1YTEzZWJjMTYwNDI2MDg4NjJkMTU3ZWUwYmJjNDEyZSIsInNlc3Npb25fc3RhdGUiOiI0ZTQ0NmRmMS0zN2IxLTQzOTEtYmYxZC04NTYxY2NiYmIwMTIiLCJhY3IiOiIxIiwicmVhbG1fYWNjZXNzIjp7InJvbGVzIjpbImdhbGF4eS1hY2Nlc3Mtcm9sZSIsIm9mZmxpbmVfYWNjZXNzIiwiZGVmYXVsdC1yb2xlcy1neHlyZWFsbSIsInVtYV9hdXRob3JpemF0aW9uIl19LCJzY29wZSI6Im9wZW5pZCBwcm9maWxlIGVtYWlsIGh0dHBzOi8vZ2FsYXh5cHJvamVjdC5vcmcvYXBpOioiLCJzaWQiOiI0ZTQ0NmRmMS0zN2IxLTQzOTEtYmYxZC04NTYxY2NiYmIwMTIiLCJlbWFpbF92ZXJpZmllZCI6dHJ1ZSwibmFtZSI6IlRlc3QgR2FsYXh5VXNlciIsInByZWZlcnJlZF91c2VybmFtZSI6Imd4eXVzZXJfbG9nZ2VkX2luX29uY2UiLCJnaXZlbl9uYW1lIjoiVGVzdCIsImZhbWlseV9uYW1lIjoiR2FsYXh5VXNlciIsImVtYWlsIjoiZ3h5dXNlcl9sb2dnZWRfaW5fb25jZUBnYWxheHkub3JnIn0.P3--pUsoc_NoOR07cnmsLBRxUeCPE2C1tAk9neGsQxmlhYdaE27_-FGil2TEiCI3r79gzrvUn89iWi_h61mXUqBpz_DxUYs7Zt-Lq1wVZRf6i27KSFNk9s_Z-Cph10Gcrg9P0NfR5DwNJkT2ikYXk6yuf1DeYefLtCBXB7z-4it5RIhqmDrydraGQcFNP0hcZmT5s3EsQKUQe0HUDJksa-dYEPzycq3VHwuFLK85nSZzGgE4CV_Lec22rfZsFKZZ6I_ynwsdSUowi92MXc9VAH9WHmNs9cx_undGXSrLDRDaall_xLiuWuDMh12BeaXnM-6qN4-ygQ9Hj0zdLhxpCg","expires_in":6,"refresh_expires_in":1799,"refresh_token":"eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.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.syBnD5J-oa_W6f1SSguTPW7Z1-YDflZhotkwfG5tMWc","token_type":"Bearer","id_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.QZprtR-JS0cG5iL_SKD6QyTsUljgRG1NmB7c-ythvW8hdgyRQoiJjOQV9XNt0xatErkVPvUp2axdrXhqu6wjCK16uvcWEEiIG-Om1mS-fy6oXfpK5dl-0QrUNOFlPfTjUj0tq097PxkYBvzEVnRfEKSRPRwBg5QDyqupfxiZ8m6YxkS9nQ3hINwVrwHHDHjEjkt2_qasobpnO2v6kvPKwj1lHbfIHoLZs-tN8gVcmszUuxGePj_WhCoZAn0O0s3f520bi3mzkNBPtbfF6yzGLDTsQetPaBudD0VrNR3FNJDrZ_uXrEw2v7KUFkujzCzauSqLRM_UAgOUR9qkco1ckA","not-before-policy":0,"session_state":"4e446df1-37b1-4391-bf1d-8561ccbbb012","scope":"openid profile email https://galaxyproject.org/api:*"}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,010 [pN:main,p:38658,tN:WSGI_0] Invoking 0 token response hooks.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,010 [pN:main,p:38658,tN:WSGI_0] Obtained token {'access_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.P3--pUsoc_NoOR07cnmsLBRxUeCPE2C1tAk9neGsQxmlhYdaE27_-FGil2TEiCI3r79gzrvUn89iWi_h61mXUqBpz_DxUYs7Zt-Lq1wVZRf6i27KSFNk9s_Z-Cph10Gcrg9P0NfR5DwNJkT2ikYXk6yuf1DeYefLtCBXB7z-4it5RIhqmDrydraGQcFNP0hcZmT5s3EsQKUQe0HUDJksa-dYEPzycq3VHwuFLK85nSZzGgE4CV_Lec22rfZsFKZZ6I_ynwsdSUowi92MXc9VAH9WHmNs9cx_undGXSrLDRDaall_xLiuWuDMh12BeaXnM-6qN4-ygQ9Hj0zdLhxpCg', 'expires_in': 6, 'refresh_expires_in': 1799, 'refresh_token': 'eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.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.syBnD5J-oa_W6f1SSguTPW7Z1-YDflZhotkwfG5tMWc', 'token_type': 'Bearer', 'id_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.QZprtR-JS0cG5iL_SKD6QyTsUljgRG1NmB7c-ythvW8hdgyRQoiJjOQV9XNt0xatErkVPvUp2axdrXhqu6wjCK16uvcWEEiIG-Om1mS-fy6oXfpK5dl-0QrUNOFlPfTjUj0tq097PxkYBvzEVnRfEKSRPRwBg5QDyqupfxiZ8m6YxkS9nQ3hINwVrwHHDHjEjkt2_qasobpnO2v6kvPKwj1lHbfIHoLZs-tN8gVcmszUuxGePj_WhCoZAn0O0s3f520bi3mzkNBPtbfF6yzGLDTsQetPaBudD0VrNR3FNJDrZ_uXrEw2v7KUFkujzCzauSqLRM_UAgOUR9qkco1ckA', 'not-before-policy': 0, 'session_state': '4e446df1-37b1-4391-bf1d-8561ccbbb012', 'scope': ['openid', 'profile', 'email', 'https://galaxyproject.org/api:*'], 'expires_at': 1708514468.010566}.
INFO: 127.0.0.1:52191 - "GET /authnz/keycloak/callback?state=7nV8LoTnnpuen5nLRYKRCF3CScmJZ1&session_state=4e446df1-37b1-4391-bf1d-8561ccbbb012&code=ebbdd785-25fe-42d7-9a4e-f0c7e01988b7.4e446df1-37b1-4391-bf1d-8561ccbbb012.52e25e17-fdb7-423a-83ab-90c27711d391 HTTP/1.1" 302 Found
INFO: 127.0.0.1:52191 - "GET /user/external_ids?notification=Your%20Keycloak%20identity%20has%20been%20linked%20to%20your%20Galaxy%20account. HTTP/1.1" 200 OK
INFO: 127.0.0.1:52195 - "GET /api/whoami HTTP/1.1" 200 OK
PASSEDINFO: 127.0.0.1:52197 - "GET /api/jobs?state=running HTTP/1.1" 500 Internal Server Error
ERROR: Exception in ASGI application
+ Exception Group Traceback (most recent call last):
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 87, in collapse_excgroups
| yield
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 190, in __call__
| async with anyio.create_task_group() as task_group:
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 678, in __aexit__
| raise BaseExceptionGroup(
| ExceptionGroup: unhandled errors in a TaskGroup (1 sub-exception)
+-+---------------- 1 ----------------
| Traceback (most recent call last):
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/protocols/http/h11_impl.py", line 412, in run_asgi
| result = await app( # type: ignore[func-returns-value]
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 84, in __call__
| return await self.app(scope, receive, send)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/applications.py", line 1054, in __call__
| await super().__call__(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/applications.py", line 123, in __call__
| await self.middleware_stack(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 186, in __call__
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 164, in __call__
| await self.app(scope, receive, _send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette_context/middleware/raw_middleware.py", line 92, in __call__
| await self.app(scope, receive, send_wrapper)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 189, in __call__
| with collapse_excgroups():
| File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 158, in __exit__
| self.gen.throw(typ, value, traceback)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 93, in collapse_excgroups
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 191, in __call__
| response = await self.dispatch_func(request, call_next)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
| response = await call_next(request)
| ^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 165, in call_next
| raise app_exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 151, in coro
| await self.app(scope, receive_or_disconnect, send_no_error)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 62, in __call__
| await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
| await app(scope, receive, sender)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 758, in __call__
| await self.middleware_stack(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 778, in app
| await route.handle(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 299, in handle
| await self.app(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 79, in app
| await wrap_app_handling_exceptions(app, request)(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
| await app(scope, receive, sender)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 74, in app
| response = await func(request)
| ^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 299, in app
| raise e
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 294, in app
| raw_response = await run_endpoint_function(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 193, in run_endpoint_function
| return await run_in_threadpool(dependant.call, **values)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/concurrency.py", line 42, in run_in_threadpool
| return await anyio.to_thread.run_sync(func, *args)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/to_thread.py", line 56, in run_sync
| return await get_async_backend().run_sync_in_worker_thread(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 2134, in run_sync_in_worker_thread
| return await future
| ^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 851, in run
| result = context.run(func, *args)
| ^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/jobs.py", line 248, in index
| return self.service.index(trans, payload)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/services/jobs.py", line 83, in index
| jobs = self.job_manager.index_query(trans, payload)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/managers/jobs.py", line 211, in index_query
| stmt = stmt.where(Job.user_id == trans.user.id)
| ^^^^^^^^^^^^^
| AttributeError: 'NoneType' object has no attribute 'id'
+------------------------------------
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/protocols/http/h11_impl.py", line 412, in run_asgi
result = await app( # type: ignore[func-returns-value]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 84, in __call__
return await self.app(scope, receive, send)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/applications.py", line 1054, in __call__
await super().__call__(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/applications.py", line 123, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 186, in __call__
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 164, in __call__
await self.app(scope, receive, _send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette_context/middleware/raw_middleware.py", line 92, in __call__
await self.app(scope, receive, send_wrapper)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 189, in __call__
with collapse_excgroups():
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 158, in __exit__
self.gen.throw(typ, value, traceback)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 93, in collapse_excgroups
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 191, in __call__
response = await self.dispatch_func(request, call_next)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
response = await call_next(request)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 165, in call_next
raise app_exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 151, in coro
await self.app(scope, receive_or_disconnect, send_no_error)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 62, in __call__
await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
await app(scope, receive, sender)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 758, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 778, in app
await route.handle(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 299, in handle
await self.app(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 79, in app
await wrap_app_handling_exceptions(app, request)(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
await app(scope, receive, sender)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 74, in app
response = await func(request)
^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 299, in app
raise e
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 294, in app
raw_response = await run_e
ndpoint_function(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 193, in run_endpoint_function
return await run_in_threadpool(dependant.call, **values)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/concurrency.py", line 42, in run_in_threadpool
return await anyio.to_thread.run_sync(func, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/to_thread.py", line 56, in run_sync
return await get_async_backend().run_sync_in_worker_thread(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 2134, in run_sync_in_worker_thread
return await future
^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 851, in run
result = context.run(func, *args)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/jobs.py", line 248, in index
return self.service.index(trans, payload)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/services/jobs.py", line 83, in index
jobs = self.job_manager.index_query(trans, payload)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/managers/jobs.py", line 211, in index_query
stmt = stmt.where(Job.user_id == trans.user.id)
^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'id'
test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_auth_by_access_token_never_logged_in INFO: 127.0.0.1:52199 - "GET /api/users/current HTTP/1.1" 401 Unauthorized
PASSEDINFO: 127.0.0.1:52200 - "GET /api/jobs?state=running HTTP/1.1" 500 Internal Server Error
test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_auth_with_expired_token ERROR: Exception in ASGI application
+ Exception Group Traceback (most recent call last):
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 87, in collapse_excgroups
| yield
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 190, in __call__
| async with anyio.create_task_group() as task_group:
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 678, in __aexit__
| raise BaseExceptionGroup(
| ExceptionGroup: unhandled errors in a TaskGroup (1 sub-exception)
+-+---------------- 1 ----------------
| Traceback (most recent call last):
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/protocols/http/h11_impl.py", line 412, in run_asgi
| result = await app( # type: ignore[func-returns-value]
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 84, in __call__
| return await self.app(scope, receive, send)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/applications.py", line 1054, in __call__
| await super().__call__(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/applications.py", line 123, in __call__
| await self.middleware_stack(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 186, in __call__
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 164, in __call__
| await self.app(scope, receive, _send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette_context/middleware/raw_middleware.py", line 92, in __call__
| await self.app(scope, receive, send_wrapper)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 189, in __call__
| with collapse_excgroups():
| File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 158, in __exit__
| self.gen.throw(typ, value, traceback)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 93, in collapse_excgroups
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 191, in __call__
| response = await self.dispatch_func(request, call_next)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
| response = await call_next(request)
| ^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 165, in call_next
| raise app_exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 151, in coro
| await self.app(scope, receive_or_disconnect, send_no_error)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 62, in __call__
| await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
| await app(scope, receive, sender)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 758, in __call__
| await self.middleware_stack(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 778, in app
| await route.handle(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 299, in handle
| await self.app(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 79, in app
| await wrap_app_handling_exceptions(app, request)(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
| await app(scope, receive, sender)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 74, in app
| response = await func(request)
| ^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 299, in app
| raise e
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 294, in app
| raw_response = await run_endpoint_function(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 193, in run_endpoint_function
| return await run_in_threadpool(dependant.call, **values)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/concurrency.py", line 42, in run_in_threadpool
| return await anyio.to_thread.run_sync(func, *args)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/to_thread.py", line 56, in run_sync
| return await get_async_backend().run_sync_in_worker_thread(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 2134, in run_sync_in_worker_thread
| return await future
| ^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 851, in run
| result = context.run(func, *args)
| ^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/jobs.py", line 248, in index
| return self.service.index(trans, payload)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/services/jobs.py", line 83, in index
| jobs = self.job_manager.index_query(trans, payload)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/managers/jobs.py", line 211, in index_query
| stmt = stmt.where(Job.user_id == trans.user.id)
| ^^^^^^^^^^^^^
| AttributeError: 'NoneType' object has no attribute 'id'
+------------------------------------
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/protocols/http/h11_impl.py", line 412, in run_asgi
result = await app( # type: ignore[func-returns-value]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 84, in __call__
return await self.app(scope, receive, send)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/applications.py", line 1054, in __call__
await super().__call__(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/applications.py", line 123, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 186, in __call__
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 164, in __call__
await self.app(scope, receive, _send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette_context/middleware/raw_middleware.py", line 92, in __call__
await self.app(scope, receive, send_wrapper)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 189, in __call__
with collapse_excgroups():
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 158, in __exit__
self.gen.throw(typ, value, traceback)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 93, in collapse_excgroups
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 191, in __call__
response = await self.dispatch_func(request, call_next)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
response = await call_next(request)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 165, in call_next
raise app_exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 151, in coro
await self.app(scope, receive_or_disconnect, send_no_error)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 62, in __call__
await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
await app(scope, receive, sender)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 758, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 778, in app
await route.handle(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 299, in handle
await self.app(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 79, in app
await wrap_app_handling_exceptions(app, request)(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
await app(scope, receive, sender)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 74, in app
response = await func(request)
^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 299, in app
raise e
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 294, in app
raw_response = await run_endpoint_function(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 193, in run_endpoint_function
return await run_in_threadpool(dependant.call, **values)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/concurrency.py", line 42, in run_in_threadpool
return await anyio.to_thread.run_sync(func, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/to_thread.py", line 56, in run_sync
return await get_async_backend().run_sync_in_worker_thread(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 2134, in run_sync_in_worker_thread
return await future
^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 851, in run
result = context.run(func, *args)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/jobs.py", line 248, in index
return self.service.index(trans, payload)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/services/jobs.py", line 83, in index
jobs = self.job_manager.index_query(trans, payload)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/managers/jobs.py", line 211, in index_query
stmt = stmt.where(Job.user_id == trans.user.id)
^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'id'
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,188 [pN:main,p:38658,tN:WSGI_0] Generated new state 8ynREEu7zbGFOV08Vnr4YcS5BzRMRx.
INFO: 127.0.0.1:52201 - "GET /authnz/keycloak/login HTTP/1.1" 200 OK
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,227 [pN:main,p:38658,tN:WSGI_0] Encoding `client_id` "gxyclient" with `client_secret` as Basic auth credentials.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,228 [pN:main,p:38658,tN:WSGI_0] Requesting url https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token using method POST.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,228 [pN:main,p:38658,tN:WSGI_0] Supplying headers {'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0'} and data {'grant_type': 'authorization_code', 'code': '60455d82-b504-41c0-b2d9-709ff9dd9007.3d97e81f-b39b-4d85-8235-8f3ef90fd8e3.52e25e17-fdb7-423a-83ab-90c27711d391', 'redirect_uri': 'http://127.0.0.1:9500/authnz/keycloak/callback'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,228 [pN:main,p:38658,tN:WSGI_0] Passing through key word arguments {'timeout': None, 'auth': <requests.auth.HTTPBasicAuth object at 0x2c7580910>, 'verify': False, 'proxies': None, 'cert': None}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,239 [pN:main,p:38658,tN:WSGI_0] Request to fetch token completed with status 200.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,239 [pN:main,p:38658,tN:WSGI_0] Request url was https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,239 [pN:main,p:38658,tN:WSGI_0] Request headers were {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0', 'Content-Length': '219', 'Content-Type': 'application/x-www-form-urlencoded'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,239 [pN:main,p:38658,tN:WSGI_0] Request body was grant_type=authorization_code&code=60455d82-b504-41c0-b2d9-709ff9dd9007.3d97e81f-b39b-4d85-8235-8f3ef90fd8e3.52e25e17-fdb7-423a-83ab-90c27711d391&redirect_uri=http%3A%2F%2F127.0.0.1%3A9500%2Fauthnz%2Fkeycloak%2Fcallback
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,239 [pN:main,p:38658,tN:WSGI_0] Response headers were {'Referrer-Policy': 'no-referrer', 'X-Frame-Options': 'SAMEORIGIN', 'Strict-Transport-Security': 'max-age=31536000; includeSubDomains', 'Cache-Control': 'no-store', 'X-Content-Type-Options': 'nosniff', 'Pragma': 'no-cache', 'X-XSS-Protection': '1; mode=block', 'Content-Type': 'application/json', 'content-length': '3824'} and content {"access_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.XIO8w8OFywmLS0EIVCH8UWNbdK83HWLnKb34o4ZgfcxY72CHpMZCHQHNPFHGEDKG5amvXulCQ30QLYeURYwZ9zOLusO7z9GPvnIj47soJO7E9bhEVkY5DHsZtJt0Ih7XHUXQEYrRiUMx94A7K7PuJXdUtipEn_faZq44uKYAehAQHrba7plNMLErE4gbM4W5hsiAy9YZ9GEYt4coRJW5AkUImWJXW_xtzXg7qeZX504sjTIZgjr_C9FIaTftIz9I_hUl9yTCdw64kFSWnIdZgQ6HV5JEyOgUWSr8B-xNDWbufIcZmN6mH0BEFIkm-JXdg_mjC7XFtevNSWgKHOgCFQ","expires_in":6,"refresh_expires_in":1800,"refresh_token":"eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.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.fZpr7BXVWK-ST4f6RReituXjFTYZMnApgD1c6kqtFtA","token_type":"Bearer","id_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.A_5Nq_TE3mLS2K98cg18IUA2EnXaaORt0F9h06oIoMoDnCQKkRAVaIrC2zZmUqfciQYLU3flqNhJ-L9vHRmxLwEt2vrC0PMgdmR6vriJQUx_KF0Tm6l4M2exZTwuO9NCsUNHxXaRh8Fhlt2VGBHADiWH8S8cQ6sXvjtTY5e-VUwS66UU_GtgkHnMVMs5JiN333ER-uBcBTOKx12BOEwBcV8Q61wlGi3_kQpHkx4JrVfYME7xYc7LbBaPGGYzbXqxQhlDCDcmjtTswOZkGk3MkrPyZWKL7CoUuYh5u-ksGT8rUAOMXUlGLUJq04lN4LI92k-aXC-iKOakLJv3lSZXyw","not-before-policy":0,"session_state":"3d97e81f-b39b-4d85-8235-8f3ef90fd8e3","scope":"openid profile email https://galaxyproject.org/api:*"}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,239 [pN:main,p:38658,tN:WSGI_0] Invoking 0 token response hooks.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:02,239 [pN:main,p:38658,tN:WSGI_0] Obtained token {'access_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.XIO8w8OFywmLS0EIVCH8UWNbdK83HWLnKb34o4ZgfcxY72CHpMZCHQHNPFHGEDKG5amvXulCQ30QLYeURYwZ9zOLusO7z9GPvnIj47soJO7E9bhEVkY5DHsZtJt0Ih7XHUXQEYrRiUMx94A7K7PuJXdUtipEn_faZq44uKYAehAQHrba7plNMLErE4gbM4W5hsiAy9YZ9GEYt4coRJW5AkUImWJXW_xtzXg7qeZX504sjTIZgjr_C9FIaTftIz9I_hUl9yTCdw64kFSWnIdZgQ6HV5JEyOgUWSr8B-xNDWbufIcZmN6mH0BEFIkm-JXdg_mjC7XFtevNSWgKHOgCFQ', 'expires_in': 6, 'refresh_expires_in': 1800, 'refresh_token': 'eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.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.fZpr7BXVWK-ST4f6RReituXjFTYZMnApgD1c6kqtFtA', 'token_type': 'Bearer', 'id_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.A_5Nq_TE3mLS2K98cg18IUA2EnXaaORt0F9h06oIoMoDnCQKkRAVaIrC2zZmUqfciQYLU3flqNhJ-L9vHRmxLwEt2vrC0PMgdmR6vriJQUx_KF0Tm6l4M2exZTwuO9NCsUNHxXaRh8Fhlt2VGBHADiWH8S8cQ6sXvjtTY5e-VUwS66UU_GtgkHnMVMs5JiN333ER-uBcBTOKx12BOEwBcV8Q61wlGi3_kQpHkx4JrVfYME7xYc7LbBaPGGYzbXqxQhlDCDcmjtTswOZkGk3MkrPyZWKL7CoUuYh5u-ksGT8rUAOMXUlGLUJq04lN4LI92k-aXC-iKOakLJv3lSZXyw', 'not-before-policy': 0, 'session_state': '3d97e81f-b39b-4d85-8235-8f3ef90fd8e3', 'scope': ['openid', 'profile', 'email', 'https://galaxyproject.org/api:*'], 'expires_at': 1708514468.239349}.
INFO: 127.0.0.1:52201 - "GET /authnz/keycloak/callback?state=8ynREEu7zbGFOV08Vnr4YcS5BzRMRx&session_state=3d97e81f-b39b-4d85-8235-8f3ef90fd8e3&code=60455d82-b504-41c0-b2d9-709ff9dd9007.3d97e81f-b39b-4d85-8235-8f3ef90fd8e3.52e25e17-fdb7-423a-83ab-90c27711d391 HTTP/1.1" 302 Found
INFO: 127.0.0.1:52201 - "GET / HTTP/1.1" 200 OK
INFO: 127.0.0.1:52205 - "GET /api/users/current HTTP/1.1" 200 OK
INFO: 127.0.0.1:52219 - "GET /api/users/current HTTP/1.1" 200 OK
galaxy.authnz.managers ERROR 2024-02-21 12:21:12,346 [pN:main,p:38658,tN:AnyIO worker thread] Could not decode access token
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/authnz/managers.py", line 441, in _match_access_token_to_user_in_provider
user, jwt = backend.decode_user_access_token(sa_session, access_token)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/authnz/custos_authnz.py", line 515, in decode_user_access_token
decoded_jwt = jwt.decode(
^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/jwt/api_jwt.py", line 210, in decode
decoded = self.decode_complete(
^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/jwt/api_jwt.py", line 162, in decode_complete
self._validate_claims(
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/jwt/api_jwt.py", line 248, in _validate_claims
self._validate_exp(payload, now, leeway)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/jwt/api_jwt.py", line 306, in _validate_exp
raise ExpiredSignatureError("Signature has expired")
jwt.exceptions.ExpiredSignatureError: Signature has expired
INFO: 127.0.0.1:52254 - "GET /api/users/current HTTP/1.1" 401 Unauthorized
PASSEDINFO: 127.0.0.1:52255 - "GET /api/jobs?state=running HTTP/1.1" 500 Internal Server Error
test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_auth_with_another_authorized_client ERROR: Exception in ASGI application
+ Exception Group Traceback (most recent call last):
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 87, in collapse_excgroups
| yield
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 190, in __call__
| async with anyio.create_task_group() as task_group:
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 678, in __aexit__
| raise BaseExceptionGroup(
| ExceptionGroup: unhandled errors in a TaskGroup (1 sub-exception)
+-+---------------- 1 ----------------
| Traceback (most recent call last):
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/protocols/http/h11_impl.py", line 412, in run_asgi
| result = await app( # type: ignore[func-returns-value]
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 84, in __call__
| return await self.app(scope, receive, send)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/applications.py", line 1054, in __call__
| await super().__call__(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/applications.py", line 123, in __call__
| await self.middleware_stack(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 186, in __call__
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 164, in __call__
| await self.app(scope, receive, _send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette_context/middleware/raw_middleware.py", line 92, in __call__
| await self.app(scope, receive, send_wrapper)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 189, in __call__
| with collapse_excgroups():
| File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 158, in __exit__
| self.gen.throw(typ, value, traceback)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 93, in collapse_excgroups
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 191, in __call__
| response = await self.dispatch_func(request, call_next)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
| response = await call_next(request)
| ^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 165, in call_next
| raise app_exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 151, in coro
| await self.app(scope, receive_or_disconnect, send_no_error)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 62, in __call__
| await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
| await app(scope, receive, sender)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 758, in __call__
| await self.middleware_stack(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 778, in app
| await route.handle(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 299, in handle
| await self.app(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 79, in app
| await wrap_app_handling_exceptions(app, request)(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
| await app(scope, receive, sender)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 74, in app
| response = await func(request)
| ^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 299, in app
| raise e
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 294, in app
| raw_response = await run_endpoint_function(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 193, in run_endpoint_function
| return await run_in_threadpool(dependant.call, **values)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/concurrency.py", line 42, in run_in_threadpool
| return await anyio.to_thread.run_sync(func, *args)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/to_thread.py", line 56, in run_sync
| return await get_async_backend().run_sync_in_worker_thread(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 2134, in run_sync_in_worker_thread
| return await future
| ^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 851, in run
| result = context.run(func, *args)
| ^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/jobs.py", line 248, in index
| return self.service.index(trans, payload)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/services/jobs.py", line 83, in index
| jobs = self.job_manager.index_query(trans, payload)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/managers/jobs.py", line 211, in index_query
| stmt = stmt.where(Job.user_id == trans.user.id)
| ^^^^^^^^^^^^^
| AttributeError: 'NoneType' object has no attribute 'id'
+------------------------------------
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/protocols/http/h11_impl.py", line 412, in run_asgi
result = await app( # type: ignore[func-returns-value]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 84, in __call__
return await self.app(scope, receive, send)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/applications.py", line 1054, in __call__
await super().__call__(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/applications.py", line 123, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 186, in __call__
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 164, in __call__
await self.app(scope, receive, _send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette_context/middleware/raw_middleware.py", line 92, in __call__
await self.app(scope, receive, send_wrapper)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 189, in __call__
with collapse_excgroups():
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 158, in __exit__
self.gen.throw(typ, value, traceback)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 93, in collapse_excgroups
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 191, in __call__
response = await self.dispatch_func(request, call_next)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
response = await call_next(request)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 165, in call_next
raise app_exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 151, in coro
await self.app(scope, receive_or_disconnect, send_no_error)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 62, in __call__
await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
await app(scope, receive, sender)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 758, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 778, in app
await route.handle(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 299, in handle
await self.app(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 79, in app
await wrap_app_handling_exceptions(app, request)(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
await app(scope, receive, sender)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 74, in app
response = await func(request)
^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 299, in app
raise e
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 294, in app
raw_response = await run_endpoint_function(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 193, in run_endpoint_function
return await run_in_threadpool(dependant.call, **values)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/concurrency.py", line 42, in run_in_threadpool
return await anyio.to_thread.run_sync(func, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/to_thread.py", line 56, in run_sync
return await get_async_backend().run_sync_in_worker_thread(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 2134, in run_sync_in_worker_thread
return await future
^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 851, in run
result = context.run(func, *args)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/jobs.py", line 248, in index
return self.service.index(trans, payload)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/services/jobs.py", line 83, in index
jobs = self.job_manager.index_query(trans, payload)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/managers/jobs.py", line 211, in index_query
stmt = stmt.where(Job.user_id == trans.user.id)
^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'id'
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,380 [pN:main,p:38658,tN:WSGI_0] Generated new state 2JhxJrZXZivO6H8CO6MRmL3flRKD5t.
INFO: 127.0.0.1:52256 - "GET /authnz/keycloak/login HTTP/1.1" 200 OK
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,521 [pN:main,p:38658,tN:WSGI_0] Encoding `client_id` "gxyclient" with `client_secret` as Basic auth credentials.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,521 [pN:main,p:38658,tN:WSGI_0] Requesting url https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token using method POST.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,521 [pN:main,p:38658,tN:WSGI_0] Supplying headers {'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0'} and data {'grant_type': 'authorization_code', 'code': '4919c34e-185d-4ce5-b0f4-1704722462a5.ff477fa5-7d46-4832-9cdb-a673d732f24b.52e25e17-fdb7-423a-83ab-90c27711d391', 'redirect_uri': 'http://127.0.0.1:9500/authnz/keycloak/callback'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,521 [pN:main,p:38658,tN:WSGI_0] Passing through key word arguments {'timeout': None, 'auth': <requests.auth.HTTPBasicAuth object at 0x2c7203410>, 'verify': False, 'proxies': None, 'cert': None}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,539 [pN:main,p:38658,tN:WSGI_0] Request to fetch token completed with status 200.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,539 [pN:main,p:38658,tN:WSGI_0] Request url was https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,539 [pN:main,p:38658,tN:WSGI_0] Request headers were {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0', 'Content-Length': '219', 'Content-Type': 'application/x-www-form-urlencoded'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,539 [pN:main,p:38658,tN:WSGI_0] Request body was grant_type=authorization_code&code=4919c34e-185d-4ce5-b0f4-1704722462a5.ff477fa5-7d46-4832-9cdb-a673d732f24b.52e25e17-fdb7-423a-83ab-90c27711d391&redirect_uri=http%3A%2F%2F127.0.0.1%3A9500%2Fauthnz%2Fkeycloak%2Fcallback
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,539 [pN:main,p:38658,tN:WSGI_0] Response headers were {'Referrer-Policy': 'no-referrer', 'X-Frame-Options': 'SAMEORIGIN', 'Strict-Transport-Security': 'max-age=31536000; includeSubDomains', 'Cache-Control': 'no-store', 'X-Content-Type-Options': 'nosniff', 'Pragma': 'no-cache', 'X-XSS-Protection': '1; mode=block', 'Content-Type': 'application/json', 'content-length': '3824'} and content {"access_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.McRQqhwnhCcFUz8D9mDte90fV1ZCb-rbNo5dnGDHQjEXTNLYVGFiMGpPVB5iveuSq9ErYVkjo4EhIae3iz38sZo488npHnjZAMCtJ4lRhZ-DILDCnqwvA5q5b6YUKiR_0vfLn3-IIIy7CVhx3DDYcbx5uXjheTf5yEGgDvPCcpVwD1u4CSS-AIhX3gWh_8Wr4hAfAVxhimnTRuc79SPR0qxlx6Ern-rvDpSSmsbyoZ8TQQlcVxbQZK6Sy6yobNwPKoqWdskRj_lCSsYDDnp-h7n68Wix8596RAkNVEY7Z1y32gYlYyq7Zh3PPbxzSv0fIDb0-kdiojOROki7lDYRxg","expires_in":6,"refresh_expires_in":1800,"refresh_token":"eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.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.vWDZlZxKTi81KuMbLRfAMLg2WJVVzYKcHwET3CDRFZM","token_type":"Bearer","id_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.eyJleHAiOjE3MDg1MTQ0NzgsImlhdCI6MTcwODUxNDQ3MiwiYXV0aF90aW1lIjoxNzA4NTE0NDcyLCJqdGkiOiI3MWVkMzhjZC0zYTgyLTQyZWYtOGQ0Yy1jNTgzMjZmOThlNWQiLCJpc3MiOiJodHRwczovL2xvY2FsaG9zdDo5NDQzL3JlYWxtcy9neHlyZWFsbSIsImF1ZCI6Imd4eWNsaWVudCIsInN1YiI6IjI0ZmZhM2ZmLWQzNTEtNGQ1ZS1iMTBiLThkNjE1MDgyZWM5YyIsInR5cCI6IklEIiwiYXpwIjoiZ3h5Y2xpZW50Iiwibm9uY2UiOiI3ZDdlMjZkYjlkYTg4ZGI4NTQzYjA5MjVmYWRlY2I0YzM0YmI5MzRlNWE1NTc2YTQwMGE1YmVjMjk1ZWU5MGI1Iiwic2Vzc2lvbl9zdGF0ZSI6ImZmNDc3ZmE1LTdkNDYtNDgzMi05Y2RiLWE2NzNkNzMyZjI0YiIsImF0X2hhc2giOiJiVHJoRlJFcDFSMkZMWjBhdUF1N0x3IiwiYWNyIjoiMSIsInNpZCI6ImZmNDc3ZmE1LTdkNDYtNDgzMi05Y2RiLWE2NzNkNzMyZjI0YiIsImVtYWlsX3ZlcmlmaWVkIjp0cnVlLCJuYW1lIjoiVGVzdCBHYWxheHlVc2VyIiwicHJlZmVycmVkX3VzZXJuYW1lIjoiZ3h5dXNlciIsImdpdmVuX25hbWUiOiJUZXN0IiwiZmFtaWx5X25hbWUiOiJHYWxheHlVc2VyIiwiZW1haWwiOiJneHl1c2VyQGdhbGF4eS5vcmcifQ.stoc-Q4BgFEYDJg88c-69e9rBMYZI-UKQ5kN40e4QhgGpthv4Mx1Tb7uata8vK9Rpnn7_Aj2rOIa9LxVKe1_Ua9iFUbipxJPSXnb047M0Uj8mA_Ceb_yo8ayOuNbzi9bDYLFPvU15r2MOgsqtyL75bxvysmHhSyN_yA7LKlL32eBZjHZf9qmdTmquzmzu58ElmneWEI0E0RGzMDbVaD8xasP-NsWP7nFT7WLl8zMUq1HBKE3PP84fpYwFinYoLPzgBaLfN7x5iazPBsNDlLDK3cmkgogC8Cl-jV0SMbG_M4gWTItul_crkCLcJEtblEtN-e-P3GzpKx1o0tvWoroHw","not-before-policy":0,"session_state":"ff477fa5-7d46-4832-9cdb-a673d732f24b","scope":"openid profile email https://galaxyproject.org/api:*"}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,542 [pN:main,p:38658,tN:WSGI_0] Invoking 0 token response hooks.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,542 [pN:main,p:38658,tN:WSGI_0] Obtained token {'access_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.McRQqhwnhCcFUz8D9mDte90fV1ZCb-rbNo5dnGDHQjEXTNLYVGFiMGpPVB5iveuSq9ErYVkjo4EhIae3iz38sZo488npHnjZAMCtJ4lRhZ-DILDCnqwvA5q5b6YUKiR_0vfLn3-IIIy7CVhx3DDYcbx5uXjheTf5yEGgDvPCcpVwD1u4CSS-AIhX3gWh_8Wr4hAfAVxhimnTRuc79SPR0qxlx6Ern-rvDpSSmsbyoZ8TQQlcVxbQZK6Sy6yobNwPKoqWdskRj_lCSsYDDnp-h7n68Wix8596RAkNVEY7Z1y32gYlYyq7Zh3PPbxzSv0fIDb0-kdiojOROki7lDYRxg', 'expires_in': 6, 'refresh_expires_in': 1800, 'refresh_token': 'eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI2ZjhlMjMwYi1iYjMyLTRiMmMtYWNhNS0yOTdkZmNmMDQxNGQifQ.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.vWDZlZxKTi81KuMbLRfAMLg2WJVVzYKcHwET3CDRFZM', 'token_type': 'Bearer', 'id_token': 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.stoc-Q4BgFEYDJg88c-69e9rBMYZI-UKQ5kN40e4QhgGpthv4Mx1Tb7uata8vK9Rpnn7_Aj2rOIa9LxVKe1_Ua9iFUbipxJPSXnb047M0Uj8mA_Ceb_yo8ayOuNbzi9bDYLFPvU15r2MOgsqtyL75bxvysmHhSyN_yA7LKlL32eBZjHZf9qmdTmquzmzu58ElmneWEI0E0RGzMDbVaD8xasP-NsWP7nFT7WLl8zMUq1HBKE3PP84fpYwFinYoLPzgBaLfN7x5iazPBsNDlLDK3cmkgogC8Cl-jV0SMbG_M4gWTItul_crkCLcJEtblEtN-e-P3GzpKx1o0tvWoroHw', 'not-before-policy': 0, 'session_state': 'ff477fa5-7d46-4832-9cdb-a673d732f24b', 'scope': ['openid', 'profile', 'email', 'https://galaxyproject.org/api:*'], 'expires_at': 1708514478.5426219}.
INFO: 127.0.0.1:52256 - "GET /authnz/keycloak/callback?state=2JhxJrZXZivO6H8CO6MRmL3flRKD5t&session_state=ff477fa5-7d46-4832-9cdb-a673d732f24b&code=4919c34e-185d-4ce5-b0f4-1704722462a5.ff477fa5-7d46-4832-9cdb-a673d732f24b.52e25e17-fdb7-423a-83ab-90c27711d391 HTTP/1.1" 302 Found
INFO: 127.0.0.1:52256 - "GET / HTTP/1.1" 200 OK
INFO: 127.0.0.1:52264 - "GET /api/users/current HTTP/1.1" 200 OK
PASSEDINFO: 127.0.0.1:52265 - "GET /api/jobs?state=running HTTP/1.1" 500 Internal Server Error
test/integration/oidc/test_auth_oidc.py::TestGalaxyOIDCLoginIntegration::test_auth_with_authorized_client_but_unauthorized_audience ERROR: Exception in ASGI application
+ Exception Group Traceback (most recent call last):
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 87, in collapse_excgroups
| yield
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 190, in __call__
| async with anyio.create_task_group() as task_group:
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 678, in __aexit__
| raise BaseExceptionGroup(
| ExceptionGroup: unhandled errors in a TaskGroup (1 sub-exception)
+-+---------------- 1 ----------------
| Traceback (most recent call last):
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/protocols/http/h11_impl.py", line 412, in run_asgi
| result = await app( # type: ignore[func-returns-value]
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 84, in __call__
| return await self.app(scope, receive, send)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/applications.py", line 1054, in __call__
| await super().__call__(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/applications.py", line 123, in __call__
| await self.middleware_stack(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 186, in __call__
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 164, in __call__
| await self.app(scope, receive, _send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette_context/middleware/raw_middleware.py", line 92, in __call__
| await self.app(scope, receive, send_wrapper)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 189, in __call__
| with collapse_excgroups():
| File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 158, in __exit__
| self.gen.throw(typ, value, traceback)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 93, in collapse_excgroups
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 191, in __call__
| response = await self.dispatch_func(request, call_next)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
| response = await call_next(request)
| ^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 165, in call_next
| raise app_exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 151, in coro
| await self.app(scope, receive_or_disconnect, send_no_error)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 62, in __call__
| await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
| await app(scope, receive, sender)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 758, in __call__
| await self.middleware_stack(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 778, in app
| await route.handle(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 299, in handle
| await self.app(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 79, in app
| await wrap_app_handling_exceptions(app, request)(scope, receive, send)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
| raise exc
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
| await app(scope, receive, sender)
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 74, in app
| response = await func(request)
| ^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 299, in app
| raise e
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 294, in app
| raw_response = await run_endpoint_function(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 193, in run_endpoint_function
| return await run_in_threadpool(dependant.call, **values)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/concurrency.py", line 42, in run_in_threadpool
| return await anyio.to_thread.run_sync(func, *args)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/to_thread.py", line 56, in run_sync
| return await get_async_backend().run_sync_in_worker_thread(
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 2134, in run_sync_in_worker_thread
| return await future
| ^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 851, in run
| result = context.run(func, *args)
| ^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/jobs.py", line 248, in index
| return self.service.index(trans, payload)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/services/jobs.py", line 83, in index
| jobs = self.job_manager.index_query(trans, payload)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/Users/mvandenb/src/galaxy/lib/galaxy/managers/jobs.py", line 211, in index_query
| stmt = stmt.where(Job.user_id == trans.user.id)
| ^^^^^^^^^^^^^
| AttributeError: 'NoneType' object has no attribute 'id'
+------------------------------------
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/protocols/http/h11_impl.py", line 412, in run_asgi
result = await app( # type: ignore[func-returns-value]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 84, in __call__
return await self.app(scope, receive, send)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/applications.py", line 1054, in __call__
await super().__call__(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/applications.py", line 123, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 186, in __call__
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/errors.py", line 164, in __call__
await self.app(scope, receive, _send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette_context/middleware/raw_middleware.py", line 92, in __call__
await self.app(scope, receive, send_wrapper)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 189, in __call__
with collapse_excgroups():
File "/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 158, in __exit__
self.gen.throw(typ, value, traceback)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_utils.py", line 93, in collapse_excgroups
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 191, in __call__
response = await self.dispatch_func(request, call_next)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
response = await call_next(request)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 165, in call_next
raise app_exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/base.py", line 151, in coro
await self.app(scope, receive_or_disconnect, send_no_error)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 62, in __call__
await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
await app(scope, receive, sender)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 758, in __call__
await self.middleware_stack(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 778, in app
await route.handle(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 299, in handle
await self.app(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 79, in app
await wrap_app_handling_exceptions(app, request)(scope, receive, send)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
raise exc
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
await app(scope, receive, sender)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/routing.py", line 74, in app
response = await func(request)
^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 299, in app
raise e
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 294, in app
raw_response = await run_endpoint_function(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/fastapi/routing.py", line 193, in run_endpoint_function
return await run_in_threadpool(dependant.call, **values)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/starlette/concurrency.py", line 42, in run_in_threadpool
return await anyio.to_thread.run_sync(func, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/to_thread.py", line 56, in run_sync
return await get_async_backend().run_sync_in_worker_thread(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 2134, in run_sync_in_worker_thread
return await future
^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 851, in run
result = context.run(func, *args)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/jobs.py", line 248, in index
return self.service.index(trans, payload)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/services/jobs.py", line 83, in index
jobs = self.job_manager.index_query(trans, payload)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/managers/jobs.py", line 211, in index_query
stmt = stmt.where(Job.user_id == trans.user.id)
^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'id'
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,638 [pN:main,p:38658,tN:WSGI_0] Generated new state NIxUJtjjlkLd6J55PGzcOMhfpTNhV0.
INFO: 127.0.0.1:52266 - "GET /authnz/keycloak/login HTTP/1.1" 200 OK
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,682 [pN:main,p:38658,tN:WSGI_0] Encoding `client_id` "gxyclient" with `client_secret` as Basic auth credentials.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,682 [pN:main,p:38658,tN:WSGI_0] Requesting url https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token using method POST.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,682 [pN:main,p:38658,tN:WSGI_0] Supplying headers {'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0'} and data {'grant_type': 'authorization_code', 'code': 'fb97102f-f3eb-4f6e-ba6a-9562855a04bd.257301be-5d92-4aea-8f7b-18474871cfe4.52e25e17-fdb7-423a-83ab-90c27711d391', 'redirect_uri': 'http://127.0.0.1:9500/authnz/keycloak/callback'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,682 [pN:main,p:38658,tN:WSGI_0] Passing through key word arguments {'timeout': None, 'auth': <requests.auth.HTTPBasicAuth object at 0x2c80486d0>, 'verify': False, 'proxies': None, 'cert': None}.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,697 [pN:main,p:38658,tN:WSGI_0] Request to fetch token completed with status 200.
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,697 [pN:main,p:38658,tN:WSGI_0] Request url was https://localhost:9443/realms/gxyrealm/protocol/openid-connect/token
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,697 [pN:main,p:38658,tN:WSGI_0] Request headers were {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Authorization': 'Basic Z3h5Y2xpZW50OmR1bW15Y2xpZW50c2VjcmV0', 'Content-Length': '219', 'Content-Type': 'application/x-www-form-urlencoded'}
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,697 [pN:main,p:38658,tN:WSGI_0] Request body was grant_type=authorization_code&code=fb97102f-f3eb-4f6e-ba6a-9562855a04bd.257301be-5d92-4aea-8f7b-18474871cfe4.52e25e17-fdb7-423a-83ab-90c27711d391&redirect_uri=http%3A%2F%2F127.0.0.1%3A9500%2Fauthnz%2Fkeycloak%2Fcallback
requests_oauthlib.oauth2_session DEBUG 2024-02-21 12:21:12,697 [pN:main,p:38658,tN:WSGI_0] Response headers were {'Referrer-Policy': 'no-referrer', 'X-Frame-Options': 'SAMEORIGIN', 'Strict-Transport-Security': 'max-age=31536000; includeSubDomains', 'Cache-Control': 'no-store', 'X-Content-Type-Options': 'nosniff', 'Pragma': 'no-cache', 'X-XSS-Protection': '1; mode=block', 'Content-Type': 'application/json', 'content-length': '3553'} and content {"access_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJsaG9TQlV4bC1HNW1nUHpqemZZR183ZEdMbUc4X0VQN3A2MnVwTzZ3RlRZIn0.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.rdjHIK-ELCpGFtvszv_sD7um1l4508ZHbh1_dBC6z1Yiu9iPWL4QAzlTDILw6U0J7lyHNz
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