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Galaxy log 20/03/18
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| CloudMan from Galaxy | |
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| The entire log file (/mnt/galaxy/galaxy-app/main.log) is shown. Show latest | Back to admin view | |
| galaxy.queue_worker INFO 2018-03-20 10:27:44,664 Initializing main Galaxy Queue Worker on sqlalchemy+postgres://galaxy@localhost:5930/galaxy | |
| tool_shed.tool_shed_registry DEBUG 2018-03-20 10:27:44,712 Loading references to tool sheds from /mnt/galaxy/galaxy-app/config/tool_sheds_conf.xml | |
| tool_shed.tool_shed_registry DEBUG 2018-03-20 10:27:44,712 Loaded reference to tool shed: Galaxy Main Tool Shed | |
| tool_shed.tool_shed_registry DEBUG 2018-03-20 10:27:44,712 Loaded reference to tool shed: Galaxy Test Tool Shed | |
| galaxy.app DEBUG 2018-03-20 10:27:44,715 Using "galaxy.ini" config file: /mnt/galaxy/galaxy-app/config/galaxy.ini | |
| migrate.versioning.repository DEBUG 2018-03-20 10:27:44,815 Loading repository lib/galaxy/model/migrate... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,819 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,822 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,822 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,823 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,823 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,823 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,823 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,823 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,824 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... | |
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| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,824 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,825 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,825 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,825 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully | |
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| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,826 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py... | |
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| migrate.versioning.script.base DEBUG 2018-03-20 10:27:44,826 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py... | |
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| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,223 Script lib/galaxy/model/tool_shed_install/migrate/versions/0005_add_tool_shed_repository_table_columns.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,223 Loading script lib/galaxy/model/tool_shed_install/migrate/versions/0006_add_tool_version_tables.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,223 Script lib/galaxy/model/tool_shed_install/migrate/versions/0006_add_tool_version_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,223 Loading script lib/galaxy/model/tool_shed_install/migrate/versions/0007_add_migrate_tools_table.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,223 Script lib/galaxy/model/tool_shed_install/migrate/versions/0007_add_migrate_tools_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,223 Loading script lib/galaxy/model/tool_shed_install/migrate/versions/0008_add_ctx_rev_column.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,223 Script lib/galaxy/model/tool_shed_install/migrate/versions/0008_add_ctx_rev_column.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,223 Loading script lib/galaxy/model/tool_shed_install/migrate/versions/0009_add_tool_dependency_table.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,223 Script lib/galaxy/model/tool_shed_install/migrate/versions/0009_add_tool_dependency_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,223 Loading script lib/galaxy/model/tool_shed_install/migrate/versions/0010_alter_tool_dependency_table_version_column.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,224 Script lib/galaxy/model/tool_shed_install/migrate/versions/0010_alter_tool_dependency_table_version_column.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,224 Loading script lib/galaxy/model/tool_shed_install/migrate/versions/0011_drop_installed_changeset_revision_column.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,224 Script lib/galaxy/model/tool_shed_install/migrate/versions/0011_drop_installed_changeset_revision_column.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,224 Loading script lib/galaxy/model/tool_shed_install/migrate/versions/0012_add_tool_dependency_status_columns.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,224 Script lib/galaxy/model/tool_shed_install/migrate/versions/0012_add_tool_dependency_status_columns.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,224 Loading script lib/galaxy/model/tool_shed_install/migrate/versions/0013_add_tool_shed_repository_status_columns.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,224 Script lib/galaxy/model/tool_shed_install/migrate/versions/0013_add_tool_shed_repository_status_columns.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,224 Loading script lib/galaxy/model/tool_shed_install/migrate/versions/0014_add_repository_dependency_tables.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,225 Script lib/galaxy/model/tool_shed_install/migrate/versions/0014_add_repository_dependency_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,225 Loading script lib/galaxy/model/tool_shed_install/migrate/versions/0015_update_migrate_tools_table.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,225 Script lib/galaxy/model/tool_shed_install/migrate/versions/0015_update_migrate_tools_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,225 Loading script lib/galaxy/model/tool_shed_install/migrate/versions/0016_update_migrate_tools_table_again.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,225 Script lib/galaxy/model/tool_shed_install/migrate/versions/0016_update_migrate_tools_table_again.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,225 Loading script lib/galaxy/model/tool_shed_install/migrate/versions/0017_drop_update_available_col_add_tool_shed_status_col.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,225 Script lib/galaxy/model/tool_shed_install/migrate/versions/0017_drop_update_available_col_add_tool_shed_status_col.py loaded successfully | |
| migrate.versioning.repository DEBUG 2018-03-20 10:27:45,225 Repository lib/galaxy/model/tool_shed_install/migrate loaded successfully | |
| migrate.versioning.repository DEBUG 2018-03-20 10:27:45,225 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'ToolShedInstall'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) | |
| galaxy.model.tool_shed_install.migrate.check INFO 2018-03-20 10:27:45,249 At database version 17 | |
| migrate.versioning.repository DEBUG 2018-03-20 10:27:45,254 Loading repository lib/tool_shed/galaxy_install/migrate... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,258 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,258 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,258 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,258 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,258 Loading script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,258 Script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,258 Loading script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,258 Script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,258 Loading script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,258 Script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,258 Loading script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,258 Script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,258 Loading script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,259 Script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,259 Loading script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,259 Script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,259 Loading script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,259 Script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,259 Loading script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,259 Script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,259 Loading script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,259 Script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,259 Loading script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-03-20 10:27:45,259 Script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py loaded successfully | |
| migrate.versioning.repository DEBUG 2018-03-20 10:27:45,259 Repository lib/tool_shed/galaxy_install/migrate loaded successfully | |
| migrate.versioning.repository DEBUG 2018-03-20 10:27:45,259 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))]) | |
| tool_shed.galaxy_install.migrate.check INFO 2018-03-20 10:27:45,265 At migrate_tools version 12 | |
| galaxy.config INFO 2018-03-20 10:27:45,282 Install database using its own connection sqlite:////mnt/galaxy/galaxy-app/config/galaxy_install_db.sqlite?isolation_level=IMMEDIATE | |
| /mnt/galaxy/galaxy-app/lib/galaxy/datatypes/registry.py:98: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. | |
| if root_dir and config: | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,503 Exception importing proprietary code file /mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,504 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,504 Exception importing proprietary code file /mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/binary: No module named binary | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,504 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,504 Exception importing proprietary code file /mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,504 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,504 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,510 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,511 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 2018-03-20 10:27:45,512 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,512 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,512 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,512 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,525 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,525 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 2018-03-20 10:27:45,525 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,525 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,525 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,525 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,532 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,532 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,532 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,532 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,532 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,533 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,533 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,533 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,533 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,533 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,534 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,534 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,534 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,534 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,534 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,534 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,534 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,535 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,535 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,535 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,535 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,535 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,535 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,536 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,536 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,536 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,536 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,536 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,536 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,537 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,537 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,537 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,537 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,537 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,537 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,538 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,538 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,538 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,538 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,538 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,538 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,539 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,539 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,539 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,539 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,539 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,539 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,539 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,540 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,540 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,540 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,540 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,540 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,541 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,541 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,541 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,541 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,541 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,541 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,541 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,542 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,542 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,542 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,542 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,542 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,542 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,543 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,543 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,543 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,543 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,543 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,543 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,544 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,544 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,544 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,544 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,544 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,544 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,545 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,545 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,545 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,545 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,545 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,545 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,546 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,546 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,546 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,546 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,546 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,546 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,546 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,547 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,547 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,547 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,547 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,547 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,552 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,552 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 2018-03-20 10:27:45,552 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,552 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,552 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,552 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,594 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,598 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,598 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 2018-03-20 10:27:45,599 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,599 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,599 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,599 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,612 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,612 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,617 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,617 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 2018-03-20 10:27:45,617 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,617 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,617 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,617 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,631 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,631 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,631 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,631 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,636 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,636 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 2018-03-20 10:27:45,636 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,636 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,636 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,636 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,650 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,650 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,650 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,650 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,654 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,655 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 2018-03-20 10:27:45,655 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,655 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,655 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,655 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,667 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,667 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,667 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,667 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,672 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,672 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 2018-03-20 10:27:45,672 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,672 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,672 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,672 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,685 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,685 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,685 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,686 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,690 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,690 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 2018-03-20 10:27:45,691 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,691 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,691 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,691 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,705 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,705 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,705 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,705 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,710 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,710 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 2018-03-20 10:27:45,710 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,710 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,710 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,710 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,724 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,724 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,724 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,724 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,729 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,729 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 2018-03-20 10:27:45,729 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,729 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,729 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,729 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,741 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,741 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,742 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,742 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,746 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,746 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 2018-03-20 10:27:45,746 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,747 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,747 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,747 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,759 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,759 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,759 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,759 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,764 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,764 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 2018-03-20 10:27:45,764 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,764 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,764 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,764 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,776 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,776 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,776 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,776 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,781 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,781 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 2018-03-20 10:27:45,781 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,781 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,781 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,781 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,793 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,793 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,793 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,793 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,798 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,798 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 2018-03-20 10:27:45,798 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,798 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,798 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,798 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,810 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,810 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,810 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,810 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,815 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,815 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 2018-03-20 10:27:45,815 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,815 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,815 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,815 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,827 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,827 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,828 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,828 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,832 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,832 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 2018-03-20 10:27:45,832 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,832 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,832 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,833 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,844 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,844 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,844 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,844 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,849 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,849 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 2018-03-20 10:27:45,849 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,849 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,849 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,849 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,861 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,861 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,861 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,861 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,865 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,866 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 2018-03-20 10:27:45,866 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,866 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,866 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,866 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,878 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,878 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,878 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,878 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,882 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,882 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 2018-03-20 10:27:45,882 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,883 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,883 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,883 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,894 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,894 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,895 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,895 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,899 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,899 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 2018-03-20 10:27:45,899 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,899 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,900 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,900 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,912 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,912 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,912 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,912 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from . | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,917 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,917 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 2018-03-20 10:27:45,917 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,917 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,917 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,917 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,929 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,934 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,934 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 2018-03-20 10:27:45,934 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,934 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,934 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,934 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,954 Loading datatypes from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,954 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,955 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,955 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,956 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,956 Overriding conflicting datatype with extension 'asn1', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,956 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,956 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,956 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,956 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,956 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,956 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,957 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,957 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,957 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,957 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,958 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,958 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,958 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,958 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,958 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,958 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,959 Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,959 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,960 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,960 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,960 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,960 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,960 Overriding conflicting datatype with extension 'data', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,960 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,961 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,961 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,961 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,961 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,961 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,961 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,961 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,961 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,961 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,962 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,962 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,962 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,962 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,962 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,962 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,962 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,962 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,962 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,963 Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,963 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,963 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,963 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,963 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,963 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,964 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,964 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,964 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,964 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,964 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,964 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,964 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,965 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,965 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,965 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,965 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,965 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,965 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,965 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,965 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,965 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,965 Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,965 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,969 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,969 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,970 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,970 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,970 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,970 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,970 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,970 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,970 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,971 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,971 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,971 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,971 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,971 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,971 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,971 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,971 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,971 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,972 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,972 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,972 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,972 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,972 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,972 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,972 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,972 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,972 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,973 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,973 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,973 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,973 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,973 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,973 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,973 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,973 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,974 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,974 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,974 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,974 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,975 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,975 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,975 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,975 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,975 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,975 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,975 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,975 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,975 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,976 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,976 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,976 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,976 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,976 Roadmaps is not lower case, that could cause troubles in the future. Please change it to lower case | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,976 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,976 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,976 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,976 Sequences is not lower case, that could cause troubles in the future. Please change it to lower case | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,977 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,977 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,977 Overriding conflicting datatype with extension 'snpeffdb', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,977 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,977 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,977 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,977 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,977 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,977 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,978 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,978 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,978 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,978 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,978 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,978 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,978 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,978 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,978 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,978 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,979 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,979 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,979 Overriding conflicting datatype with extension 'bcf_bgzip', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,979 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,979 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,979 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,979 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,979 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,980 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,980 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,980 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,983 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,984 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,984 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,984 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,984 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,984 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,984 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,984 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,985 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,985 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,985 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,985 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,985 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,985 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,985 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,985 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,986 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,986 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,986 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,986 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,988 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,988 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,990 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,990 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,990 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,990 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,990 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,990 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,991 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,991 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,991 Overriding conflicting datatype with extension 'btwisted', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,991 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,991 Overriding conflicting datatype with extension 'cai', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,991 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,991 Overriding conflicting datatype with extension 'charge', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,991 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,991 Overriding conflicting datatype with extension 'checktrans', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,992 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,992 Overriding conflicting datatype with extension 'chips', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,992 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,992 Overriding conflicting datatype with extension 'codcmp', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,992 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,992 Overriding conflicting datatype with extension 'coderet', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,992 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,992 Overriding conflicting datatype with extension 'compseq', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,992 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,993 Overriding conflicting datatype with extension 'cpgplot', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,993 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,993 Overriding conflicting datatype with extension 'cpgreport', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,993 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,993 Overriding conflicting datatype with extension 'cusp', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,993 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,993 Overriding conflicting datatype with extension 'cut', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,993 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,993 Overriding conflicting datatype with extension 'dan', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,994 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,994 Overriding conflicting datatype with extension 'digest', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,994 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,994 Overriding conflicting datatype with extension 'dreg', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,994 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,994 Overriding conflicting datatype with extension 'einverted', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,994 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,994 Overriding conflicting datatype with extension 'epestfind', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,994 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,995 Overriding conflicting datatype with extension 'equicktandem', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,995 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,995 Overriding conflicting datatype with extension 'est2genome', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,995 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,995 Overriding conflicting datatype with extension 'etandem', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,995 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,995 Overriding conflicting datatype with extension 'freak', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,995 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,995 Overriding conflicting datatype with extension 'fuzznuc', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,996 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,996 Overriding conflicting datatype with extension 'fuzzpro', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,996 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,996 Overriding conflicting datatype with extension 'fuzztran', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,996 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,996 Overriding conflicting datatype with extension 'garnier', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,996 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,996 Overriding conflicting datatype with extension 'geecee', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,996 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,996 Overriding conflicting datatype with extension 'helixturnhelix', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,997 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,997 Overriding conflicting datatype with extension 'hmoment', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,997 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,997 Overriding conflicting datatype with extension 'isochore', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,997 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,997 Overriding conflicting datatype with extension 'match', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,997 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,997 Overriding conflicting datatype with extension 'nametable', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,997 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,998 Overriding conflicting datatype with extension 'needle', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,998 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,998 Overriding conflicting datatype with extension 'newcpgreport', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,998 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,998 Overriding conflicting datatype with extension 'newcpgseek', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,998 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,998 Overriding conflicting datatype with extension 'noreturn', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,998 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,998 Overriding conflicting datatype with extension 'palindrome', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,999 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,999 Overriding conflicting datatype with extension 'pepcoil', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,999 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,999 Overriding conflicting datatype with extension 'pepinfo', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,999 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,999 Overriding conflicting datatype with extension 'pepstats', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,999 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,999 Overriding conflicting datatype with extension 'polydot', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,999 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:45,999 Overriding conflicting datatype with extension 'preg', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,000 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,000 Overriding conflicting datatype with extension 'prettyseq', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,000 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,000 Overriding conflicting datatype with extension 'primersearch', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,000 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,000 Overriding conflicting datatype with extension 'showfeat', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,000 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,000 Overriding conflicting datatype with extension 'showorf', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,000 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,001 Overriding conflicting datatype with extension 'sixpack', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,001 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,001 Overriding conflicting datatype with extension 'strider', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,001 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,001 Overriding conflicting datatype with extension 'supermatcher', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,001 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,001 Overriding conflicting datatype with extension 'syco', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,001 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,001 Overriding conflicting datatype with extension 'textsearch', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,002 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,002 Overriding conflicting datatype with extension 'vectorstrip', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,002 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,002 Overriding conflicting datatype with extension 'wobble', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,002 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,002 Overriding conflicting datatype with extension 'wordcount', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,002 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,002 Overriding conflicting datatype with extension 'dbmotif', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,002 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,002 Overriding conflicting datatype with extension 'diffseq', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,003 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,003 Overriding conflicting datatype with extension 'excel', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,003 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,003 Overriding conflicting datatype with extension 'feattable', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,003 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,003 Overriding conflicting datatype with extension 'motif', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,003 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,003 Overriding conflicting datatype with extension 'regions', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,003 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,003 Overriding conflicting datatype with extension 'seqtable', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,004 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,004 Overriding conflicting datatype with extension 'simple', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,004 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,004 Overriding conflicting datatype with extension 'table', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,004 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,004 Overriding conflicting datatype with extension 'tagseq', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,004 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,004 Overriding conflicting datatype with extension 'acedb', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,005 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,005 Overriding conflicting datatype with extension 'clustal', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,005 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,005 Overriding conflicting datatype with extension 'codata', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,005 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,005 Overriding conflicting datatype with extension 'embl', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,005 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,005 Overriding conflicting datatype with extension 'fitch', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,005 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,005 Overriding conflicting datatype with extension 'gcg', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,006 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,006 Overriding conflicting datatype with extension 'genbank', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,006 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,006 Overriding conflicting datatype with extension 'hennig86', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,006 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,006 Overriding conflicting datatype with extension 'ig', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,006 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,006 Overriding conflicting datatype with extension 'jackknifer', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,006 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,007 Overriding conflicting datatype with extension 'jackknifernon', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,007 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,007 Overriding conflicting datatype with extension 'mega', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,007 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,007 Overriding conflicting datatype with extension 'meganon', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,007 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,007 Overriding conflicting datatype with extension 'ncbi', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,007 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,007 Overriding conflicting datatype with extension 'nexus', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,008 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,008 Overriding conflicting datatype with extension 'nexusnon', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,008 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,008 Overriding conflicting datatype with extension 'phylip', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,008 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,008 Overriding conflicting datatype with extension 'phylipnon', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,008 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,008 Overriding conflicting datatype with extension 'pir', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,008 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,008 Overriding conflicting datatype with extension 'staden', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,009 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,009 Overriding conflicting datatype with extension 'swiss', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,009 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,009 Overriding conflicting datatype with extension 'markx0', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,009 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,009 Overriding conflicting datatype with extension 'markx1', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,009 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,009 Overriding conflicting datatype with extension 'markx10', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,010 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,010 Overriding conflicting datatype with extension 'markx2', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,010 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,010 Overriding conflicting datatype with extension 'markx3', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,010 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,010 Overriding conflicting datatype with extension 'pair', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,010 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,010 Overriding conflicting datatype with extension 'score', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,010 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,010 Overriding conflicting datatype with extension 'srs', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,011 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,011 Overriding conflicting datatype with extension 'srspair', using datatype from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,012 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,013 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,013 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,013 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,013 RData is not lower case, that could cause troubles in the future. Please change it to lower case | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,013 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,013 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,013 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,013 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,013 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,014 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,014 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,015 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,015 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,015 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,015 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,016 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,016 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,019 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,019 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,019 Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,020 Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,020 Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,020 Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,020 Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,020 Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,020 Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,020 Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,024 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,024 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,024 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,024 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,025 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,025 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,025 Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,025 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,025 Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,025 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,025 Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,026 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,026 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,026 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,026 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,026 Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,026 Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,026 Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,027 Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,027 Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,027 Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,027 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,027 Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,027 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,027 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,028 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,028 Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,028 Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,028 Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,028 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,028 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,029 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,029 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,029 Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,029 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,029 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,030 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,030 Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,031 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,031 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,031 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,031 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,031 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,031 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,031 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,031 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,031 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,032 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,032 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,032 Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,032 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,032 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,032 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,032 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,032 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,032 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,033 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,034 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,034 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,034 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,034 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,034 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,035 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,035 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,035 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,035 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,035 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,035 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,035 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,035 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,035 Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,036 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,036 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,036 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,036 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,036 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,036 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,036 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,036 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,036 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,037 Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,037 Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,037 Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,037 Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,037 Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,037 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,037 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,037 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,037 Loaded sniffer for datatype 'galaxy.datatypes.text:Html' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,038 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,038 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,038 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,038 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,038 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,038 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,038 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,038 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,039 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,039 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,039 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,039 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,039 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,039 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,039 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,039 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,039 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,040 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,040 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,040 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,040 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,040 Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,040 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,040 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,040 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,041 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,041 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,042 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,042 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,042 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,042 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,042 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,042 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,042 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,042 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,043 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,043 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,043 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,043 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,043 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,043 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,043 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,043 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,044 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,044 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 2018-03-20 10:27:46,044 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,044 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,044 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:27:46,044 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,965 Loaded 235 lines from '/galaxy/data/location/all_fasta.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,965 Loaded tool data table 'all_fasta' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,968 Loaded 5 lines from '/galaxy/data/location/bfast_indexes.loc' for 'bfast_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,968 Loaded tool data table 'bfast_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,969 Loaded 4 lines from '/galaxy/data/location/blastdb.loc' for 'blastdb' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,969 Loaded tool data table 'blastdb' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,970 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/blastdb_p.loc' for 'blastdb_p' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,971 Loaded tool data table 'blastdb_p' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,973 Loaded 121 lines from '/galaxy/data/location/bowtie2_indices.loc' for 'bowtie2_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,973 Loaded tool data table 'bowtie2_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,974 Loaded 16 lines from '/galaxy/data/location/bwa_mem_index.loc' for 'bwa_mem_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,975 Loaded tool data table 'bwa_mem_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,977 Loaded 201 lines from '/galaxy/data/location/bwa_index.loc' for 'bwa_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,978 Loaded tool data table 'bwa_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,979 Loaded 9 lines from '/galaxy/data/location/bwa_index_color.loc' for 'bwa_indexes_color' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,979 Loaded tool data table 'bwa_indexes_color' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,983 Loaded 24 lines from '/galaxy/data/location/maf_index.loc' for 'indexed_maf_files' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,983 Loaded tool data table 'indexed_maf_files' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,984 Loaded 3 lines from '/galaxy/data/location/ngs_sim_fasta.loc' for 'ngs_sim_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,984 Loaded tool data table 'ngs_sim_fasta' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,986 Loaded 10 lines from '/galaxy/data/location/perm_base_index.loc' for 'perm_base_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,986 Loaded tool data table 'perm_base_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,987 Loaded 10 lines from '/galaxy/data/location/perm_color_index.loc' for 'perm_color_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,988 Loaded tool data table 'perm_color_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,990 Loaded 182 lines from '/galaxy/data/location/picard_index.loc' for 'picard_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,991 Loaded tool data table 'picard_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,992 Loaded 1 lines from '/galaxy/data/location/gatk_sorted_picard_index.loc' for 'gatk_picard_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,992 Loaded tool data table 'gatk_picard_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data WARNING 2018-03-20 10:27:46,992 Cannot find index file '/galaxy/data/location/gatk_annotations.txt' for tool data table 'gatk_annotations' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,993 Loaded tool data table 'gatk_annotations' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,994 Loaded 182 lines from '/galaxy/data/location/picard_index.loc' for 'srma_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,994 Loaded tool data table 'srma_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,997 Loaded 202 lines from '/galaxy/data/location/bowtie_indices.loc' for 'tophat_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:46,997 Loaded tool data table 'tophat_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,000 Loaded 194 lines from '/galaxy/data/location/bowtie_indices_color.loc' for 'tophat_indexes_color' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,000 Loaded tool data table 'tophat_indexes_color' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,001 Loaded 121 lines from '/galaxy/data/location/bowtie2_indices.loc' for 'tophat2_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,002 Loaded tool data table 'tophat2_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,003 Loaded 3 lines from '/galaxy/data/location/ccat_configurations.loc' for 'ccat_configurations' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,003 Loaded tool data table 'ccat_configurations' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,005 Loaded 182 lines from '/galaxy/data/location/mosaik_index.loc' for 'mosaik_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,005 Loaded tool data table 'mosaik_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,006 Loaded 202 lines from '/galaxy/data/location/bowtie_indices.loc' for 'bowtie_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,007 Loaded tool data table 'bowtie_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,008 Loaded 194 lines from '/galaxy/data/location/bowtie_indices_color.loc' for 'bowtie_indexes_color' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,008 Loaded tool data table 'bowtie_indexes_color' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,011 Loaded 191 lines from '/galaxy/data/location/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,011 Loaded tool data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,014 Loaded 180 lines from '/galaxy/data/location/sam_fa_indices.loc' for 'sam_fa_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,014 Loaded tool data table 'sam_fa_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,014 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/annovar_index.loc' for 'annovar_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,015 Loaded tool data table 'annovar_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,015 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/tophat_fusion_blastdb.loc' for 'tophat_fusion_blastdb_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,016 Loaded tool data table 'tophat_fusion_blastdb_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,018 Loaded 178 lines from '/galaxy/data/location/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,018 Loaded tool data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| requests.packages.urllib3.connectionpool INFO 2018-03-20 10:27:47,024 Starting new HTTP connection (1): igv.broadinstitute.org | |
| requests.packages.urllib3.connectionpool DEBUG 2018-03-20 10:27:47,308 "GET /genomes/genomes.txt HTTP/1.1" 200 15681 | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,309 Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/mnt/galaxy/tmp/TTDT_URL_igv_broad_genomes-WNkgTj". | |
| galaxy.tools.data WARNING 2018-03-20 10:27:47,309 Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '' characters must be used to separate fields): | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,310 Loaded 156 lines from '/mnt/galaxy/tmp/TTDT_URL_igv_broad_genomes-WNkgTj' for 'igv_broad_genomes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,310 Loaded tool data table 'igv_broad_genomes' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data WARNING 2018-03-20 10:27:47,314 Line 214 in tool data table 'liftOver' is invalid (HINT: '' characters must be used to separate fields): | |
| ce9 bruMal1 /galaxy/data/ce9/liftOver/ce9ToBruMal1.over.chain | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,319 Loaded 1180 lines from '/galaxy/data/location/liftOver.loc' for 'liftOver' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,319 Loaded tool data table 'liftOver' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,501 Loaded 1 lines from '/cvmfs/main.galaxyproject.org/galaxy/tool-data/bam_iobio.loc.sample' for 'bam_iobio' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,501 Loaded tool data table 'bam_iobio' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,503 Loaded 1 lines from '/cvmfs/main.galaxyproject.org/galaxy/tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,503 Loaded tool data table 'vcf_iobio' from file '/mnt/galaxy/galaxy-app/config/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,509 Loaded 2 lines from '/cvmfs/data.galaxyproject.org/managed/location/all_fasta_dbkeys.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,509 Loading another instance of data table 'all_fasta' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,511 Loaded 2 lines from '/cvmfs/data.galaxyproject.org/managed/location/dbkeys.loc' for '__dbkeys__' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,511 Loaded tool data table '__dbkeys__' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,513 Loaded 18 lines from '/cvmfs/data.galaxyproject.org/managed/location/all_fasta.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,513 Loading another instance of data table 'all_fasta' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,516 Loaded 19 lines from '/cvmfs/data.galaxyproject.org/managed/location/alignseq.loc' for 'alignseq_seq' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,516 Loaded tool data table 'alignseq_seq' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,517 Loaded 19 lines from '/cvmfs/data.galaxyproject.org/managed/location/twobit.loc' for 'twobit' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,517 Loaded tool data table 'twobit' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,518 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,518 Loading another instance of data table 'lastz_seqs' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,520 Loaded 33 lines from '/cvmfs/data.galaxyproject.org/managed/location/bowtie2_indices.loc' for 'bowtie2_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,520 Loading another instance of data table 'bowtie2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,522 Loaded 33 lines from '/cvmfs/data.galaxyproject.org/managed/location/tophat2_indices.loc' for 'tophat2_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,522 Loading another instance of data table 'tophat2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,525 Loaded 57 lines from '/cvmfs/data.galaxyproject.org/managed/location/hisat2_indexes.loc' for 'hisat2_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,525 Loaded tool data table 'hisat2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,526 Loaded 45 lines from '/cvmfs/data.galaxyproject.org/managed/location/bwa_mem_index.loc' for 'bwa_mem_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,527 Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,527 Attempted to add fields (['papHam1', 'papHam1', 'Baboon (Papio anubis): papHam1', '/cvmfs/data.galaxyproject.org/managed/bwa_mem_index/papHam1/papHam1.fa']) to data table 'bwa_mem_indexes', but this entry already exists and allow_duplicates is False. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,528 Loaded 18 lines from '/cvmfs/data.galaxyproject.org/managed/location/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,528 Loading another instance of data table 'fasta_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,530 Loaded 17 lines from '/cvmfs/data.galaxyproject.org/managed/location/picard_index.loc' for 'picard_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,530 Loading another instance of data table 'picard_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,532 Loaded 3 lines from '/cvmfs/data.galaxyproject.org/managed/location/kraken_databases.loc' for 'kraken_databases' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,532 Loaded tool data table 'kraken_databases' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,533 Loaded 1 lines from '/cvmfs/data.galaxyproject.org/managed/location/ncbi_taxonomy.loc' for 'ncbi_taxonomy' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,533 Loaded tool data table 'ncbi_taxonomy' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,534 Loaded 0 lines from '/cvmfs/data.galaxyproject.org/managed/location/byhand_dbkeys.loc' for '__dbkeys__' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,534 Loading another instance of data table '__dbkeys__' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,536 Loaded 12 lines from '/cvmfs/data.galaxyproject.org/managed/location/rnastar_index2.loc' for 'rnastar_index2' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,536 Loaded tool data table 'rnastar_index2' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,551 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/a9d4f71dbfb0/bowtie2_indices.loc' for 'bowtie2_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,551 Loading another instance of data table 'bowtie2_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,552 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/546ada4a9f43/bwa_mem_index.loc' for 'bwa_mem_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,552 Loading another instance of data table 'bwa_mem_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,553 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/fb2e0e1dac89/blastdb.loc' for 'blastdb' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,553 Loading another instance of data table 'blastdb' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,554 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/b4427dbb6ced/bwa_index.loc' for 'bwa_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,554 Loading another instance of data table 'bwa_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,555 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/b4427dbb6ced/bwa_index_color.loc' for 'bwa_indexes_color' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,555 Loading another instance of data table 'bwa_indexes_color' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,556 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/9ca609a2a421/bowtie_indices.loc' for 'bowtie_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,556 Loading another instance of data table 'bowtie_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,557 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/lastz/60afcc2c1d05/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,557 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,558 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/758594ed0364/bowtie2_indices.loc' for 'tophat2_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,558 Loading another instance of data table 'tophat2_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,558 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/1eb21dccc2fa/hisat2_indexes.loc' for 'hisat2_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,559 Loading another instance of data table 'hisat2_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,559 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/a6dcb86af112/sam_fa_indices.loc' for 'sam_fa_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,559 Loading another instance of data table 'sam_fa_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,560 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/85d0d479f05b/sailfish_indexes.loc' for 'sailfish_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,560 Loaded tool data table 'sailfish_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,561 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/0f32ad418df8/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,561 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,562 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/b77178f66fc3/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,562 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,563 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/a1ea9af8d5f4/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,563 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,564 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/gffread/12aeae6d8587/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,564 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,565 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/8160c8ea4eb9/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,565 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,566 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/986b63735a5e/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,566 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,567 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/tophat_fusion_post/f83394a2c2da/bowtie_indices.loc' for 'bowtie_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,567 Loading another instance of data table 'bowtie_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,568 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/tophat_fusion_post/f83394a2c2da/tophat_fusion_blastdb.loc' for 'tophat_fusion_blastdb_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,568 Loading another instance of data table 'tophat_fusion_blastdb_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,569 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/881e16ad05c6/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,569 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,569 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/bfc4517aa037/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,570 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,570 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/8cfc17e27132/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,570 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,571 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/1ebb4ecdc1ef/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,571 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,572 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/890d97772e2a/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,572 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,573 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/bamtools/ea3fc1adee75/sam_fa_indices.loc' for 'sam_fa_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,573 Loading another instance of data table 'sam_fa_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,574 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/picard/efc56ee1ade4/picard_index.loc' for 'picard_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,574 Loading another instance of data table 'picard_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,575 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/401f29f278f0/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,575 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,576 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/046b3db333bd/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,576 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,576 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/d3f4f86a18d4/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,577 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,577 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/4dba4b988d0a/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,577 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,578 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/d485f9f1aa83/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,578 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,579 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/table_annovar/08b003ee9db7/annovar_index.loc' for 'annovar_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,579 Loading another instance of data table 'annovar_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,580 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/e09ce114d240/snpeffv_genomedb.loc' for 'snpeffv_genomedb' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,580 Loaded tool data table 'snpeffv_genomedb' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,581 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/e09ce114d240/snpeffv_regulationdb.loc' for 'snpeffv_regulationdb' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,581 Loaded tool data table 'snpeffv_regulationdb' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,581 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/e09ce114d240/snpeffv_annotations.loc' for 'snpeffv_annotations' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,581 Loaded tool data table 'snpeffv_annotations' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,584 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/e09ce114d240/snpeffv_databases.loc' for 'snpeffv_databases' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,584 Loaded tool data table 'snpeffv_databases' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,585 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/99684adf84de/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,585 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,586 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/ac0235d2d459/sam_fa_indices.loc' for 'sam_fa_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,586 Loading another instance of data table 'sam_fa_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,586 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/kraken_report/9ae975c30dde/kraken_databases.loc' for 'kraken_databases' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,586 Loading another instance of data table 'kraken_databases' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,586 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/kraken_translate/b9971bca4b01/kraken_databases.loc' for 'kraken_databases' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,586 Loading another instance of data table 'kraken_databases' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,586 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/kraken_filter/fe94f318048c/kraken_databases.loc' for 'kraken_databases' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,586 Loading another instance of data table 'kraken_databases' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,587 Loaded 2 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/kraken/b2392a9dfb01/kraken_databases.loc' for 'kraken_databases' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,587 Loading another instance of data table 'kraken_databases' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,588 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/data_manager_diamond_database_builder/ce62d0912b10/diamond_database.loc' for 'diamond_database' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,588 Loaded tool data table 'diamond_database' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,589 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/98037ef3d2a9/diamond_database.loc' for 'diamond_database' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,589 Loading another instance of data table 'diamond_database' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,589 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/d844fdcce44e/ncbi_taxonomy.loc' for 'ncbi_taxonomy' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,589 Loading another instance of data table 'ncbi_taxonomy' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,590 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/cdcc4bb60bc3/all_fasta.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,590 Loading another instance of data table 'all_fasta' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,591 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/62d1fae3b7d3/all_fasta.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,591 Loading another instance of data table 'all_fasta' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,592 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/table_recalibration/30e1dd77e99c/gatk_sorted_picard_index.loc' for 'gatk_picard_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,592 Loading another instance of data table 'gatk_picard_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,592 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/984733fcab49/snpeffv_genomedb.loc' for 'snpeffv_genomedb' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,592 Loading another instance of data table 'snpeffv_genomedb' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,593 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/984733fcab49/snpeffv_regulationdb.loc' for 'snpeffv_regulationdb' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,593 Loading another instance of data table 'snpeffv_regulationdb' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,594 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/984733fcab49/snpeffv_annotations.loc' for 'snpeffv_annotations' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,594 Loading another instance of data table 'snpeffv_annotations' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,594 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/984733fcab49/snpeffv_databases.loc' for 'snpeffv_databases' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,594 Loading another instance of data table 'snpeffv_databases' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,595 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_index_builder/cc5ae94acf01/all_fasta.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,595 Loading another instance of data table 'all_fasta' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,596 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_index_builder/cc5ae94acf01/bwa_index.loc' for 'bwa_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,596 Loading another instance of data table 'bwa_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,597 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_index_builder/cc5ae94acf01/bwa_index_color.loc' for 'bwa_indexes_color' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,597 Loading another instance of data table 'bwa_indexes_color' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,598 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/700f2df51eb0/all_fasta.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,598 Loading another instance of data table 'all_fasta' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,599 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/700f2df51eb0/gatk_sorted_picard_index.loc' for 'gatk_picard_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,599 Loading another instance of data table 'gatk_picard_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,600 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/all_fasta.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,600 Loading another instance of data table 'all_fasta' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,601 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,601 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,602 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/86fa71e9b427/all_fasta.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,602 Loading another instance of data table 'all_fasta' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,603 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/86fa71e9b427/dbkeys.loc' for '__dbkeys__' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,603 Loading another instance of data table '__dbkeys__' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,604 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/fb744a070bee/all_fasta.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,604 Loading another instance of data table 'all_fasta' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,605 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/e87aeff2cf88/all_fasta.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,605 Loading another instance of data table 'all_fasta' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,606 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/e87aeff2cf88/bowtie2_indices.loc' for 'bowtie2_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,606 Loading another instance of data table 'bowtie2_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,607 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/e87aeff2cf88/tophat2_indices.loc' for 'tophat2_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,607 Loading another instance of data table 'tophat2_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,608 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/e519769cdb9c/all_fasta.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,608 Loading another instance of data table 'all_fasta' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,608 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/e519769cdb9c/bwa_mem_index.loc' for 'bwa_mem_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,609 Loading another instance of data table 'bwa_mem_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,609 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/all_fasta.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,609 Loading another instance of data table 'all_fasta' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,610 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/hisat2_indexes.loc' for 'hisat2_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,610 Loading another instance of data table 'hisat2_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,611 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_picard_index_builder/00491eabe22b/all_fasta.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,611 Loading another instance of data table 'all_fasta' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,612 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_picard_index_builder/00491eabe22b/picard_index.loc' for 'picard_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,612 Loading another instance of data table 'picard_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,613 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/avowinkel/gatk/b80ff7f43ad1/picard_index.loc' for 'picard_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,613 Loading another instance of data table 'picard_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,614 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/9946bc39c834/all_fasta.loc' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,614 Loading another instance of data table 'all_fasta' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,615 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/9946bc39c834/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,615 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,618 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/9946bc39c834/twobit.loc' for 'twobit' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,618 Loading another instance of data table 'twobit' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,619 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/9946bc39c834/alignseq.loc' for 'alignseq_seq' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,619 Loading another instance of data table 'alignseq_seq' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,622 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/b8431744eab3/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,622 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,623 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/vcftools_consensus/79f5d34da277/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,623 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,624 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/bamtools/04866f817daa/sam_fa_indices.loc' for 'sam_fa_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,624 Loading another instance of data table 'sam_fa_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,625 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/53646aaaafef/bwa_mem_index.loc' for 'bwa_mem_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,625 Loading another instance of data table 'bwa_mem_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,625 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7538e2bfcd41/blastdb.loc' for 'blastdb' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,625 Loading another instance of data table 'blastdb' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,626 While attempting to merge tool data table "blastdb", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,626 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7538e2bfcd41/blastdb_p.loc' for 'blastdb_p' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,626 Loading another instance of data table 'blastdb_p' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,626 While attempting to merge tool data table "blastdb_p", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,627 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7538e2bfcd41/blastdb_d.loc' for 'blastdb_d' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,627 Loaded tool data table 'blastdb_d' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,627 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/065d8a4d74f4/kraken_databases.loc' for 'kraken_databases' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,627 Loading another instance of data table 'kraken_databases' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,628 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/testtoolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/6f0294046f41/kraken_databases.loc' for 'kraken_databases' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,628 Loading another instance of data table 'kraken_databases' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,628 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/156b60c1530f/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,629 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,629 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/testtoolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/d731d6f785b5/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,629 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,630 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/testtoolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/64d95a7df265/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,630 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,631 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/testtoolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/265e5230925c/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,631 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,632 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/testtoolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/c3a5388628b5/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,632 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,633 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/testtoolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/f0982f54fef1/fasta_indexes.loc' for 'fasta_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,633 Loading another instance of data table 'fasta_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,633 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/aac8444d6681/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,634 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,634 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/512155688d98/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,634 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,635 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/a02cfa31e9cb/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,635 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,636 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/a1ca9bccc7f2/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,636 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,637 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/7e361d147872/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,637 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,638 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/94ca68515826/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,638 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,640 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/db940c262830/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,640 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,641 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/f8fc4e5aff9d/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,641 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,642 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/29fcfd36e90a/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,642 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,643 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/38e3f226248b/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,643 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,644 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/fd1275e01605/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,644 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,644 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/bfff7454b59a/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,645 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,645 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/5d11599b8a7d/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,645 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,648 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/81b1e3e1fc6c/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,648 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,649 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/f264afa9fa6f/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,649 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,649 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/72bfafe3330b/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,649 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,650 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/2d466b530754/lastz_seqs.loc' for 'lastz_seqs' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,650 Loading another instance of data table 'lastz_seqs' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,651 Loaded 0 lines from '/mnt/galaxy/galaxy-app/tool-data/shed_tool_data/toolshed.g2.bx.psu.edu/repos/devteam/bamtools/c1a1bea37098/sam_fa_indices.loc' for 'sam_fa_indexes' | |
| galaxy.tools.data DEBUG 2018-03-20 10:27:47,651 Loading another instance of data table 'sam_fa_indexes' from file '/mnt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content. | |
| galaxy.jobs DEBUG 2018-03-20 10:27:47,741 Loading job configuration from ./config/job_conf.xml | |
| galaxy.util.handlers DEBUG 2018-03-20 10:27:47,741 Read definition for handler 'main' | |
| galaxy.util.handlers DEBUG 2018-03-20 10:27:47,741 default set to child with id or tag 'main' | |
| galaxy.util.handlers DEBUG 2018-03-20 10:27:47,741 default set to child with id or tag 'slurm_cluster' | |
| galaxy.jobs DEBUG 2018-03-20 10:27:47,742 Done loading job configuration | |
| beaker.container DEBUG 2018-03-20 10:27:47,923 data file /mnt/galaxy/galaxy-app/database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache | |
| galaxy.tools.toolbox.base INFO 2018-03-20 10:27:48,042 Parsing the tool configuration /mnt/galaxy/galaxy-app/config/tool_conf.xml | |
| galaxy.tools.toolbox.base ERROR 2018-03-20 10:27:48,107 Error reading tool configuration file from path: genomespace/genomespace_file_browser_prod.xml | |
| galaxy.tools.toolbox.base ERROR 2018-03-20 10:27:48,331 Error reading tool configuration file from path: extract/liftOver_wrapper.xml | |
| galaxy.tools.toolbox.base INFO 2018-03-20 10:27:48,491 Parsing the tool configuration /mnt/galaxy/galaxy-app/config/shed_tool_conf.xml | |
| galaxy.tools WARNING 2018-03-20 10:27:48,828 Tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3: a when tag has not been defined for 'illuminaclip (do_illuminaclip) --> no', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:48,947 Tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1: a when tag has been defined for 'manipulation (manipulation_selector) --> modify_each_score', but does not appear to be selectable. | |
| galaxy.tools WARNING 2018-03-20 10:27:49,643 Tool toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy1: a when tag has not been defined for 'samout_conditional (samout) --> False', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:49,831 Tool toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1: a when tag has not been defined for 'D (seq_dictionary) --> false', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:49,832 Tool toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1: a when tag has not been defined for 'i (alt_indel_snp_ratio) --> false', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:49,832 Tool toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1: a when tag has not been defined for 'p (variant_filter) --> false', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:49,832 Tool toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1: a when tag has not been defined for 't (mutation_rate) --> false', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:49,975 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.2: a when tag has not been defined for 'rule_configuration (rules_selector) --> false', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:49,982 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2: a when tag has not been defined for 'format_type (format_type_selector) --> fastq', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:49,982 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2: a when tag has not been defined for 'format_type (format_type_selector) --> bed', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:49,982 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2: a when tag has not been defined for 'format_type (format_type_selector) --> yaml', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:49,982 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2: a when tag has not been defined for 'format_type (format_type_selector) --> json', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:49,982 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2: a when tag has not been defined for 'format_type (format_type_selector) --> fasta', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:49,982 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2: a when tag has been defined for 'analysis_type (analysis_type_selector) --> sort', but does not appear to be selectable. | |
| galaxy.tools WARNING 2018-03-20 10:27:50,269 Tool toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/0.0.3: a when tag has not been defined for 'adv_options (adv_options_selector) --> false', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:50,301 Tool toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/0.0.3: a when tag has not been defined for 'adv_options (adv_options_selector) --> false', assuming empty inputs. | |
| /mnt/galaxy/galaxy-app/lib/galaxy/tools/parameters/basic.py:1249: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. | |
| if elem.find('filter'): | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:50,848 Datatype class not found for extension 'snp', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:50,848 Datatype class not found for extension 'ind', which is used in the 'format' attribute of parameter 'group1' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:50,848 Datatype class not found for extension 'ind', which is used in the 'format' attribute of parameter 'group2' | |
| galaxy.tools WARNING 2018-03-20 10:27:51,582 Tool toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.22.1: a when tag has not been defined for 'genome (genome_choose) --> ', assuming empty inputs. | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:51,822 Datatype class not found for extension 'gg3', which is used in the 'format' attribute of parameter 'inputA' | |
| galaxy.tools WARNING 2018-03-20 10:27:51,835 Tool with id toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.22.0 declares a conditional test parameter as optional, this is invalid and will be ignored. | |
| galaxy.tools WARNING 2018-03-20 10:27:51,835 Tool toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.22.0: a when tag has not been defined for 'addition2 (addition2_select) --> ', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:52,334 Tool toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatellite/1.0.0: a when tag has not been defined for 'referenceFileSource (requireReference) --> false', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:52,335 Tool toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatellite/1.0.0: a when tag has not been defined for 'inputFileSource (inputFileType) --> fastq_noquals', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:52,335 Tool toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatellite/1.0.0: a when tag has not been defined for 'inputFileSource (inputFileType) --> fasta', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:52,335 Tool toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatellite/1.0.0: a when tag has not been defined for 'inputFileSource (inputFileType) --> fastq', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:52,335 Tool toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatellite/1.0.0: a when tag has not been defined for 'flankSetting (noflankdisplay) --> true', assuming empty inputs. | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:52,402 Datatype class not found for extension 'gerald', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:52,408 Datatype class not found for extension 'gerald', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:52,810 Datatype class not found for extension 'fastqsanger.gz', which is used in the 'format' attribute of parameter 'fastq_input1' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:52,810 Datatype class not found for extension 'fastqsanger.gz', which is used in the 'format' attribute of parameter 'fastq_input2' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:52,810 Datatype class not found for extension 'fastqsanger.gz', which is used in the 'format' attribute of parameter 'fastq_input1' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:52,811 Datatype class not found for extension 'fastqsanger.gz', which is used in the 'format' attribute of parameter 'fastq_input1' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:53,005 Datatype class not found for extension 'fastqsanger.gz', which is used in the 'format' attribute of parameter 'fastq_input1' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:53,005 Datatype class not found for extension 'fastqsanger.gz', which is used in the 'format' attribute of parameter 'fastq_input2' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:53,005 Datatype class not found for extension 'fastqsanger.gz', which is used in the 'format' attribute of parameter 'fastq_input1' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:53,006 Datatype class not found for extension 'fastqsanger.gz', which is used in the 'format' attribute of parameter 'fastq_input1' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:53,006 Datatype class not found for extension 'fastqsanger.gz', which is used in the 'format' attribute of parameter 'fastq_input1' | |
| galaxy.tools WARNING 2018-03-20 10:27:53,624 Tool testtoolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc1.0: a when tag has been defined for 'adv_options (adv_options_selector) --> ', but does not appear to be selectable. | |
| galaxy.tools WARNING 2018-03-20 10:27:53,624 Tool testtoolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc1.0: a when tag has not been defined for 'adv_options (adv_options_selector) --> no', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:53,682 Tool testtoolshed.g2.bx.psu.edu/repos/anton/vcfrandomsample/vcfrandomsample/0.0.1: a when tag has not been defined for 'adv_options (adv_options_selector) --> false', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:53,692 Tool testtoolshed.g2.bx.psu.edu/repos/anton/vcfvcfintersect/vcfvcfintersect/0.0.1: a when tag has not been defined for 'adv_options (adv_options_selector) --> false', assuming empty inputs. | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:54,765 Datatype class not found for extension 'fastq.gz', which is used in the 'format' attribute of parameter 'input_file' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:54,765 Datatype class not found for extension 'fastq.bz2', which is used in the 'format' attribute of parameter 'input_file' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:54,786 Datatype class not found for extension 'gb', which is used in the 'format' attribute of parameter 'inf_gbk' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:54,786 Datatype class not found for extension 'gbk', which is used in the 'format' attribute of parameter 'inf_gbk' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:54,847 Datatype class not found for extension 'fastqsanger.gz', which is used in the 'format' attribute of parameter 'fastq_input1' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:54,848 Datatype class not found for extension 'fastqsanger.gz', which is used in the 'format' attribute of parameter 'fastq_input2' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:54,848 Datatype class not found for extension 'fastqsanger.gz', which is used in the 'format' attribute of parameter 'fastq_input1' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:54,848 Datatype class not found for extension 'fastqsanger.gz', which is used in the 'format' attribute of parameter 'fastq_input1' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:54,848 Datatype class not found for extension 'fastqsanger.gz', which is used in the 'format' attribute of parameter 'long' | |
| galaxy.tools WARNING 2018-03-20 10:27:54,861 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/0.0.1: a when tag has not been defined for 'analysis_type (analysis_type_selector) --> -mapped', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:54,861 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/0.0.1: a when tag has not been defined for 'analysis_type (analysis_type_selector) --> -paired', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:54,861 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/0.0.1: a when tag has not been defined for 'analysis_type (analysis_type_selector) --> -reference', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:54,870 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.1: a when tag has not been defined for 'rule_configuration (rules_selector) --> false', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:54,876 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.1: a when tag has not been defined for 'format_type (format_type_selector) --> fastq', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:54,876 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.1: a when tag has not been defined for 'format_type (format_type_selector) --> bed', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:54,876 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.1: a when tag has not been defined for 'format_type (format_type_selector) --> yaml', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:54,876 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.1: a when tag has not been defined for 'format_type (format_type_selector) --> json', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:54,876 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.1: a when tag has not been defined for 'format_type (format_type_selector) --> fasta', assuming empty inputs. | |
| galaxy.tools WARNING 2018-03-20 10:27:54,877 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.1: a when tag has been defined for 'analysis_type (analysis_type_selector) --> sort', but does not appear to be selectable. | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:55,134 Datatype class not found for extension 'fastq.gz', which is used in the 'format' attribute of parameter 'paired_collection' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 10:27:55,139 Datatype class not found for extension 'fastq.gz', which is used in the 'format' attribute of parameter 'paired_collection' | |
| galaxy.tools.toolbox.base INFO 2018-03-20 10:27:55,141 Parsing the tool configuration /mnt/galaxy/galaxy-app/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,141 Reading tools from config files finshed (7098.655 ms) | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,141 Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,141 Loaded tool id: toolshed.g2.bx.psu.edu/repos/malex/beast/beast/1.1, version: 1.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,142 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.2, version: 2.8.1.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,142 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.2, version: 2.8.1.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,142 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.8.1.2, version: 2.8.1.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,142 Loaded tool id: upload1, version: 1.1.4 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,142 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,142 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,142 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,143 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,143 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,143 Loaded tool id: biomart, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,143 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,143 Loaded tool id: gramenemart, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,143 Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,143 Loaded tool id: flymine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,144 Loaded tool id: flymine_test, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,144 Loaded tool id: modmine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,144 Loaded tool id: mousemine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,144 Loaded tool id: ratmine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,144 Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,144 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,144 Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,145 Loaded tool id: wormbase, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,145 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,145 Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,145 Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,145 Loaded tool id: hbvar, version: 2.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,145 Loaded tool id: genomespace_importer, version: 0.0.6 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,145 Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,145 Loaded tool id: genomespace_exporter, version: 0.0.6 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,146 Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,146 Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,146 Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,146 Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,146 Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,146 Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,146 Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,146 Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.1.1, version: 0.1.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,147 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.0.6, version: 1.0.6 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,147 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.0.6, version: 1.0.6 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,147 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.0.6, version: 1.0.6 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,147 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0, version: 1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,147 Loaded tool id: toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,147 Loaded tool id: addValue, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,148 Loaded tool id: cat1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,148 Loaded tool id: Cut1, version: 1.0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,148 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,148 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,148 Loaded tool id: createInterval, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,148 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,148 Loaded tool id: Paste1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,149 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,149 Loaded tool id: random_lines1, version: 2.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,149 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,149 Loaded tool id: Show tail1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,149 Loaded tool id: trimmer, version: 0.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,149 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,149 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,149 Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,150 Loaded tool id: Filter1, version: 1.1.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,150 Loaded tool id: sort1, version: 1.0.3 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,150 Loaded tool id: Grep1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,150 Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,150 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,150 Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,150 Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,150 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,150 Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,151 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/subtract_query/subtract_query1/0.1, version: 0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,151 Loaded tool id: join1, version: 2.1.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,151 Loaded tool id: comp1, version: 1.0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,151 Loaded tool id: Grouping1, version: 2.1.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,151 Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,151 Loaded tool id: toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/fml_gff2gtf/2.1.0, version: 2.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,151 Loaded tool id: toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/fml_bed2gff/2.1.0, version: 2.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,152 Loaded tool id: toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/fml_gbk2gff/2.1.0, version: 2.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,152 Loaded tool id: toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/fml_gff2bed/2.1.0, version: 2.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,152 Loaded tool id: toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/fml_gtf2gff/2.1.0, version: 2.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,152 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,152 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.0, version: 1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,152 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,153 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,153 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,153 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,153 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,153 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,153 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,153 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,154 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,154 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,154 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,154 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,154 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,154 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,154 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,154 Loading section: Extract Features | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,155 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,155 Loading section: Fetch Sequences | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,155 Loaded tool id: Extract genomic DNA 1, version: 2.2.3 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,155 Loading section: Fetch Alignments | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,155 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,155 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,155 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,155 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,155 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,156 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,156 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,156 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,156 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,156 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,156 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,156 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,156 Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,157 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/correlation/cor2/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,157 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/generate_pc_lda_matrix/generate_matrix_for_pca_and_lda1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,157 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lda_analysis/lda_analy1/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,157 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/plot_from_lda/plot_for_lda_output1/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,157 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/mine/maximal_information_based_nonparametric_exploration/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,158 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/count_gff_features/count_gff_features/0.1, version: 0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,158 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/t_test_two_samples/t_test_two_samples/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,158 Loaded tool id: Summary_Statistics1, version: 1.1.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,158 Loaded tool id: Count1, version: 1.0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,158 Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,158 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/gmaj/gmaj_1/2.0.1, version: 2.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,158 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,159 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.3, version: 1.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,159 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/scatterplot_rpy/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,159 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ucsc_custom_track/build_ucsc_custom_track_1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,159 Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/venn_list/venn_list/0.0.9, version: 0.0.9 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,159 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,159 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,159 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,160 Loading section: FASTA manipulation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,160 Loaded tool id: toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.0, version: 0.3.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,160 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_nucleotide_changer/cshl_fasta_nucleotides_changer/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,160 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,160 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,160 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_concatenate_by_species/fasta_concatenate0/0.0.0, version: 0.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,161 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1, version: 1.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,161 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastx_collapser/cshl_fastx_collapser/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,161 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0, version: 1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,161 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0, version: 1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,161 Loading section: NGS: QC and manipulation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,161 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.1, version: 1.1.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,161 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/fastq_quality_trimmer/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,162 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/fastq_trimmer/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,162 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,162 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_splitter/fastq_paired_end_splitter/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,162 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_masker_by_quality/fastq_masker_by_quality/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,162 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,162 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,163 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_combiner/fastq_combiner/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,163 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,163 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,163 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastx_renamer/cshl_fastx_renamer/0.0.11, version: 0.0.11 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,163 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastx_quality_statistics/cshl_fastx_quality_statistics/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,164 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastx_nucleotides_distribution/cshl_fastx_nucleotides_distribution/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,164 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastx_clipper/cshl_fastx_clipper/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,164 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/cshl_fastx_barcode_splitter/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,164 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastx_artifacts_filter/cshl_fastx_artifacts_filter/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,164 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,165 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_converter/cshl_fastq_quality_converter/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,165 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_boxplot/cshl_fastq_quality_boxplot/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,165 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/short_reads_figure_score/quality_score_distribution/1.0.2, version: 1.0.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,165 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/short_reads_trim_seq/trim_reads/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,165 Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3, version: 0.32.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,166 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.0, version: 0.9.6.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,166 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.1, version: 2.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,166 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65, version: 0.65 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,166 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2, version: 0.4.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,166 Loading section: NGS: Mapping | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,167 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,167 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,167 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,167 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.1, version: 0.7.15.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,168 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.15.1, version: 0.7.15.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,168 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.5.0.0, version: 2.5.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,168 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.2.2, version: 1.2.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,168 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.2, version: 1.1.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,168 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3, version: 1.2.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,169 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_color_wrapper/1.0.2, version: 1.0.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,169 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.2.0, version: 1.2.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,169 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/megablast_xml_parser/megablast_xml_parser/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,169 | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,169 | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,169 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2, version: 2.2.6.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,170 Loading section: NGS: RNA Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,170 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/tophat_fusion_post/tophat_fusion_post/0.1, version: 0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,170 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/filter_transcripts_via_tracking/filter_combined_via_tracking/0.1, version: 0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,170 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/cuffquant/2.2.1.0, version: 2.2.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,170 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.0, version: 2.2.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,170 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.0, version: 2.2.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,171 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.0, version: 2.2.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,171 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/2.2.1.0, version: 2.2.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,171 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.3, version: 2.2.1.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,171 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.1.0, version: 1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,171 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.7.6.0, version: 0.7.6.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,171 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.1, version: 2.2.1.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,172 Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy1, version: 0.6.1galaxy1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,172 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.1.0, version: 2.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,172 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3, version: 2.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,172 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.0, version: 2.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,172 Loading section: NGS: SAMtools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,172 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_consensus/vcftools_consensus/0.1.11, version: 0.1.11 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,173 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools/bcftools_view/0.1.19.0, version: 0.1.19.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,173 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.2, version: 1.1.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,173 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_bitwise_flag_filter/sam_bw_filter/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,173 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,173 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_parser/pileup_parser/1.0.2, version: 1.0.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,173 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0, version: 2.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,174 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0, version: 2.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,174 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0, version: 2.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,174 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0, version: 2.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,174 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0, version: 2.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,174 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0, version: 2.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,174 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0, version: 2.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,175 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0, version: 2.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,175 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0, version: 2.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,175 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.1, version: 1.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,175 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0, version: 2.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,175 Loaded tool id: toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,175 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.1, version: 2.1.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,176 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.2, version: 1.0.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,176 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1, version: 2.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,176 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,176 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2, version: 1.1.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,176 Loading section: NGS: BamTools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,177 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0, version: 2.4.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,177 | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,177 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.2, version: 0.0.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,177 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/0.0.2, version: 0.0.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,177 Loading section: NGS: Picard | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,177 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,178 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,178 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,178 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,178 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,178 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,178 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,179 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/1.136.1, version: 1.136.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,179 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,179 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,179 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,179 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,179 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,180 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,180 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,180 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,180 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,180 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,180 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,181 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,181 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,181 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,181 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,181 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,182 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,182 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.136.1, version: 1.136.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,182 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,182 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,182 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/1.136.0, version: 1.136.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,182 Loading section: NGS: VCF Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,182 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,183 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,183 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,183 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,183 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,183 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,183 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,184 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/0.0.2, version: 0.0.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,184 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,184 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,184 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,184 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,184 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,185 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,185 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,185 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,185 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,185 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,186 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,186 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,186 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,186 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,186 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/0.0.4, version: 0.0.4 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,186 Loading section: NGS: Peak Calling | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,186 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sicer/peakcalling_sicer/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,187 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,187 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.7.1, version: 0.5.7.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,187 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/genetrack/genetrack/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,187 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/cwpair2/cwpair2/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,187 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/repmatch_gff3/repmatch_gff3/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,187 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/resize_coordinate_window/resize_coordinate_window/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,188 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgdiff/2.1.0.20151222.0, version: 2.1.0.20151222.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,188 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_predictd/2.1.0.20151222.0, version: 2.1.0.20151222.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,188 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_randsample/2.1.0.20151222.0, version: 2.1.0.20151222.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,188 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_filterdup/2.1.0.20151222.0, version: 2.1.0.20151222.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,188 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0, version: 2.1.0.20151222.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,189 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_refinepeak/2.1.0.20151222.0, version: 2.1.0.20151222.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,189 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0, version: 2.1.0.20151222.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,189 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgbroadcall/2.1.0.20151222.0, version: 2.1.0.20151222.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,189 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgpeakcall/2.1.0.20151222.0, version: 2.1.0.20151222.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,189 Loading section: NGS: Variant Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,189 Loaded tool id: toolshed.g2.bx.psu.edu/repos/simon-gladman/snippy/snippy-core/0.2.0, version: 0.2.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,190 Loaded tool id: toolshed.g2.bx.psu.edu/repos/simon-gladman/snippy/snippy/0.2.0, version: 0.2.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,190 Loaded tool id: toolshed.g2.bx.psu.edu/repos/ntino-krampis/viralcloud/VIGOR/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,190 Loaded tool id: toolshed.g2.bx.psu.edu/repos/ntino-krampis/viralcloud/vir_assembly/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,190 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_isec/vcftools_isec/0.1, version: 0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,190 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_merge/vcftools_merge/0.1, version: 0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,191 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_compare/vcftools_compare/0.1, version: 0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,191 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_subset/vcftools_subset/0.1, version: 0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,191 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0, version: 1.1.0.46-0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,191 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.1.0.46-0, version: 1.1.0.46-0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,192 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,192 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,192 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/varscan_version_2/varscan/0.1, version: 0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,192 Loaded tool id: toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/naive_variant_caller/0.0.2, version: 0.0.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,192 | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,192 | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,193 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2, version: 1.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,193 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/mutate_snp_codon/mutate_snp_codon_1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,193 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.0.0, version: 4.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,193 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.0.0, version: 4.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,193 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.0.0, version: 4.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,193 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/table_annovar/table_annovar/0.2, version: 0.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,193 Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,194 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,194 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/flanking_features/flanking_features_1/4.0.1, version: 4.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,194 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/annotation_profiler/Annotation_Profiler_0/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,194 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/basecoverage/gops_basecoverage_1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,194 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cluster/gops_cluster_1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,194 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/complement/gops_complement_1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,195 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,195 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,195 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,195 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,195 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,195 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,196 Loading section: CloudMap | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,196 Loaded tool id: toolshed.g2.bx.psu.edu/repos/gregory-minevich/check_snpeff_candidates/check_snpeff_candidates/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,196 Loaded tool id: toolshed.g2.bx.psu.edu/repos/gregory-minevich/snp_mapping_using_wgs/snp_mapping_using_wgs/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,196 Loaded tool id: toolshed.g2.bx.psu.edu/repos/gregory-minevich/ems_variant_density_mapping/ems_variant_density_mapping/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,196 Loaded tool id: toolshed.g2.bx.psu.edu/repos/gregory-minevich/cloudmap_in_silico_complementation/in_silico_complementation/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,196 Loaded tool id: toolshed.g2.bx.psu.edu/repos/gregory-minevich/cloudmap_variant_discovery_mapping/cloudmap_variant_discovery_mapping/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,196 Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,197 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes_wrapper/freebayes_wrapper/0.5.0, version: 0.5.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,197 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/hgv_hilbertvis/hgv_hilbertvis/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,197 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/hgv_fundo/hgv_funDo/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,197 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/divide_pg_snp/dividePgSnp/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,197 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ctd_batch/ctdBatch_1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,198 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/snpfreq/hgv_snpFreq/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,198 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2pgsnp/vcf2pgSnp/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,198 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/dgidb_annotator/dgidb_annotator/0.1, version: 0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,198 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/dgidb_annotator/dgidb_annotate/0.1, version: 0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,198 Loading section: BEDTools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,198 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,199 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,199 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,199 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,200 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,200 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,201 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,201 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,202 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,202 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,202 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,203 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,203 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,203 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,204 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,204 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,205 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,205 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,205 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,206 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,206 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,206 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.22.1, version: 2.22.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,207 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.22.1, version: 2.22.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,207 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,208 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,208 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.22.1, version: 2.22.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,208 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,209 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,209 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,209 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,210 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,210 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,211 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,211 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,211 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.22.0, version: 2.22.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,212 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,212 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,212 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,213 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,213 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,213 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.24.1, version: 2.24.1 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,214 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,214 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.24.1, version: 2.24.1 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,214 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,214 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,215 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,215 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,215 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,216 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0, version: 2.24.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,216 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,216 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,217 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,217 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,217 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,217 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,218 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.24.1, version: 2.24.1 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,218 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,218 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.24.0, version: 2.24.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,219 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,219 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,219 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,220 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.24.1, version: 2.24.1 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,220 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,220 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,221 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,221 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,221 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,221 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,222 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,222 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,222 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,223 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.24.0, version: 2.24.0 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,223 Loading section: Regional Variation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,223 Loaded tool id: toolshed.g2.bx.psu.edu/repos/guru-ananda/heatmap/heatmap_1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,223 Loaded tool id: toolshed.g2.bx.psu.edu/repos/guru-ananda/rhmm/hmm_1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,224 Loaded tool id: toolshed.g2.bx.psu.edu/repos/guru-ananda/karyotype_plot/karyotype_Plot_1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,224 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/windowsplitter/winSplitter/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,225 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/microsats_alignment_level/microsats_align1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,225 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/getindels_2way/getIndels_2way/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,225 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/microsats_mutability/microsats_mutability1/1.1.0, version: 1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,226 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/maf_cpg_filter/cpgFilter/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,226 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/getindelrates_3way/indelRates_3way/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,226 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/featurecounter/featureCoverage1/2.0.0, version: 2.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,227 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/indels_3way/indels_3way/1.0.3, version: 1.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,227 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/weightedaverage/wtavg/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,227 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/substitutions/substitutions1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,228 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/substitution_rates/subRate1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,228 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/quality_filter/qualityFilter/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,228 Loading section: Multiple Alignments | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,228 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/0.1, version: 0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,229 Loaded tool id: toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3, version: 7.221.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,229 Loading section: Metagenomic Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,229 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1, version: 0.1.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,230 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_matches/0.1.1, version: 0.1.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,230 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/gi2taxonomy/Fetch Taxonomic Ranks/1.1.0, version: 1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,230 Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/amplicon_analysis_pipeline/amplicon_analysis_pipeline/1.0.6, version: 1.0.6 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,231 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cd_hit_dup/cd_hit_dup/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,231 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/Kraken2Tax/1.1, version: 1.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,231 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/0.6.13, version: 0.6.13 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,232 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.1.6.0, version: 0.1.6.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,232 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_alignment/1.9.7.0, version: 1.9.7.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,232 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_clustering/1.9.7.0, version: 1.9.7.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,233 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_sorting/1.9.7.0, version: 1.9.7.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,233 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_shuffling/1.9.7.0, version: 1.9.7.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,233 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_search/1.9.7.0, version: 1.9.7.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,234 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_masking/1.9.7.0, version: 1.9.7.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,234 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_chimera_detection/1.9.7.0, version: 1.9.7.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,234 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/1.9.7.0, version: 1.9.7.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,235 Loaded tool id: toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.0, version: 2.6.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,235 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vegan_rarefaction/vegan_rarefaction/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,235 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vegan_fisher_alpha/vegan_fisher_alpha/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,236 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vegan_diversity/vegan_diversity/0.0.3, version: 0.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,236 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/kraken/kraken/1.2.1, version: 1.2.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,237 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/kraken_filter/kraken-filter/1.2.1, version: 1.2.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,237 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/kraken_translate/kraken-translate/1.2.1, version: 1.2.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,237 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/kraken_report/kraken-report/1.2.1, version: 1.2.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,238 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/kraken_report/kraken-mpa-report/1.2.1, version: 1.2.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,238 Loading section: Multiple regression | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,238 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/best_regression_subsets/BestSubsetsRegression1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,238 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/rcve/rcve1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,239 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/partialr_square/partialRsq/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,239 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/logistic_regression_vif/LogisticRegression/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,239 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/linear_regression/LinearRegression1/1.0.1, version: 1.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,240 Loading section: Multivariate Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,240 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2, version: 1.0.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,240 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/kernel_principal_component_analysis/kpca1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,241 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/kernel_canonical_correlation_analysis/kcca1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,241 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/canonical_correlation_analysis/cca1/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,241 Loading section: Motif Tools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,241 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.11.0.1, version: 4.11.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,242 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.0.3, version: 4.11.0.3 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,242 Loading section: STR-FM: Microsatellite Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,242 Loaded tool id: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/Profilegenerator/2.0.0, version: 2.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,243 Loaded tool id: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/PEsortedSAM2readprofile/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,243 Loaded tool id: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatpurity/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,243 Loaded tool id: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatcompat/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,244 Loaded tool id: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/heteroprob/2.0.0, version: 2.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,244 Loaded tool id: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/fetchflank/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,244 Loaded tool id: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/combineproballelecom/2.0.0, version: 2.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,245 Loaded tool id: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatellite/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,245 Loaded tool id: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/space2underscore_readname/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,245 Loaded tool id: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/GenotypeSTR/2.0.0, version: 2.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,245 Loaded tool id: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/readdepth2seqdepth/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,245 Loading section: NGS: GATK Tools (beta) | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,246 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/table_recalibration/gatk_table_recalibration/0.0.5, version: 0.0.5 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,246 Loading section: NCBI SRA Tools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,246 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.2, version: 2.8.1.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,247 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.2, version: 2.8.1.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,247 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.8.1.2, version: 2.8.1.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,247 Loading section: Assembly | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,248 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.11.1, version: 3.11.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,248 Loaded tool id: toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/velvetoptimiser/velvetoptimiser/1.0.0, version: 1.0.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,248 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/1.2.10.0, version: 1.2.10.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,249 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.0, version: 1.2.10.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,249 Loading section: GATK | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,249 Loaded tool id: toolshed.g2.bx.psu.edu/repos/avowinkel/gatk/gatk/3.4-0.d9, version: 3.4-0.d9 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,249 Loading section: NCBI: Blast Tools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,250 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,250 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,250 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,251 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,251 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_segmasker_wrapper/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,251 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,251 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,252 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,252 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,253 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_convert2blastmask_wrapper/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,253 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,253 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,254 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,254 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,254 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.2.00, version: 0.2.00 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,254 Loading section: Annotation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,255 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2, version: 0.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,255 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_not-knowlegde-based/0.2, version: 0.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,255 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2, version: 0.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,255 Loading section: Vcflib | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,256 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfannotategenotypes/vcfannotategenotypes/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,256 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfprimers/vcfprimers/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,256 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfbreakcreatemulti/vcfbreakcreatemulti/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,257 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfcombine/vcfcombine/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,257 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfvcfintersect/vcfvcfintersect/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,257 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfbedintersect/vcfbedintersect/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,258 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfrandomsample/vcfrandomsample/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,258 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfcheck/vcfcheck/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,258 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfcommonsamples/vcfcommonsamples/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,259 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcffilter/vcffilter/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,259 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcffixup/vcffixup/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,259 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfgeno2haplo/vcfgeno2haplo/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,260 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfaddinfo/vcfaddinfo/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,260 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfleftalign/vcfleftalign/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,260 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfgenotypes/vcfgenotypes/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,261 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfselectsamples/vcfselectsamples/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,261 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfannotate/vcfannotate/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,261 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfsort/vcfsort/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,262 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfallelicprimitives/vcfallelicprimitives/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,262 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcf2tsv/vcf2tsv/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,262 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfdistance/vcfdistance/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,263 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/anton/vcfhethom/vcfhethom/0.0.1, version: 0.0.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,263 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,264 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,264 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,265 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,265 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,266 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,266 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,267 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,267 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,267 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,268 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,268 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,269 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,269 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,270 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,270 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/0.0.2, version: 0.0.2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,271 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,271 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,272 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,272 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,273 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,273 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,273 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc1.0, version: 1.0.0_rc1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,274 Loading section: quasitools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,274 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/quasitools/aavariants/0.1.0, version: 0.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,274 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/quasitools/consensus/0.1.0, version: 0.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,275 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/quasitools/callcodonvar/0.1.0, version: 0.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,275 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/quasitools/aacoverage/0.1.0, version: 0.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,275 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/quasitools/dnds/0.1.0, version: 0.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,276 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/quasitools/drmutations/0.1.0, version: 0.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,276 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/quasitools/callntvar/0.1.0, version: 0.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,276 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/quasitools/hydra/0.1.0, version: 0.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,276 Loading section: Deeptools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,277 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,277 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,278 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,278 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,278 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,279 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,279 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,279 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,280 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,280 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,281 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,281 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,282 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,282 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,282 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,283 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,283 Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0, version: 2.5.1.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,283 Loading section: NGS: Assembly | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,284 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.9.0, version: 3.9.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,284 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/abyss/abyss-pe/2.0.1.0, version: 2.0.1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,284 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.5, version: 4.5 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,285 Loaded tool id: toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0, version: 1.12.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,285 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.4.0, version: 0.4.4.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 10:27:55,285 Loading tool panel finished (144.037 ms) | |
| galaxy.tools.search DEBUG 2018-03-20 10:27:55,310 Starting to build toolbox index. | |
| docutils WARNING 2018-03-20 10:27:55,925 :38: (ERROR/3) Document may not end with a transition. | |
| docutils WARNING 2018-03-20 10:27:57,882 :61: (ERROR/3) Document may not end with a transition. | |
| docutils WARNING 2018-03-20 10:27:58,927 :11: (ERROR/3) At least one body element must separate transitions; adjacent transitions are not allowed. | |
| docutils WARNING 2018-03-20 10:28:01,212 :35: (ERROR/3) Document may not end with a transition. | |
| docutils WARNING 2018-03-20 10:28:02,796 :16: (ERROR/3) Unexpected indentation. | |
| docutils WARNING 2018-03-20 10:28:03,630 :22: (ERROR/3) Document may not end with a transition. | |
| docutils WARNING 2018-03-20 10:28:03,659 :30: (WARNING/2) Duplicate explicit target name: "krona". | |
| docutils WARNING 2018-03-20 10:28:03,662 :4: (ERROR/3) Duplicate target name, cannot be used as a unique reference: "krona". | |
| docutils WARNING 2018-03-20 10:28:03,663 :28: (ERROR/3) Duplicate target name, cannot be used as a unique reference: "krona". | |
| docutils WARNING 2018-03-20 10:28:03,938 :16: (ERROR/3) Document may not end with a transition. | |
| docutils WARNING 2018-03-20 10:28:04,149 :50: (ERROR/3) Document may not end with a transition. | |
| galaxy.tools.search DEBUG 2018-03-20 10:28:05,599 Toolbox index finished (10288.760 ms) | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,617 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/bgruening/data_manager_diamond_database_builder/data_manager/diamond_database_builder/0.0.1 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,624 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/data_manager/data_manager_snpeff_databases/0.0.1 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,628 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/data_manager/data_manager_snpeff_download/0.0.1 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,633 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_index_builder/data_manager/bwa_index_builder/0.0.1 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,637 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_index_builder/data_manager/bwa_color_space_index_builder/0.0.1 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,641 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/data_manager/gatk_picard_index_builder/0.0.1 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,645 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/data_manager/sam_fasta_index_builder/0.0.1 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,653 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/fetch_genome_all_fasta_dbkeys/0.0.1 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,660 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/data_manager/fetch_genome_all_fasta/0.0.1 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,664 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/data_manager/bowtie2_index_builder/2.2.6 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,668 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/data_manager/bwa_mem_index_builder/0.0.1 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,674 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder/0.0.1 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,678 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_picard_index_builder/data_manager/picard_index_builder/0.0.1 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,682 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/data_manager/twobit_builder/0.0.2 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,687 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/data_manager/kraken_database_builder/1.0.0 | |
| galaxy.tools.data_manager.manager DEBUG 2018-03-20 10:28:05,694 Loaded Data Manager: testtoolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/data_manager/kraken_database_builder/1.0.0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,697 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,701 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,738 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,739 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,741 Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,741 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,742 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,745 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,746 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,749 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,750 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,752 Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,758 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,786 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,787 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,792 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,800 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,803 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,869 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,872 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,875 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,910 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,912 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,914 Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,914 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,951 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. | |
| galaxy.datatypes.display_applications.application ERROR 2018-03-20 10:28:05,952 Error loading a set of Dynamic Display Application links: Unable to find data table named "biom_simple_display". | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,952 Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,953 Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,954 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,954 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,955 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,955 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,955 Adding inherited display application 'ensembl_interval' to datatype 'bed12' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,955 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,955 Adding inherited display application 'rviewer_interval' to datatype 'bed12' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,955 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,962 Adding inherited display application 'ensembl_interval' to datatype 'bed' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,962 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,962 Adding inherited display application 'rviewer_interval' to datatype 'bed' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,962 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,966 Adding inherited display application 'ensembl_gff' to datatype 'gtf' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,966 Adding inherited display application 'igv_gff' to datatype 'gtf' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,967 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,967 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,967 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,967 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,969 Adding inherited display application 'ensembl_gff' to datatype 'gff3' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,969 Adding inherited display application 'igv_gff' to datatype 'gff3' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,972 Adding inherited display application 'ensembl_interval' to datatype 'chrint' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,973 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,973 Adding inherited display application 'rviewer_interval' to datatype 'chrint' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,973 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,973 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,973 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,973 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,973 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,975 Adding inherited display application 'ensembl_interval' to datatype 'bed6' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,975 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,975 Adding inherited display application 'rviewer_interval' to datatype 'bed6' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,975 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' | |
| galaxy.datatypes.registry ERROR 2018-03-20 10:28:05,977 Error loading converter (./lib/galaxy/datatypes/converters) | |
| Traceback (most recent call last): | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/datatypes/registry.py", line 540, in load_datatype_converters | |
| converter = toolbox.load_tool(config_path, use_cached=use_cached) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 748, in load_tool | |
| tool = self.create_tool(config_file=config_file, repository_id=repository_id, guid=guid, **kwds) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 262, in create_tool | |
| raise e | |
| IOError: [Errno 2] No such file or directory: './lib/galaxy/datatypes/converters/bam_to_bai.xml' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,983 Loaded converter: CONVERTER_bam_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,985 Loaded converter: CONVERTER_bed_to_gff_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,987 Loaded converter: CONVERTER_bed_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,988 Loaded converter: CONVERTER_bed_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,990 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,993 Loaded converter: CONVERTER_bed_to_fli_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,994 Loaded converter: CONVERTER_bedgraph_to_bigwig | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,996 Loaded converter: CONVERTER_len_to_linecount | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:05,998 Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,000 Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,001 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,003 Loaded converter: CONVERTER_fasta_to_tabular | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,004 Loaded converter: CONVERTER_fasta_to_bowtie_base_index | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,006 Loaded converter: CONVERTER_fasta_to_bowtie_color_index | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,007 Loaded converter: CONVERTER_fasta_to_2bit | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,009 Loaded converter: CONVERTER_fasta_to_len | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,010 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,012 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,013 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,014 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,015 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,017 Loaded converter: CONVERTER_gff_to_bed_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,018 Loaded converter: CONVERTER_gff_to_interval_index_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,019 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,021 Loaded converter: CONVERTER_gff_to_fli_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,022 Loaded converter: CONVERTER_gff_to_interval_index_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,023 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,024 Loaded converter: CONVERTER_interval_to_bed_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,026 Loaded converter: CONVERTER_interval_to_bedstrict_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,027 Loaded converter: CONVERTER_interval_to_bed6_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,029 Loaded converter: CONVERTER_interval_to_bed12_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,030 Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,031 Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,032 Loaded converter: CONVERTER_interval_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,034 Loaded converter: CONVERTER_picard_interval_list_to_bed6 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,036 Loaded converter: CONVERTER_maf_to_fasta_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,037 Loaded converter: CONVERTER_maf_to_interval_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,039 Loaded converter: CONVERTER_encodepeak_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,040 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,041 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,042 Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,043 Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,045 Loaded converter: CONVERTER_sam_to_bam | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,047 Loaded converter: CONVERTER_sam_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,048 Loaded converter: tabular_to_dbnsfp | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,050 Loaded converter: CONVERTER_vcf_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,051 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,053 Loaded converter: CONVERTER_vcf_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,054 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry ERROR 2018-03-20 10:28:06,054 Error loading converter (./lib/galaxy/datatypes/converters) | |
| Traceback (most recent call last): | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/datatypes/registry.py", line 540, in load_datatype_converters | |
| converter = toolbox.load_tool(config_path, use_cached=use_cached) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 748, in load_tool | |
| tool = self.create_tool(config_file=config_file, repository_id=repository_id, guid=guid, **kwds) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 262, in create_tool | |
| raise e | |
| IOError: [Errno 2] No such file or directory: './lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml' | |
| galaxy.datatypes.registry ERROR 2018-03-20 10:28:06,055 Error loading converter (./lib/galaxy/datatypes/converters) | |
| Traceback (most recent call last): | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/datatypes/registry.py", line 540, in load_datatype_converters | |
| converter = toolbox.load_tool(config_path, use_cached=use_cached) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 748, in load_tool | |
| tool = self.create_tool(config_file=config_file, repository_id=repository_id, guid=guid, **kwds) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 262, in create_tool | |
| raise e | |
| IOError: [Errno 2] No such file or directory: './lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,056 Loaded converter: CONVERTER_wig_to_bigwig | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,058 Loaded converter: CONVERTER_wiggle_to_interval_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,059 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,061 Loaded converter: lped2fpedconvert | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,063 Loaded converter: lped2pbedconvert | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,064 Loaded converter: pbed2lpedconvert | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,066 Loaded converter: pbed2ldindepconvert | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,068 Loaded converter: CONVERTER_SMILES_to_sdf | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,069 Loaded converter: CONVERTER_SMILES_to_inchi | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,071 Loaded converter: CONVERTER_SMILES_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,073 Loaded converter: CONVERTER_SMILES_to_MOL | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,075 Loaded converter: CONVERTER_SMILES_to_MOL2 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,077 Loaded converter: CONVERTER_smiles_to_smiles | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,079 Loaded converter: CONVERTER_sdf_to_smiles | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,081 Loaded converter: CONVERTER_sdf_to_inchi | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,083 Loaded converter: CONVERTER_sdf_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,085 Loaded converter: CONVERTER_sdf_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,086 Loaded converter: CONVERTER_inchi_to_smi | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,088 Loaded converter: CONVERTER_inchi_to_sdf | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,090 Loaded converter: CONVERTER_inchi_to_mol | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,092 Loaded converter: CONVERTER_inchi_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,094 Loaded converter: CONVERTER_inchi_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,096 Loaded converter: CONVERTER_mol_to_smi | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,097 Loaded converter: CONVERTER_mol_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,099 Loaded converter: CONVERTER_mol_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,101 Loaded converter: CONVERTER_mol_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,102 Loaded converter: CONVERTER_mol2_to_smi | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,104 Loaded converter: CONVERTER_mol2_to_sdf | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,106 Loaded converter: CONVERTER_mol2_to_inchi | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,108 Loaded converter: CONVERTER_mol2_to_mol | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,109 Loaded converter: CONVERTER_mol2_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,111 Loaded converter: CONVERTER_cml_to_smiles | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,113 Loaded converter: CONVERTER_cml_to_inchi | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,114 Loaded converter: CONVERTER_cml_to_sdf | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,116 Loaded converter: CONVERTER_cml_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,118 Loaded converter: CONVERTER_ref_to_seq_taxomony | |
| galaxy.datatypes.registry DEBUG 2018-03-20 10:28:06,120 Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2018-03-20 10:28:06,125 Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2018-03-20 10:28:06,126 Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.web.base.pluginframework INFO 2018-03-20 10:28:06,132 VisualizationsRegistry, loaded plugin: charts | |
| galaxy.visualization.plugins.config_parser INFO 2018-03-20 10:28:06,133 Visualizations plugin disabled: Circster. Skipping... | |
| galaxy.visualization.plugins.config_parser INFO 2018-03-20 10:28:06,134 template syntax is deprecated: use entry_point instead | |
| galaxy.web.base.pluginframework INFO 2018-03-20 10:28:06,134 VisualizationsRegistry, loaded plugin: csg | |
| galaxy.visualization.plugins.config_parser INFO 2018-03-20 10:28:06,135 template syntax is deprecated: use entry_point instead | |
| galaxy.web.base.pluginframework INFO 2018-03-20 10:28:06,136 VisualizationsRegistry, loaded plugin: graphviz | |
| galaxy.web.base.pluginframework INFO 2018-03-20 10:28:06,137 VisualizationsRegistry, loaded plugin: phyloviz | |
| galaxy.web.base.pluginframework INFO 2018-03-20 10:28:06,138 VisualizationsRegistry, loaded plugin: scatterplot | |
| galaxy.visualization.plugins.config_parser INFO 2018-03-20 10:28:06,139 Visualizations plugin disabled: Sweepster. Skipping... | |
| galaxy.web.base.pluginframework INFO 2018-03-20 10:28:06,140 VisualizationsRegistry, loaded plugin: trackster | |
| galaxy.visualization.plugins.config_parser INFO 2018-03-20 10:28:06,141 template syntax is deprecated: use entry_point instead | |
| galaxy.web.base.pluginframework INFO 2018-03-20 10:28:06,142 VisualizationsRegistry, loaded plugin: unipept | |
| galaxy.web.base.pluginframework INFO 2018-03-20 10:28:06,144 VisualizationsRegistry, loaded plugin: bam_iobio | |
| galaxy.web.base.pluginframework INFO 2018-03-20 10:28:06,147 VisualizationsRegistry, loaded plugin: ethercalc | |
| galaxy.web.base.pluginframework INFO 2018-03-20 10:28:06,150 VisualizationsRegistry, loaded plugin: hicbrowser | |
| galaxy.web.base.pluginframework INFO 2018-03-20 10:28:06,151 VisualizationsRegistry, loaded plugin: jupyter | |
| galaxy.web.base.pluginframework INFO 2018-03-20 10:28:06,152 VisualizationsRegistry, loaded plugin: neo | |
| galaxy.web.base.pluginframework INFO 2018-03-20 10:28:06,153 VisualizationsRegistry, loaded plugin: phinch | |
| galaxy.visualization.plugins.config_parser INFO 2018-03-20 10:28:06,155 template syntax is deprecated: use entry_point instead | |
| galaxy.web.base.pluginframework INFO 2018-03-20 10:28:06,155 VisualizationsRegistry, loaded plugin: rstudio | |
| galaxy.tours INFO 2018-03-20 10:28:06,166 Loaded tour 'core.scratchbook' | |
| galaxy.tours INFO 2018-03-20 10:28:06,195 Loaded tour 'core.galaxy_ui' | |
| galaxy.tours INFO 2018-03-20 10:28:06,215 Loaded tour 'core.history' | |
| galaxy.webhooks WARNING 2018-03-20 10:28:06,216 directory not found: /mnt/galaxy/galaxy-app/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config | |
| galaxy.openid.providers DEBUG 2018-03-20 10:28:06,266 Loaded OpenID provider: GenomeSpace (genomespace) | |
| galaxy.openid.providers DEBUG 2018-03-20 10:28:06,267 Loaded OpenID provider: Yahoo! (yahoo) | |
| galaxy.openid.providers DEBUG 2018-03-20 10:28:06,268 Loaded OpenID provider: AOL/AIM (aol) | |
| galaxy.openid.providers DEBUG 2018-03-20 10:28:06,269 Loaded OpenID provider: Launchpad (launchpad) | |
| galaxy.jobs.manager DEBUG 2018-03-20 10:28:06,277 Starting job handler | |
| galaxy.jobs INFO 2018-03-20 10:28:06,277 Handler 'main' will load specified runner plugins: slurm | |
| galaxy.jobs.runners.state_handler_factory DEBUG 2018-03-20 10:28:06,281 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit | |
| pulsar.managers.util.drmaa DEBUG 2018-03-20 10:28:06,316 Initializing DRMAA session from thread MainThread | |
| galaxy.jobs.runners DEBUG 2018-03-20 10:28:06,317 Starting 4 SlurmRunner workers | |
| galaxy.jobs DEBUG 2018-03-20 10:28:06,318 Loaded job runner 'galaxy.jobs.runners.slurm:SlurmJobRunner' as 'slurm' | |
| galaxy.jobs.handler DEBUG 2018-03-20 10:28:06,318 Loaded job runners plugins: slurm | |
| galaxy.jobs.handler INFO 2018-03-20 10:28:06,318 job handler stop queue started | |
| galaxy.jobs.handler INFO 2018-03-20 10:28:06,359 job handler queue started | |
| galaxy.sample_tracking.external_service_types DEBUG 2018-03-20 10:28:06,372 Loaded external_service_type: Simple unknown sequencer 1.0.0 | |
| galaxy.sample_tracking.external_service_types DEBUG 2018-03-20 10:28:06,375 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 | |
| galaxy.workflow.scheduling_manager DEBUG 2018-03-20 10:28:06,381 Starting workflow schedulers | |
| galaxy.app INFO 2018-03-20 10:28:06,382 Galaxy app startup finished (21810.835 ms) | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,393 Enabling 'history' controller, class: HistoryController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,400 Enabling 'admin' controller, class: AdminGalaxy | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,738 Enabling 'admin_toolshed' controller, class: AdminGalaxy | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,740 Enabling 'admin_toolshed' controller, class: AdminToolshed | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,742 Enabling 'async' controller, class: ASync | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,743 Enabling 'biostar' controller, class: BiostarController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,744 Enabling 'data_manager' controller, class: DataManager | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,748 Enabling 'dataset' controller, class: DatasetInterface | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,749 Enabling 'error' controller, class: Error | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,753 Enabling 'external_service' controller, class: ExternalService | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,754 Enabling 'external_services' controller, class: ExternalServiceController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,756 Enabling 'forms' controller, class: Forms | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,757 Enabling 'interactive_environments' controller, class: InteractiveEnvironmentsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,766 Enabling 'library' controller, class: Library | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,768 Enabling 'library_admin' controller, class: LibraryAdmin | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,768 Enabling 'library_common' controller, class: LibraryCommon | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,772 Enabling 'page' controller, class: PageController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,774 Enabling 'request_type' controller, class: RequestType | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,776 Enabling 'requests' controller, class: Requests | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,778 Enabling 'requests_admin' controller, class: RequestsAdmin | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,778 Enabling 'requests_common' controller, class: RequestsCommon | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,781 Enabling 'root' controller, class: RootController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,782 Enabling 'tag' controller, class: TagsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,783 Enabling 'tool_runner' controller, class: ToolRunner | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,785 Enabling 'user' controller, class: User | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,786 Enabling 'userskeys' controller, class: User | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,789 Enabling 'visualization' controller, class: VisualizationController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,793 Enabling 'workflow' controller, class: WorkflowController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,797 Enabling 'visualizations' API controller, class: VisualizationsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,798 Enabling 'toolshed' API controller, class: ToolShedController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,801 Enabling 'tools' API controller, class: ToolsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,802 Enabling 'workflows' API controller, class: WorkflowsAPIController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,803 Enabling 'tours' API controller, class: ToursController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,804 Enabling 'tool_data' API controller, class: ToolData | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,806 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,807 Enabling 'webhooks' API controller, class: WebhooksController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,807 Enabling 'requests' API controller, class: RequestsAPIController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,845 Enabling 'search' API controller, class: SearchController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,847 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,848 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,848 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,849 Enabling 'quotas' API controller, class: QuotaAPIController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,852 Enabling 'request_types' API controller, class: RequestTypeAPIController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,852 Enabling 'roles' API controller, class: RoleAPIController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,855 Enabling 'users' API controller, class: UserAPIController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,859 Enabling 'library_datasets' API controller, class: LibraryDatasetsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,859 Enabling 'page_revisions' API controller, class: PageRevisionsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,862 Enabling 'remote_files' API controller, class: RemoteFilesAPIController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,863 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,865 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,865 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,866 Enabling 'authenticate' API controller, class: AuthenticationController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,867 Enabling 'configuration' API controller, class: ConfigurationController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,868 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,870 Enabling 'datasets' API controller, class: DatasetsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,871 Enabling 'datatypes' API controller, class: DatatypesController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,872 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,872 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,873 Enabling 'folder_contents' API controller, class: FolderContentsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,875 Enabling 'folders' API controller, class: FoldersController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,876 Enabling 'forms' API controller, class: FormDefinitionAPIController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,876 Enabling 'genomes' API controller, class: GenomesController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,877 Enabling 'group_roles' API controller, class: GroupRolesAPIController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,878 Enabling 'group_users' API controller, class: GroupUsersAPIController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,879 Enabling 'groups' API controller, class: GroupAPIController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,882 Enabling 'histories' API controller, class: HistoriesController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,886 Enabling 'history_contents' API controller, class: HistoryContentsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,887 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,888 Enabling 'history_tags' API controller, class: HistoryTagsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,888 Enabling 'workflow_tags' API controller, class: WorkflowTagsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,889 Enabling 'job_files' API controller, class: JobFilesAPIController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,890 Enabling 'jobs' API controller, class: JobController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,893 Enabling 'libraries' API controller, class: LibrariesController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,895 Enabling 'library_contents' API controller, class: LibraryContentsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,896 Enabling 'metrics' API controller, class: MetricsController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,898 Enabling 'pages' API controller, class: PagesController | |
| galaxy.web.framework.base DEBUG 2018-03-20 10:28:06,899 Enabling 'samples' API controller, class: SamplesAPIController | |
| galaxy.webapps.util DEBUG 2018-03-20 10:28:07,286 Enabling 'paste.httpexceptions' middleware | |
| galaxy.webapps.util DEBUG 2018-03-20 10:28:07,288 Enabling 'RecursiveMiddleware' middleware | |
| galaxy.webapps.util DEBUG 2018-03-20 10:28:07,299 Enabling 'ErrorMiddleware' middleware | |
| galaxy.webapps.util DEBUG 2018-03-20 10:28:07,300 Enabling 'TransLogger' middleware | |
| galaxy.webapps.util DEBUG 2018-03-20 10:28:07,301 Enabling 'XForwardedHostMiddleware' middleware | |
| galaxy.webapps.util DEBUG 2018-03-20 10:28:07,302 Enabling 'RequestIDMiddleware' middleware | |
| galaxy.webapps.util DEBUG 2018-03-20 10:28:07,303 Enabling 'BatchMiddleware' middleware | |
| galaxy.queue_worker INFO 2018-03-20 10:28:07,304 Binding and starting galaxy control worker for main | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-03-20 10:28:07,304 Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 140561648047936)> is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-03-20 10:28:07,304 Prior to webapp return, Galaxy thread is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-03-20 10:28:07,304 Prior to webapp return, Galaxy thread is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-03-20 10:28:07,304 Prior to webapp return, Galaxy thread is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-03-20 10:28:07,305 Prior to webapp return, Galaxy thread is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-03-20 10:28:07,305 Prior to webapp return, Galaxy thread is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-03-20 10:28:07,305 Prior to webapp return, Galaxy thread is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-03-20 10:28:07,305 Prior to webapp return, Galaxy thread is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-03-20 10:28:07,305 Prior to webapp return, Galaxy thread is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-03-20 10:28:07,305 Prior to webapp return, Galaxy thread is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-03-20 10:28:07,305 Prior to webapp return, Galaxy thread is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-03-20 10:28:07,305 Prior to webapp return, Galaxy thread is alive. | |
| Starting server in PID 2780. | |
| serving on http://127.0.0.1:8080 | |
| 127.0.0.1 - - [20/Mar/2018:10:28:20 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:28:20 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:28:32 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:28:32 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:28:42 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:28:42 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:28:58 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:28:58 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:29:09 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:29:09 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:29:25 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:29:25 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:29:36 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:29:36 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:29:52 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:29:52 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:30:07 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:30:07 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:30:23 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:30:23 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:30:39 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:30:39 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:30:50 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:30:50 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:31:06 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:31:06 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:31:22 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:31:22 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:31:34 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:31:34 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:31:44 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:31:44 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:32:00 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:32:00 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:32:16 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:32:16 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:32:32 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:32:32 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:32:42 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:32:42 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:32:58 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:32:58 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:33:09 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:33:09 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:33:20 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:33:20 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:33:56 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:33:56 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:34:32 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:34:32 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:35:08 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:35:08 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:35:39 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:35:39 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:36:10 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:36:10 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:36:46 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:36:46 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:37:21 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:37:21 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:37:57 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:37:57 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:39:02 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:39:02 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:40:08 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:40:08 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:41:13 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:41:13 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:42:18 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:42:18 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:43:24 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:43:24 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:44:29 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:44:29 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:45:35 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:45:35 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:46:40 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:46:40 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:47:45 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:47:45 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:48:51 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:48:51 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:49:56 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:49:56 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:50:28 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:50:28 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:50:44 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:50:44 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:51:00 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:51:00 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| /mnt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. | |
| 'strategies for improved performance.' % expr) | |
| 94.125.130.125 - - [20/Mar/2018:10:51:14 +0000] "GET / HTTP/1.0" 200 - "-" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:51:15 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:51:15 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:15 +0000] "GET /api/webhooks/history-menu/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:15 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:15 +0000] "GET /api/webhooks/masthead/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:15 +0000] "GET /api/datatypes?extension_only=False HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:15 +0000] "GET /api/genomes HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:16 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:16 +0000] "GET /welcome HTTP/1.0" 302 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:16 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:16 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:16 +0000] "GET /api/histories/cbbbf59e8f08c98c?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:18 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:19 +0000] "PUT /api/histories/cbbbf59e8f08c98c/contents/datasets/ed249e2c46dcfb26 HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:20 +0000] "PUT /api/histories/cbbbf59e8f08c98c/contents/datasets/1a303bb7245cf54f HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:20 +0000] "PUT /api/histories/cbbbf59e8f08c98c/contents/datasets/1a303bb7245cf54f HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:20 +0000] "PUT /api/histories/cbbbf59e8f08c98c/contents/datasets/6aa46477e65e50f0 HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:21 +0000] "PUT /api/histories/cbbbf59e8f08c98c/contents/datasets/6aa46477e65e50f0 HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:21 +0000] "PUT /api/histories/cbbbf59e8f08c98c/contents/datasets/03d50517628a21aa HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:25 +0000] "GET /api/tools?q=ref HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:29 +0000] "GET /api/tools?q=ref_seq HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:51:31 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:51:31 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:31 +0000] "GET /api/tools?q=refs HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:32 +0000] "GET /api/tools?q=refseq HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:34 +0000] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1/build?version=0.1.1&__identifer=1w1zjfjy2tb&tool_version=0.1.1 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:34 +0000] "GET /api/webhooks/tool-menu/all HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:34 +0000] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1/citations HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:37 +0000] "POST /api/tools/toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1/build HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:40 +0000] "POST /api/tools/toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1/build HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.tools DEBUG 2018-03-20 10:51:42,823 Validated and populated state for tool request (23.413 ms) | |
| galaxy.tools.actions INFO 2018-03-20 10:51:42,892 Handled output named output_path_tab for tool toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1 (36.032 ms) | |
| galaxy.tools.actions INFO 2018-03-20 10:51:42,901 Added output datasets to history (9.680 ms) | |
| galaxy.tools.actions INFO 2018-03-20 10:51:42,923 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1] (12.654 ms) | |
| galaxy.tools.actions INFO 2018-03-20 10:51:42,924 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1] complete, ready to flush (22.157 ms) | |
| galaxy.tools.actions INFO 2018-03-20 10:51:42,975 Flushed transaction for job Job[id=5437,tool_id=toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1] (50.825 ms) | |
| galaxy.tools.execute DEBUG 2018-03-20 10:51:42,975 Tool [toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1] created job [5437] (128.344 ms) | |
| galaxy.tools.execute DEBUG 2018-03-20 10:51:42,994 Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1 request: (170.653 ms) | |
| 94.125.130.125 - - [20/Mar/2018:10:51:42 +0000] "POST /api/tools HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.jobs DEBUG 2018-03-20 10:51:43,025 (5437) Working directory for job is: /mnt/galaxy/tmp/job_working_directory/005/5437 | |
| galaxy.jobs.handler DEBUG 2018-03-20 10:51:43,029 (5437) Dispatching to slurm runner | |
| galaxy.jobs DEBUG 2018-03-20 10:51:43,054 (5437) Persisting job destination (destination id: slurm_cluster) | |
| galaxy.jobs.runners DEBUG 2018-03-20 10:51:43,062 Job [5437] queued (32.504 ms) | |
| galaxy.jobs.handler INFO 2018-03-20 10:51:43,076 (5437) Job dispatched | |
| 94.125.130.125 - - [20/Mar/2018:10:51:43 +0000] "GET /api/webhooks/tool HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:43 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A30.661Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.util.object_wrapper WARNING 2018-03-20 10:51:43,344 Unable to create dynamic subclass for , None: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases | |
| 94.125.130.125 - - [20/Mar/2018:10:51:43 +0000] "GET /api/histories/cbbbf59e8f08c98c?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 10:51:43,615 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@0.1.1 refseq_masher=0.1.1 | |
| 127.0.0.1 - - [20/Mar/2018:10:51:46 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:51:46 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:47 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A51%3A43.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:47 +0000] "GET /api/histories/cbbbf59e8f08c98c?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:50 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:51 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:51 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:52 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:52 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:52 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:53 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:53 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:53 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:53 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:54 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:55 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:55 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:55 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:55 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:56 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:56 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:56 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:57 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:58 +0000] "GET /api/histories/null/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 400 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:58 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:58 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:51:59 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:00 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:02 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A56%3A12.530Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:52:02 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:52:02 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:06 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A52%3A02.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:09 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:10 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:10 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:11 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:11 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:11 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:12 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:13 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:16 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A56%3A26.139Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:52:18 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:52:18 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:21 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A52%3A16.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher 0.1.1* -> python 3.5* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 10:52:21,569 Removing failed conda install of [CondaTarget[refseq_masher,version=0.1.1]] | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 10:52:21,570 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@0.1.1 refseq_masher=0.1.1 | |
| 94.125.130.125 - - [20/Mar/2018:10:52:26 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A52%3A21.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:52:29 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:52:29 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:31 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A52%3A26.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher 0.1.1* -> python 3.6* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 10:52:34,495 Removing failed conda install of refseq_masher, version '0.1.1' | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 10:52:34,495 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@_uv_ refseq_masher | |
| 94.125.130.125 - - [20/Mar/2018:10:52:36 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A52%3A31.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:41 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A52%3A36.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:52:45 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:52:45 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:46 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A52%3A41.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher -> python 3.5* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 10:52:47,403 Removing failed conda install of [CondaTarget[refseq_masher,unversioned]] | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 10:52:47,403 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@_uv_ refseq_masher | |
| 94.125.130.125 - - [20/Mar/2018:10:52:51 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A52%3A46.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:52 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:52 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:52 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:54 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:54 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:54 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:54 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:52:57 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:52:57 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:57 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:52:59 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A57%3A08.801Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher -> python 3.5* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 10:53:01,681 Removing failed conda install of refseq_masher, version 'None' | |
| galaxy.jobs.command_factory INFO 2018-03-20 10:53:01,703 Built script [/mnt/galaxy/tmp/job_working_directory/005/5437/tool_script.sh] for tool command [ln -s "/mnt/galaxy/files/000/dataset_864.dat" "718138_S1_L001_R1_001.fastq_1.fastq" && ln -s "/mnt/galaxy/files/000/dataset_853.dat" "718138_S1_L001_R2_001.fastq_2.fastq" && refseq_masher -vv contains --output refseq_masher-contains.tab --output-type tab --top-n-results 0 --parallelism "${GALAXY_SLOTS:-1}" --min-identity 0.9 --max-pvalue 0.01 "718138_S1_L001_R1_001.fastq_1.fastq" "718138_S1_L001_R2_001.fastq_2.fastq"] | |
| galaxy.tools.deps DEBUG 2018-03-20 10:53:01,841 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 10:53:01,842 Using dependency bcftools version 1.5 of type conda | |
| galaxy.jobs.runners DEBUG 2018-03-20 10:53:01,847 (5437) command is: rm -rf working; mkdir -p working; cd working; /mnt/galaxy/tmp/job_working_directory/005/5437/tool_script.sh; return_code=$?; if [ -f /mnt/galaxy/tmp/job_working_directory/005/5437/working/refseq_masher-contains.tab ] ; then cp /mnt/galaxy/tmp/job_working_directory/005/5437/working/refseq_masher-contains.tab /mnt/galaxy/files/008/dataset_8239.dat ; fi; cd '/mnt/galaxy/tmp/job_working_directory/005/5437'; | |
| [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True | |
| export PATH=$PATH:'/mnt/galaxy/tool_dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; export PATH=$PATH:'/mnt/galaxy/tool_dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; python "/mnt/galaxy/tmp/job_working_directory/005/5437/set_metadata_Q0uhmA.py" "/mnt/galaxy/tmp/job_working_directory/005/5437/registry.xml" "/mnt/galaxy/tmp/job_working_directory/005/5437/working/galaxy.json" "/mnt/galaxy/tmp/job_working_directory/005/5437/metadata_in_HistoryDatasetAssociation_8822_S4WGsT,/mnt/galaxy/tmp/job_working_directory/005/5437/metadata_kwds_HistoryDatasetAssociation_8822_ktA5ji,/mnt/galaxy/tmp/job_working_directory/005/5437/metadata_out_HistoryDatasetAssociation_8822_1EPGq1,/mnt/galaxy/tmp/job_working_directory/005/5437/metadata_results_HistoryDatasetAssociation_8822_vreAxO,/mnt/galaxy/files/008/dataset_8239.dat,/mnt/galaxy/tmp/job_working_directory/005/5437/metadata_override_HistoryDatasetAssociation_8822_tdHNio" 5242880; sh -c "exit $return_code" | |
| galaxy.jobs.runners.drmaa DEBUG 2018-03-20 10:53:01,870 (5437) submitting file /mnt/galaxy/tmp/job_working_directory/005/5437/galaxy_5437.sh | |
| galaxy.jobs.runners.drmaa INFO 2018-03-20 10:53:01,884 (5437) queued as 2 | |
| galaxy.jobs DEBUG 2018-03-20 10:53:01,884 (5437) Persisting job destination (destination id: slurm_cluster) | |
| galaxy.jobs.runners.drmaa DEBUG 2018-03-20 10:53:02,592 (5437/2) state change: job is queued and active | |
| 94.125.130.125 - - [20/Mar/2018:10:53:04 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A52%3A59.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:53:07 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:53:07 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:09 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A53%3A04.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:14 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A53%3A09.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:19 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A53%3A14.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:53:23 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:53:23 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:24 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A53%3A19.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:28 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A53%3A24.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:30 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:30 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:30 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:31 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:31 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:31 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:32 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:34 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:36 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A57%3A46.331Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:40 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A53%3A36.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:44 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A53%3A40.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:53:44 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:53:44 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:48 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A53%3A44.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:53:50 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:53:50 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:52 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A53%3A48.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:53:57 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A53%3A53.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:01 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A53%3A57.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:05 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A01.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:54:05 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:54:05 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:09 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A05.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:13 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A09.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:17 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A13.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:54:21 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:54:21 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:21 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A17.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:26 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A21.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:30 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A26.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:34 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A30.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:54:37 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:54:37 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:38 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A34.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:42 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A38.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:46 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A42.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:54:48 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:54:48 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:50 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A46.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:55 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A50.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:54:59 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A55.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:55:03 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A54%3A59.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:55:04 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:55:04 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:55:07 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A03.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:55:11 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A07.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:55:15 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A11.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:55:19 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A15.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:55:19 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:55:19 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:55:23 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A19.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:55:28 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A24.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:55:32 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A28.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:55:35 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:55:35 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:55:36 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A32.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:55:40 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A36.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:55:44 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A40.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:55:48 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A44.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:55:51 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:55:51 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:55:52 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A48.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:55:57 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A52.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:56:01 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A55%3A57.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:56:05 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A56%3A01.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:56:06 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:56:06 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:10:56:09 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A56%3A05.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:56:13 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A56%3A09.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:56:17 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A56%3A13.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:56:21 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A56%3A17.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:56:22 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:56:22 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| galaxy.jobs.runners.drmaa DEBUG 2018-03-20 10:56:23,101 (5437/2) state change: job is running | |
| 94.125.130.125 - - [20/Mar/2018:10:56:26 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A56%3A22.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.jobs.runners.drmaa DEBUG 2018-03-20 10:56:30,211 (5437/2) state change: job finished normally | |
| galaxy.jobs.output_checker INFO 2018-03-20 10:56:30,241 Job 5437: Fatal error: Exit code 127 () | |
| galaxy.jobs.output_checker DEBUG 2018-03-20 10:56:30,241 Tool exit code indicates an error, failing job. | |
| galaxy.jobs DEBUG 2018-03-20 10:56:30,333 (5437) setting dataset 8239 state to ERROR | |
| 94.125.130.125 - - [20/Mar/2018:10:56:30 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A56%3A26.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.jobs INFO 2018-03-20 10:56:30,474 Collecting metrics for Job 5437 | |
| galaxy.jobs DEBUG 2018-03-20 10:56:30,498 job 5437 ended (finish() executed in (260.856 ms)) | |
| galaxy.tools.error_reports DEBUG 2018-03-20 10:56:30,512 Bug report plugin generated response None | |
| 94.125.130.125 - - [20/Mar/2018:10:56:34 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T10%3A56%3A30.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:10:56:34 +0000] "GET /api/histories/cbbbf59e8f08c98c?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:10:56:38 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:56:38 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:56:53 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:56:53 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:57:10 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:57:10 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:57:21 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:57:21 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:57:36 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:57:36 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:57:52 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:57:52 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:58:03 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:58:03 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:58:19 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:58:19 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:58:31 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:58:31 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:58:43 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:58:43 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:58:54 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:58:54 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:59:05 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:59:05 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:59:17 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:59:17 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:59:28 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:59:28 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:59:44 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:59:44 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:59:55 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:10:59:55 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:00:07 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:00:07 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:00:18 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:00:18 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:00:35 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:00:35 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:00:47 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:00:47 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:00:59 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:00:59 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:01:10 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:01:10 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:01:17 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents/datasets/255f6b16db8a3b32 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:01:21 +0000] "GET /datasets/255f6b16db8a3b32/show_params HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:01:21 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/datasets/255f6b16db8a3b32/show_params" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:01:22 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:01:22 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:01:33 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:01:33 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:01:34 +0000] "GET /api/datasets/255f6b16db8a3b32 HTTP/1.0" 200 - "http://52.54.147.188/datasets/error?dataset_id=255f6b16db8a3b32&__identifer=0ssou692cw9n" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:01:34 +0000] "GET /api/jobs/b5d0a911015ba239?full=True HTTP/1.0" 200 - "http://52.54.147.188/datasets/error?dataset_id=255f6b16db8a3b32&__identifer=0ssou692cw9n" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:01:39 +0000] "GET /admin HTTP/1.0" 200 - "http://52.54.147.188/datasets/error?dataset_id=255f6b16db8a3b32&__identifer=0ssou692cw9n" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:01:40 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:01:40 +0000] "GET /api/webhooks/masthead/all HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:01:40 +0000] "GET /admin/center?message=&status=done HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:01:40 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin/center?message=&status=done" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:01:43 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:01:43 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:02:00 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:02:00 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:02:11 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:02:11 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:02:23 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:02:23 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:02:34 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:02:34 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:02:46 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:02:46 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:02:57 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:02:57 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:03:09 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:03:09 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:21 +0000] "GET / HTTP/1.0" 302 - "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/49.0.2623.75 Safari/537.36 Google Favicon" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:21 +0000] "GET /root/login?redirect=%2F HTTP/1.0" 200 - "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/49.0.2623.75 Safari/537.36 Google Favicon" | |
| 127.0.0.1 - - [20/Mar/2018:11:03:41 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:03:41 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:44 +0000] "GET / HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:45 +0000] "GET /api/webhooks/history-menu/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:45 +0000] "GET /api/datatypes?extension_only=False HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:45 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:45 +0000] "GET /api/webhooks/masthead/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:45 +0000] "GET /api/genomes HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:45 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:45 +0000] "GET /welcome HTTP/1.0" 302 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:45 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:45 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&details=255f6b16db8a3b32&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:46 +0000] "GET /api/histories/cbbbf59e8f08c98c?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:47 +0000] "GET /history/view_multiple HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:47 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/history/view_multiple" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:48 +0000] "GET /api/webhooks/masthead/all HTTP/1.0" 200 - "http://52.54.147.188/history/view_multiple" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:50 +0000] "GET /api/histories?limit=1&offset=0&order=update_time&view=dev-detailed&q=encoded_id-in&qv=cbbbf59e8f08c98c HTTP/1.0" 200 - "http://52.54.147.188/history/view_multiple" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:50 +0000] "GET /api/histories?limit=10&offset=0&order=update_time&view=dev-detailed&q=deleted&q=purged&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/history/view_multiple" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:50 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&details=255f6b16db8a3b32&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/history/view_multiple" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:51 +0000] "GET /api/histories/be8c8ac3dbd1dd54/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/history/view_multiple" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:51 +0000] "GET /api/histories/e8d3f6db536fde44/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/history/view_multiple" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:51 +0000] "GET /api/histories/32d48e3506ae8cf7/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/history/view_multiple" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:03:52 +0000] "GET /api/histories/96d9e11f37f34b29/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/history/view_multiple" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:04:12 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:04:12 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:04:49 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:04:49 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 115.231.219.29 - - [20/Mar/2018:11:04:56 +0000] "GET /manager/html HTTP/1.0" 404 - "-" "Mozilla/3.0 (compatible; Indy Library)" | |
| 127.0.0.1 - - [20/Mar/2018:11:05:20 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:05:20 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:39 +0000] "GET / HTTP/1.0" 200 - "-" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:40 +0000] "GET /api/webhooks/history-menu/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:41 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:41 +0000] "GET /api/webhooks/masthead/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:41 +0000] "GET /api/genomes HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:41 +0000] "GET /api/datatypes?extension_only=False HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:41 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:41 +0000] "GET /welcome HTTP/1.0" 302 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:41 +0000] "GET /api/users/a799d38679e985db HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:41 +0000] "GET /api/histories/70eec96181a992f8/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:41 +0000] "GET /api/histories/70eec96181a992f8?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:43 +0000] "GET /api/histories/70eec96181a992f8/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:44 +0000] "GET /api/histories/70eec96181a992f8/contents/dataset_collections/a3c8c801a73b991c HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:48 +0000] "GET /api/histories/70eec96181a992f8/contents/dataset_collections/dcccc52cd332be44 HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:05:51 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:05:51 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:05:53 +0000] "GET /datasets/fc9144aebb7028b7/display/?preview=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:06:28 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:06:28 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:06:31 +0000] "GET /datasets/2e9f4e0e2a64f8bb/display/?preview=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:06:41 +0000] "GET /datasets/be9b3cb16975f357/display/?preview=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:06:47 +0000] "GET /datasets/ca52bc6731bc608f/display/?preview=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:07:00 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:07:00 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:07:10 +0000] "GET /datasets/d398bf448c0ad552/display/?preview=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:07:12 +0000] "GET /datasets/bf275650290955c0/display/?preview=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:07:14 +0000] "GET /datasets/6de7412240dd9f10/display/?preview=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:07:15 +0000] "GET /datasets/9c505520e5c7fc69/display/?preview=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:07:18 +0000] "GET /datasets/46dfcb6eed6349c4/display/?preview=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:07:31 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:07:31 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:07:34 +0000] "GET /datasets/4d245df0eb33c748/display/?preview=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:07:36 +0000] "GET /datasets/08dd6d3c4cb4ddc9/display/?preview=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:07:38 +0000] "GET /datasets/43cb9a4bf8d07722/display/?preview=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:07:40 +0000] "GET /datasets/28d4ce5c28982210/display/?preview=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:08:03 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:08:03 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:09:03 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:09:03 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:10:09 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:10:09 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:11:13 +0000] "GET /api/histories/70eec96181a992f8/contents/28d4ce5c28982210 HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:11:14 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:11:14 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:12:20 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:12:20 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:13:25 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:13:25 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:14:30 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:14:30 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:15:36 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:15:36 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 117.50.7.159 - - [20/Mar/2018:11:15:47 +0000] "GET / HTTP/1.0" 302 - "-" "-" | |
| 127.0.0.1 - - [20/Mar/2018:11:16:41 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:16:41 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:17:47 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:17:47 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:18:52 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:18:52 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:19:57 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:19:57 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:21:03 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:21:03 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:22:08 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:22:08 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:23:13 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:23:13 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:24:19 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:24:19 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:25:24 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:25:24 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:26:29 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:26:29 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| galaxy.webapps.galaxy.controllers.user WARNING 2018-03-20 11:27:24,549 Redirect URL is outside of Galaxy, will redirect to Galaxy root instead: http://yandex.ru/clck/jsredir?from=yandex.ru%3Bsearch%3Bweb%3B%3B&text=&etext=1733.W1rqh-rMeS8x3janyrG7eHX4vcXBC_gfWYzbKcI53AhddPhbSLmcK_4DfVLZ5tJP.bddb95756e6f089f5971dfc02fac47c2c5a9948d&uuid=&state=_BLhILn4SxNIvvL0W45KSic66uCIg23qh8iRG98qeIXmeppkgUc0YGHEttDsYq_w3pSJtejupWg&data=UlNrNmk5WktYejR0eWJFYk1LdmtxdnE5NmFDRTloS2dqQ2xKdWNkV0pLbGE1Wi1pWE4wREtZbk9pd1VYaXE4R1A5aFRuMUxUYWp0SkZ3X21lQnhVSUdIV0Y3WVA4TGxNN09nVnZtMkhWbTYwdUljZlhnR3hCZzR1a05nOEVPdkFtOGpXWnhmdUZYVQ&b64e=2&sign=ed0745a40e7bcd87762e3b4216457b03&keyno=0&cst=AiuY0DBWFJ7IXge4WdYJQe3IrxbPWIv4xPR30fL-gDVjlpQARilzOXcMbl_9nGn3_N-CQkpFsZf85mwm2fL3Zharoy9fUrgp8LTzWR-XGVaAUS1MidkUTtPEpMNCW-X7gH9IuivM1-o7MIRQeyQG-rzGhEyGKSzN&ref=orjY4mGPRjk5boDnW0uvlrrd71vZw9kp5uQozpMtKCXdCnh-_wii4fFyhNqsOT0UsViSF7k5DI2HJuQnJz1pn_okcqHPnEtFvNKSi2LFcdMmjne9jzGMWQ&l10n=ru&cts=1521545023864&mc=4.87414073231 | |
| 176.14.37.74 - - [20/Mar/2018:11:27:24 +0000] "GET /user/login?use_panels=True HTTP/1.0" 200 - "http://yandex.ru/clck/jsredir?from=yandex.ru%3Bsearch%3Bweb%3B%3B&text=&etext=1733.W1rqh-rMeS8x3janyrG7eHX4vcXBC_gfWYzbKcI53AhddPhbSLmcK_4DfVLZ5tJP.bddb95756e6f089f5971dfc02fac47c2c5a9948d&uuid=&state=_BLhILn4SxNIvvL0W45KSic66uCIg23qh8iRG98qeIXmeppkgUc0YGHEttDsYq_w3pSJtejupWg&data=UlNrNmk5WktYejR0eWJFYk1LdmtxdnE5NmFDRTloS2dqQ2xKdWNkV0pLbGE1Wi1pWE4wREtZbk9pd1VYaXE4R1A5aFRuMUxUYWp0SkZ3X21lQnhVSUdIV0Y3WVA4TGxNN09nVnZtMkhWbTYwdUljZlhnR3hCZzR1a05nOEVPdkFtOGpXWnhmdUZYVQ&b64e=2&sign=ed0745a40e7bcd87762e3b4216457b03&keyno=0&cst=AiuY0DBWFJ7IXge4WdYJQe3IrxbPWIv4xPR30fL-gDVjlpQARilzOXcMbl_9nGn3_N-CQkpFsZf85mwm2fL3Zharoy9fUrgp8LTzWR-XGVaAUS1MidkUTtPEpMNCW-X7gH9IuivM1-o7MIRQeyQG-rzGhEyGKSzN&ref=orjY4mGPRjk5boDnW0uvlrrd71vZw9kp5uQozpMtKCXdCnh-_wii4fFyhNqsOT0UsViSF7k5DI2HJuQnJz1pn_okcqHPnEtFvNKSi2LFcdMmjne9jzGMWQ&l10n=ru&cts=1521545023864&mc=4.87414073231" "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.132 YaBrowser/18.1.1.839 Yowser/2.5 Safari/537.36" | |
| 176.14.37.74 - - [20/Mar/2018:11:27:26 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/user/login?use_panels=True" "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.132 YaBrowser/18.1.1.839 Yowser/2.5 Safari/537.36" | |
| 176.14.37.74 - - [20/Mar/2018:11:27:28 +0000] "GET /api/webhooks/masthead/all HTTP/1.0" 200 - "http://52.54.147.188/user/login?use_panels=True" "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.132 YaBrowser/18.1.1.839 Yowser/2.5 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:27:35 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:27:35 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:28:15 +0000] "GET / HTTP/1.0" 200 - "http://52.54.147.188/history/view_multiple" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:28:16 +0000] "GET /api/webhooks/history-menu/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:28:16 +0000] "GET /api/datatypes?extension_only=False HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:28:16 +0000] "GET /api/webhooks/masthead/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:28:16 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:28:16 +0000] "GET /api/genomes HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:28:16 +0000] "GET /welcome HTTP/1.0" 302 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:28:16 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:28:17 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:28:17 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&details=255f6b16db8a3b32&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:28:17 +0000] "GET /api/histories/cbbbf59e8f08c98c?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:28:19 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&details=255f6b16db8a3b32&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:28:40 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:28:40 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:29:46 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:29:46 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:30:51 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:30:51 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:31:56 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:31:56 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:33:02 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:33:02 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:34:07 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:34:07 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:35:13 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:35:13 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:36:18 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:36:18 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:37:23 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:37:23 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:38:29 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:38:29 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:06 +0000] "GET /admin HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:06 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:06 +0000] "GET /api/webhooks/masthead/all HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:06 +0000] "GET /admin/center?message=&status=done HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:07 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin/center?message=&status=done" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:16 +0000] "GET /admin_toolshed/browse_repositories HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:19 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_repositories" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:26 +0000] "GET /admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_repositories" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:26 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:28 +0000] "GET /admin_toolshed/browse_repositories?operation=update+tool+shed+status&id=44015a2f24f1f430 HTTP/1.0" 302 - "http://52.54.147.188/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:29 +0000] "GET /admin_toolshed/update_tool_shed_status_for_installed_repository?id=44015a2f24f1f430 HTTP/1.0" 302 - "http://52.54.147.188/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:29 +0000] "GET /admin_toolshed/browse_repositories?status=ok&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Erefseq_masher%3C%2Fb%3E. HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:32 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_repositories?status=ok&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Erefseq_masher%3C%2Fb%3E." "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:39:34 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:39:34 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:42 +0000] "GET /admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_repositories?status=ok&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Erefseq_masher%3C%2Fb%3E." "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:42 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:44 +0000] "GET /admin_toolshed/browse_repositories?operation=update+tool+shed+status&id=44015a2f24f1f430 HTTP/1.0" 302 - "http://52.54.147.188/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:44 +0000] "GET /admin_toolshed/update_tool_shed_status_for_installed_repository?id=44015a2f24f1f430 HTTP/1.0" 302 - "http://52.54.147.188/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:45 +0000] "GET /admin_toolshed/browse_repositories?status=ok&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Erefseq_masher%3C%2Fb%3E. HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:48 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_repositories?status=ok&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Erefseq_masher%3C%2Fb%3E." "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:53 +0000] "GET /admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_repositories?status=ok&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Erefseq_masher%3C%2Fb%3E." "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:53 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:58 +0000] "GET /admin_toolshed/browse_repositories?operation=deactivate+or+uninstall&id=44015a2f24f1f430 HTTP/1.0" 302 - "http://52.54.147.188/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:58 +0000] "GET /admin_toolshed/deactivate_or_uninstall_repository?id=44015a2f24f1f430 HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:39:59 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/deactivate_or_uninstall_repository?id=44015a2f24f1f430" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| tool_shed.galaxy_install.installed_repository_manager DEBUG 2018-03-20 11:40:02,119 Removed repository installation directory: /mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/26df66c32861 | |
| 94.125.130.125 - - [20/Mar/2018:11:40:01 +0000] "POST /admin_toolshed/deactivate_or_uninstall_repository HTTP/1.0" 302 - "http://52.54.147.188/admin_toolshed/deactivate_or_uninstall_repository?id=44015a2f24f1f430" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.tools.toolbox.watcher DEBUG 2018-03-20 11:40:02,439 The file '/mnt/galaxy/galaxy-app/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker DEBUG 2018-03-20 11:40:02,440 Executing toolbox reload on 'main' | |
| galaxy.tools.toolbox.base INFO 2018-03-20 11:40:02,868 Parsing the tool configuration /mnt/galaxy/galaxy-app/config/tool_conf.xml | |
| galaxy.tools.toolbox.base ERROR 2018-03-20 11:40:02,880 Error reading tool configuration file from path: genomespace/genomespace_file_browser_prod.xml | |
| galaxy.tools.toolbox.base ERROR 2018-03-20 11:40:02,895 Error reading tool configuration file from path: extract/liftOver_wrapper.xml | |
| galaxy.tools.toolbox.base INFO 2018-03-20 11:40:02,904 Parsing the tool configuration /mnt/galaxy/galaxy-app/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base INFO 2018-03-20 11:40:03,562 Parsing the tool configuration /mnt/galaxy/galaxy-app/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,564 Reading tools from config files finshed (696.101 ms) | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,564 Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,571 Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,571 Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,572 Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,572 Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,577 Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,577 Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,579 Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,580 Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,586 Loading section: Extract Features | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,588 Loading section: Fetch Sequences | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,588 Loading section: Fetch Alignments | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,590 Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,593 Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,596 Loading section: FASTA manipulation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,598 Loading section: NGS: QC and manipulation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,603 Loading section: NGS: Mapping | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,608 Loading section: NGS: RNA Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,613 Loading section: NGS: SAMtools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,620 Loading section: NGS: BamTools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,622 Loading section: NGS: Picard | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,630 Loading section: NGS: VCF Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,637 Loading section: NGS: Peak Calling | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,643 Loading section: NGS: Variant Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,650 Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,653 Loading section: CloudMap | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,655 Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,657 Loading section: BEDTools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,682 Loading section: Regional Variation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,686 Loading section: Multiple Alignments | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,687 Loading section: Metagenomic Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,693 Loading section: Multiple regression | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,694 Loading section: Multivariate Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,695 Loading section: Motif Tools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,696 Loading section: STR-FM: Microsatellite Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,699 Loading section: NGS: GATK Tools (beta) | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,700 Loading section: NCBI SRA Tools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,701 Loading section: Assembly | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,702 Loading section: GATK | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,702 Loading section: NCBI: Blast Tools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,707 Loading section: Annotation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,708 Loading section: Vcflib | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,725 Loading section: quasitools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,729 Loading section: Deeptools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,734 Loading section: NGS: Assembly | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:03,736 Loading tool panel finished (171.821 ms) | |
| galaxy.datatypes.registry ERROR 2018-03-20 11:40:03,839 Error loading converter (./lib/galaxy/datatypes/converters) | |
| Traceback (most recent call last): | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/datatypes/registry.py", line 540, in load_datatype_converters | |
| converter = toolbox.load_tool(config_path, use_cached=use_cached) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 748, in load_tool | |
| tool = self.create_tool(config_file=config_file, repository_id=repository_id, guid=guid, **kwds) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 262, in create_tool | |
| raise e | |
| IOError: [Errno 2] No such file or directory: './lib/galaxy/datatypes/converters/bam_to_bai.xml' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,840 Loaded converter: CONVERTER_bam_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,840 Loaded converter: CONVERTER_bed_to_gff_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,840 Loaded converter: CONVERTER_bed_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,840 Loaded converter: CONVERTER_bed_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,841 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,841 Loaded converter: CONVERTER_bed_to_fli_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,841 Loaded converter: CONVERTER_bedgraph_to_bigwig | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,841 Loaded converter: CONVERTER_len_to_linecount | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,844 Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,845 Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,845 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,845 Loaded converter: CONVERTER_fasta_to_tabular | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,846 Loaded converter: CONVERTER_fasta_to_bowtie_base_index | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,846 Loaded converter: CONVERTER_fasta_to_bowtie_color_index | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,846 Loaded converter: CONVERTER_fasta_to_2bit | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,846 Loaded converter: CONVERTER_fasta_to_len | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,847 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,847 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,847 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,847 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,847 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,847 Loaded converter: CONVERTER_gff_to_bed_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,848 Loaded converter: CONVERTER_gff_to_interval_index_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,848 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,848 Loaded converter: CONVERTER_gff_to_fli_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,848 Loaded converter: CONVERTER_gff_to_interval_index_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,848 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,849 Loaded converter: CONVERTER_interval_to_bed_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,849 Loaded converter: CONVERTER_interval_to_bedstrict_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,849 Loaded converter: CONVERTER_interval_to_bed6_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,849 Loaded converter: CONVERTER_interval_to_bed12_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,849 Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,850 Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,851 Loaded converter: CONVERTER_interval_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,851 Loaded converter: CONVERTER_picard_interval_list_to_bed6 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,851 Loaded converter: CONVERTER_maf_to_fasta_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,852 Loaded converter: CONVERTER_maf_to_interval_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,852 Loaded converter: CONVERTER_encodepeak_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,852 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,853 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,853 Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,853 Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,853 Loaded converter: CONVERTER_sam_to_bam | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,853 Loaded converter: CONVERTER_sam_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,853 Loaded converter: tabular_to_dbnsfp | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,854 Loaded converter: CONVERTER_vcf_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,854 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,854 Loaded converter: CONVERTER_vcf_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,854 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry ERROR 2018-03-20 11:40:03,854 Error loading converter (./lib/galaxy/datatypes/converters) | |
| Traceback (most recent call last): | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/datatypes/registry.py", line 540, in load_datatype_converters | |
| converter = toolbox.load_tool(config_path, use_cached=use_cached) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 748, in load_tool | |
| tool = self.create_tool(config_file=config_file, repository_id=repository_id, guid=guid, **kwds) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 262, in create_tool | |
| raise e | |
| IOError: [Errno 2] No such file or directory: './lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml' | |
| galaxy.datatypes.registry ERROR 2018-03-20 11:40:03,855 Error loading converter (./lib/galaxy/datatypes/converters) | |
| Traceback (most recent call last): | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/datatypes/registry.py", line 540, in load_datatype_converters | |
| converter = toolbox.load_tool(config_path, use_cached=use_cached) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 748, in load_tool | |
| tool = self.create_tool(config_file=config_file, repository_id=repository_id, guid=guid, **kwds) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 262, in create_tool | |
| raise e | |
| IOError: [Errno 2] No such file or directory: './lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,855 Loaded converter: CONVERTER_wig_to_bigwig | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,855 Loaded converter: CONVERTER_wiggle_to_interval_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,855 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,858 Loaded converter: lped2fpedconvert | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,858 Loaded converter: lped2pbedconvert | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,859 Loaded converter: pbed2lpedconvert | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,860 Loaded converter: pbed2ldindepconvert | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,860 Loaded converter: CONVERTER_SMILES_to_sdf | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,860 Loaded converter: CONVERTER_SMILES_to_inchi | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,860 Loaded converter: CONVERTER_SMILES_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,860 Loaded converter: CONVERTER_SMILES_to_MOL | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,860 Loaded converter: CONVERTER_SMILES_to_MOL2 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,861 Loaded converter: CONVERTER_smiles_to_smiles | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,862 Loaded converter: CONVERTER_sdf_to_smiles | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,862 Loaded converter: CONVERTER_sdf_to_inchi | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,862 Loaded converter: CONVERTER_sdf_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,862 Loaded converter: CONVERTER_sdf_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,862 Loaded converter: CONVERTER_inchi_to_smi | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,862 Loaded converter: CONVERTER_inchi_to_sdf | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,862 Loaded converter: CONVERTER_inchi_to_mol | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,862 Loaded converter: CONVERTER_inchi_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,863 Loaded converter: CONVERTER_inchi_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,863 Loaded converter: CONVERTER_mol_to_smi | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,863 Loaded converter: CONVERTER_mol_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,863 Loaded converter: CONVERTER_mol_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,864 Loaded converter: CONVERTER_mol_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,866 Loaded converter: CONVERTER_mol2_to_smi | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,866 Loaded converter: CONVERTER_mol2_to_sdf | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,866 Loaded converter: CONVERTER_mol2_to_inchi | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,866 Loaded converter: CONVERTER_mol2_to_mol | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,866 Loaded converter: CONVERTER_mol2_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,866 Loaded converter: CONVERTER_cml_to_smiles | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,866 Loaded converter: CONVERTER_cml_to_inchi | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,867 Loaded converter: CONVERTER_cml_to_sdf | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,867 Loaded converter: CONVERTER_cml_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,867 Loaded converter: CONVERTER_ref_to_seq_taxomony | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:03,875 Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2018-03-20 11:40:03,880 Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2018-03-20 11:40:03,884 Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.queue_worker INFO 2018-03-20 11:40:03,887 Queuing async task rebuild_toolbox_search_index for main. | |
| galaxy.queue_worker DEBUG 2018-03-20 11:40:03,928 Toolbox reload (1488.650 ms) | |
| galaxy.queue_worker INFO 2018-03-20 11:40:04,937 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2018-03-20 11:40:04,937 Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2018-03-20 11:40:06,049 Toolbox index finished (1112.381 ms) | |
| 94.125.130.125 - - [20/Mar/2018:11:40:02 +0000] "GET /admin_toolshed/browse_repositories?status=done&message=The+repository+named+%3Cb%3Erefseq_masher%3C%2Fb%3E+has+been+uninstalled.++ HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/deactivate_or_uninstall_repository?id=44015a2f24f1f430" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:40:07 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_repositories?status=done&message=The+repository+named+%3Cb%3Erefseq_masher%3C%2Fb%3E+has+been+uninstalled.++" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:40:11 +0000] "GET /admin_toolshed/browse_tool_sheds HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:40:12 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:40:12 +0000] "GET /admin_toolshed/browse_tool_shed?tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.0" 302 - "http://52.54.147.188/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.tools.deps DEBUG 2018-03-20 11:40:25,391 Dependency refseq_masher not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:40:25,392 Dependency refseq_masher not found. | |
| 94.125.130.125 - - [20/Mar/2018:11:40:25 +0000] "GET /admin_toolshed/prepare_for_install?changeset_revisions=26df66c32861&repository_ids=df2fa11538368649&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.0" 200 - "-" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:40:26 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install?changeset_revisions=26df66c32861&repository_ids=df2fa11538368649&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2018-03-20 11:40:33,484 Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:34,125 Appending to tool panel section: Metagenomic Analysis | |
| tool_shed.util.repository_util DEBUG 2018-03-20 11:40:34,157 Updating an existing row for repository 'refseq_masher' in the tool_shed_repository table, status set to 'New'. | |
| tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2018-03-20 11:40:34,178 Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:34,179 Appending to tool panel section: Metagenomic Analysis | |
| 94.125.130.125 - - [20/Mar/2018:11:40:33 +0000] "POST /admin_toolshed/prepare_for_install HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install?changeset_revisions=26df66c32861&repository_ids=df2fa11538368649&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:40:34 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:34,633 Appending to tool panel section: Metagenomic Analysis | |
| 94.125.130.125 - - [20/Mar/2018:11:40:37 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:40:40 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:40:40 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 11:40:40,320 Datatype class not found for extension 'fastq.gz', which is used in the 'format' attribute of parameter 'paired_collection' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 11:40:40,328 Datatype class not found for extension 'fastq.gz', which is used in the 'format' attribute of parameter 'paired_collection' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 11:40:40,886 Datatype class not found for extension 'fastq.gz', which is used in the 'format' attribute of parameter 'paired_collection' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 11:40:40,889 Datatype class not found for extension 'fastq.gz', which is used in the 'format' attribute of parameter 'paired_collection' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 11:40:40,892 Datatype class not found for extension 'fastq.gz', which is used in the 'format' attribute of parameter 'paired_collection' | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 11:40:40,895 Datatype class not found for extension 'fastq.gz', which is used in the 'format' attribute of parameter 'paired_collection' | |
| 94.125.130.125 - - [20/Mar/2018:11:40:41 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 11:40:41,922 Datatype class not found for extension 'fastq.gz', which is used in the 'format' attribute of parameter 'paired_collection' | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:41,924 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1, version: 0.1.1 into tool panel.... | |
| galaxy.tools.parameters.basic WARNING 2018-03-20 11:40:41,932 Datatype class not found for extension 'fastq.gz', which is used in the 'format' attribute of parameter 'paired_collection' | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:41,936 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_matches/0.1.1, version: 0.1.1 into tool panel.... | |
| galaxy.tools.toolbox.watcher DEBUG 2018-03-20 11:40:42,411 The file '/mnt/galaxy/galaxy-app/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker DEBUG 2018-03-20 11:40:42,411 Executing toolbox reload on 'main' | |
| galaxy.tools.toolbox.base INFO 2018-03-20 11:40:42,467 Parsing the tool configuration /mnt/galaxy/galaxy-app/config/tool_conf.xml | |
| galaxy.tools.toolbox.base ERROR 2018-03-20 11:40:42,469 Error reading tool configuration file from path: genomespace/genomespace_file_browser_prod.xml | |
| galaxy.tools.toolbox.base ERROR 2018-03-20 11:40:42,473 Error reading tool configuration file from path: extract/liftOver_wrapper.xml | |
| galaxy.tools.toolbox.base INFO 2018-03-20 11:40:42,475 Parsing the tool configuration /mnt/galaxy/galaxy-app/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base INFO 2018-03-20 11:40:42,565 Parsing the tool configuration /mnt/galaxy/galaxy-app/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,565 Reading tools from config files finshed (98.511 ms) | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,565 Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,568 Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,568 Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,568 Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,568 Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,570 Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,570 Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,571 Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,571 Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,573 Loading section: Extract Features | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,573 Loading section: Fetch Sequences | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,573 Loading section: Fetch Alignments | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,575 Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,578 Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,579 Loading section: FASTA manipulation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,580 Loading section: NGS: QC and manipulation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,583 Loading section: NGS: Mapping | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,585 Loading section: NGS: RNA Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,587 Loading section: NGS: SAMtools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,589 Loading section: NGS: BamTools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,590 Loading section: NGS: Picard | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,593 Loading section: NGS: VCF Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,595 Loading section: NGS: Peak Calling | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,597 Loading section: NGS: Variant Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,600 Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,601 Loading section: CloudMap | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,602 Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,603 Loading section: BEDTools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,614 Loading section: Regional Variation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,617 Loading section: Multiple Alignments | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,618 Loading section: Metagenomic Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,618 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1, version: 0.1.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,618 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_matches/0.1.1, version: 0.1.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,621 Loading section: Multiple regression | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,621 Loading section: Multivariate Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,622 Loading section: Motif Tools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,622 Loading section: STR-FM: Microsatellite Analysis | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,623 Loading section: NGS: GATK Tools (beta) | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,623 Loading section: NCBI SRA Tools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,624 Loading section: Assembly | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,624 Loading section: GATK | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,625 Loading section: NCBI: Blast Tools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,626 Loading section: Annotation | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,627 Loading section: Vcflib | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,639 Loading section: quasitools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,641 Loading section: Deeptools | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,644 Loading section: NGS: Assembly | |
| galaxy.tools.toolbox.base DEBUG 2018-03-20 11:40:42,644 Loading tool panel finished (79.072 ms) | |
| galaxy.datatypes.registry ERROR 2018-03-20 11:40:42,673 Error loading converter (./lib/galaxy/datatypes/converters) | |
| Traceback (most recent call last): | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/datatypes/registry.py", line 540, in load_datatype_converters | |
| converter = toolbox.load_tool(config_path, use_cached=use_cached) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 748, in load_tool | |
| tool = self.create_tool(config_file=config_file, repository_id=repository_id, guid=guid, **kwds) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 262, in create_tool | |
| raise e | |
| IOError: [Errno 2] No such file or directory: './lib/galaxy/datatypes/converters/bam_to_bai.xml' | |
| galaxy.datatypes.registry ERROR 2018-03-20 11:40:42,674 Error loading converter (./lib/galaxy/datatypes/converters) | |
| Traceback (most recent call last): | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/datatypes/registry.py", line 540, in load_datatype_converters | |
| converter = toolbox.load_tool(config_path, use_cached=use_cached) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 748, in load_tool | |
| tool = self.create_tool(config_file=config_file, repository_id=repository_id, guid=guid, **kwds) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 262, in create_tool | |
| raise e | |
| IOError: [Errno 2] No such file or directory: './lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml' | |
| galaxy.datatypes.registry ERROR 2018-03-20 11:40:42,674 Error loading converter (./lib/galaxy/datatypes/converters) | |
| Traceback (most recent call last): | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/datatypes/registry.py", line 540, in load_datatype_converters | |
| converter = toolbox.load_tool(config_path, use_cached=use_cached) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 748, in load_tool | |
| tool = self.create_tool(config_file=config_file, repository_id=repository_id, guid=guid, **kwds) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 262, in create_tool | |
| raise e | |
| IOError: [Errno 2] No such file or directory: './lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml' | |
| galaxy.datatypes.registry DEBUG 2018-03-20 11:40:42,675 Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2018-03-20 11:40:42,676 Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2018-03-20 11:40:42,678 Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.queue_worker INFO 2018-03-20 11:40:42,678 Queuing async task rebuild_toolbox_search_index for main. | |
| galaxy.queue_worker DEBUG 2018-03-20 11:40:42,683 Toolbox reload (271.470 ms) | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 11:40:42,784 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@0.1.1 refseq_masher=0.1.1 | |
| galaxy.queue_worker INFO 2018-03-20 11:40:43,400 Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2018-03-20 11:40:43,400 Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2018-03-20 11:40:44,139 Toolbox index finished (738.953 ms) | |
| 94.125.130.125 - - [20/Mar/2018:11:40:45 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:40:49 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:40:53 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:40:57 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:41:01 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:41:05 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:41:09 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher 0.1.1* -> python 3.6* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 11:41:11,774 Removing failed conda install of [CondaTarget[refseq_masher,version=0.1.1]] | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 11:41:11,775 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@0.1.1 refseq_masher=0.1.1 | |
| 94.125.130.125 - - [20/Mar/2018:11:41:13 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:41:17 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:41:21 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:41:25 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:41:29 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:41:33 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:41:37 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:41:41 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:41:45 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:41:45 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:41:45 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher 0.1.1* -> python 3.6* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 11:41:47,537 Removing failed conda install of refseq_masher, version '0.1.1' | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 11:41:47,537 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@_uv_ refseq_masher | |
| 94.125.130.125 - - [20/Mar/2018:11:41:49 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:41:53 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:41:57 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher -> python 3.5* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 11:42:00,433 Removing failed conda install of [CondaTarget[refseq_masher,unversioned]] | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 11:42:00,434 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@_uv_ refseq_masher | |
| 94.125.130.125 - - [20/Mar/2018:11:42:01 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:42:05 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:42:09 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:42:12 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:42:12 +0000] "GET /admin HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:42:13 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:42:13 +0000] "GET /api/webhooks/masthead/all HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:42:13 +0000] "GET /admin/center?message=&status=done HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:42:13 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin/center?message=&status=done" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher -> python 3.5* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 11:42:13,519 Removing failed conda install of refseq_masher, version 'None' | |
| 94.125.130.125 - - [20/Mar/2018:11:40:34 +0000] "POST /admin_toolshed/manage_repositories HTTP/1.0" 302 - "http://52.54.147.188/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| ---------------------------------------- | |
| Exception happened during processing of request from ('127.0.0.1', 60275) | |
| Traceback (most recent call last): | |
| File "/mnt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread | |
| self.finish_request(request, client_address) | |
| File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request | |
| self.RequestHandlerClass(request, client_address, self) | |
| File "/usr/lib/python2.7/SocketServer.py", line 651, in __init__ | |
| self.finish() | |
| File "/usr/lib/python2.7/SocketServer.py", line 710, in finish | |
| self.wfile.close() | |
| File "/usr/lib/python2.7/socket.py", line 279, in close | |
| self.flush() | |
| File "/usr/lib/python2.7/socket.py", line 303, in flush | |
| self._sock.sendall(view[write_offset:write_offset+buffer_size]) | |
| error: [Errno 32] Broken pipe | |
| ---------------------------------------- | |
| 94.125.130.125 - - [20/Mar/2018:11:42:16 +0000] "GET /admin_toolshed/monitor_repository_installation?installing_repository_ids=44015a2f24f1f430 HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:42:17 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/monitor_repository_installation?installing_repository_ids=44015a2f24f1f430" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:42:18 +0000] "GET /admin_toolshed/browse_repositories HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:42:21 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_repositories" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:42:50 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:42:50 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:43:56 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:43:56 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:45:02 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:45:02 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,859 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,862 Dependency galaxy_sequence_utils not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,869 Using dependency vcflib version 586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,874 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,877 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,879 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,881 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,888 Using dependency fastx_toolkit version 0.0.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,896 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,898 Using dependency biopython version 1.61 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,901 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,903 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,907 Using dependency cutadapt version 1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,908 Using dependency fastqc version 0.11.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,908 Dependency amplicon_analysis_pipeline not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,909 Using dependency sickle version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,909 Using dependency bioawk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,910 Using dependency pandaseq version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,911 Using dependency spades version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,912 Using dependency qiime version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,912 Using dependency blast version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,912 Dependency fasta-splitter not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,913 Dependency rdp-classifier not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,913 Dependency r-base not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,913 Using dependency vsearch version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,914 Dependency microbiomeutil not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,914 Dependency fasta_number not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,919 Using dependency cd-hit-auxtools version 0.5-2012-03-07-fix-dan-gh-0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,923 Using dependency ucsc-fatotwobit version 324 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,928 Using dependency anaconda version 2.3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,934 Using dependency kraken version 0.10.6-eaf8fb68 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,936 Using dependency kraken version 0.10.6_eaf8fb68 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,940 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,943 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,948 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,949 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,952 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,953 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,955 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,962 Using dependency bwa version 0.5.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,967 Using dependency R version 3.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,969 Using dependency vegan version 2.3-0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,972 Using dependency mafft version 7.221 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,975 Dependency kraken not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,980 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,980 Dependency tabix not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,983 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,984 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,986 Using dependency kernlab version 0.1-4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,986 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,988 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,992 Using dependency unicycler version 0.4.4 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:24,997 Using dependency gatk version 1.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,000 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,005 Using dependency galaxy_sequence_utils version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,010 Using dependency R version 3.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,012 Using dependency deseq2 version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,015 Using dependency diffbind version 1.8.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,026 Using dependency snpEff version 4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,030 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,031 Using dependency limma version 3.25.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,032 Using dependency biopython version 1.65 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,036 Using dependency lastz version 1.02.00 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,040 Using dependency spades version 3.11.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,045 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,045 Dependency ucsc-fatotwobit not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,046 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,049 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,051 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,055 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,056 Using dependency RHmm version 1.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,060 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,060 Using dependency htslib version 1.3.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,061 Using dependency vcftools version 0.1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,064 Using dependency velvet version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,070 Using dependency snpEff version 4.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,073 Using dependency spades version 3.9.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,078 Using dependency galaxy_sequence_utils version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,082 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,082 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,084 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,089 Using dependency freebayes version 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,090 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,095 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,095 Dependency openbabel not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,098 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,102 Using dependency package_r_for_gatk_3_4_0 version 3.1.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,103 Using dependency gatk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,106 Dependency annovar not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,110 Using dependency sailfish version 0.7.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,116 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,119 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,123 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,125 Using dependency cummeRbund version 2.8.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,128 Dependency refseq_masher not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,132 Using dependency MINE version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,135 Using dependency freebayes version 0_9_20_b040236 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,135 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,139 Using dependency diamond version 0.6.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,143 Using dependency python version 2.7.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,143 Using dependency deeptools version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,146 Using dependency velvet version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,151 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,154 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,158 Using dependency blast version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,162 Using dependency prokka version 1.12 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,166 Using dependency macs version 1.3.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,168 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,169 Dependency rpy2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,174 Using dependency bamtools version 2.4.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,175 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,177 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,177 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,177 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,179 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,179 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,179 Using dependency bcftools version 1.5 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,183 Using dependency clustalw2 version 2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,183 Dependency gnuplot not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,188 Using dependency fontconfig version 2.11.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,188 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,189 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,192 Using dependency krona version 2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,195 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,199 Using dependency varscan version 2.3.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,202 Dependency deeptools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,205 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,206 Using dependency bioc_qvalue version 1.34.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,208 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,208 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,208 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,208 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,208 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,214 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,218 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,219 Dependency htslib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,224 Using dependency bwa version 0.7.15 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,224 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,225 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,225 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,226 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,229 Using dependency abyss version 2.0.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,233 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,236 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,236 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,239 Dependency biopython not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,242 Using dependency stringtie version 1.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,247 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,247 Using dependency bioc_hilbertvis version 1.18.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,251 Using dependency sra-tools version 2.8.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,254 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,255 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,259 Dependency quast not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,262 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,262 Using dependency tabix version 0.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,265 Using dependency htseq version 0.6.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,267 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,267 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,268 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,271 Using dependency bedtools version 2.22 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,275 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,277 Using dependency snippy version 3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,281 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,281 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,284 Using dependency FastQC version 0.11.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,289 Using dependency hisat version 2.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,293 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,295 Using dependency pyBamParser version 0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,296 Using dependency pyBamTools version 0.0.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,300 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,300 Dependency bowtie not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,303 Using dependency vsearch version 1.9.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,306 Using dependency pear version 0.9.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,308 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,308 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,310 Using dependency gawk version 4.1.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,310 Using dependency parallel version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,311 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,314 Using dependency blast+ version 2.2.28 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,314 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,315 Using dependency tophat2 version 2.0.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,319 Using dependency sputnik version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,322 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,327 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,329 Using dependency galaxy-ops version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,330 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,330 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,333 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,333 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,335 Using dependency yacca version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,335 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,339 Using dependency cutadapt version 1.8 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,339 Dependency cutadapt not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,346 Using dependency hisat version 2.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,346 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,348 Dependency hisat2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,349 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,356 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,364 Using dependency blast+ version 2.2.26+ of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,365 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,369 Using dependency imagemagick version 6.9.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,372 Using dependency meme version 4.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,375 Dependency perl not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,376 Dependency python not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,382 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,382 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,386 Using dependency trimmomatic version 0.32 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,390 Using dependency SICER version 1.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,390 Dependency gnuplot-py not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,394 Using dependency datamash version 1.0.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,397 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,404 Using dependency taxonomy version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,407 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,407 Using dependency gb_taxonomy version 8d245994d7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,410 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,413 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,415 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,415 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,415 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,417 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,420 Using dependency bowtie2 version 2.2.5 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,421 Using dependency tophat version 2.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,423 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,424 Using dependency gtools version 3.4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,427 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,428 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,432 Using dependency quasitools version 0.2.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,478 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,479 Dependency galaxy_sequence_utils not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,480 Using dependency vcflib version 586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,484 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,484 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,484 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,484 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,486 Using dependency fastx_toolkit version 0.0.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,487 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,487 Using dependency biopython version 1.61 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,489 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,489 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,491 Using dependency cutadapt version 1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,492 Using dependency fastqc version 0.11.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,492 Dependency amplicon_analysis_pipeline not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,492 Using dependency sickle version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,492 Using dependency bioawk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,492 Using dependency pandaseq version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,492 Using dependency spades version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,492 Using dependency qiime version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,493 Using dependency blast version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,493 Dependency fasta-splitter not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,493 Dependency rdp-classifier not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,493 Dependency r-base not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,493 Using dependency vsearch version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,493 Dependency microbiomeutil not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,493 Dependency fasta_number not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,495 Using dependency cd-hit-auxtools version 0.5-2012-03-07-fix-dan-gh-0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,497 Using dependency ucsc-fatotwobit version 324 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,498 Using dependency anaconda version 2.3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,500 Using dependency kraken version 0.10.6-eaf8fb68 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,500 Using dependency kraken version 0.10.6_eaf8fb68 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,502 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,502 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,503 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,503 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,505 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,505 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,505 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,507 Using dependency bwa version 0.5.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,508 Using dependency R version 3.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,508 Using dependency vegan version 2.3-0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,510 Using dependency mafft version 7.221 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,511 Dependency kraken not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,512 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,513 Dependency tabix not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,514 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,514 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,515 Using dependency kernlab version 0.1-4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,515 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,515 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,516 Using dependency unicycler version 0.4.4 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,518 Using dependency gatk version 1.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,518 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,520 Using dependency galaxy_sequence_utils version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,523 Using dependency R version 3.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,524 Using dependency deseq2 version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,525 Using dependency diffbind version 1.8.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,529 Using dependency snpEff version 4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,534 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,534 Using dependency limma version 3.25.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,535 Using dependency biopython version 1.65 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,539 Using dependency lastz version 1.02.00 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,555 Using dependency spades version 3.11.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,559 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,560 Dependency ucsc-fatotwobit not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,561 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,564 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,564 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,567 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,567 Using dependency RHmm version 1.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,572 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,573 Using dependency htslib version 1.3.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,574 Using dependency vcftools version 0.1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,578 Using dependency velvet version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,582 Using dependency snpEff version 4.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,589 Using dependency spades version 3.9.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,593 Using dependency galaxy_sequence_utils version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,598 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,598 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,601 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,604 Using dependency freebayes version 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,604 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,606 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,606 Dependency openbabel not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,609 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,613 Using dependency package_r_for_gatk_3_4_0 version 3.1.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,613 Using dependency gatk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,615 Dependency annovar not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,616 Using dependency sailfish version 0.7.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,619 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,619 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,620 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,620 Using dependency cummeRbund version 2.8.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,622 Dependency refseq_masher not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,623 Using dependency MINE version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,625 Using dependency freebayes version 0_9_20_b040236 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,625 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,626 Using dependency diamond version 0.6.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,628 Using dependency python version 2.7.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,628 Using dependency deeptools version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,630 Using dependency velvet version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,631 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,633 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,634 Using dependency blast version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,636 Using dependency prokka version 1.12 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,640 Using dependency macs version 1.3.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,640 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,641 Dependency rpy2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,642 Using dependency bamtools version 2.4.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,642 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,645 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,646 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,646 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,646 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,646 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,646 Using dependency bcftools version 1.5 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,648 Using dependency clustalw2 version 2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,648 Dependency gnuplot not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,650 Using dependency fontconfig version 2.11.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,650 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,650 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,652 Using dependency krona version 2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,653 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,655 Using dependency varscan version 2.3.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,656 Dependency deeptools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,658 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,658 Using dependency bioc_qvalue version 1.34.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,659 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,660 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,660 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,660 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,660 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,662 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,663 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,663 Dependency htslib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,665 Using dependency bwa version 0.7.15 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,665 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,665 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,666 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,666 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,667 Using dependency abyss version 2.0.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,669 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,670 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,670 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,672 Dependency biopython not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,675 Using dependency stringtie version 1.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,676 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,676 Using dependency bioc_hilbertvis version 1.18.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,677 Using dependency sra-tools version 2.8.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,681 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,681 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,686 Dependency quast not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,687 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,688 Using dependency tabix version 0.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,689 Using dependency htseq version 0.6.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,689 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,689 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,689 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,691 Using dependency bedtools version 2.22 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,692 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,694 Using dependency snippy version 3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,696 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,696 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,697 Using dependency FastQC version 0.11.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,699 Using dependency hisat version 2.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,700 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,700 Using dependency pyBamParser version 0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,701 Using dependency pyBamTools version 0.0.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,702 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,703 Dependency bowtie not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,704 Using dependency vsearch version 1.9.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,706 Using dependency pear version 0.9.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,708 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,708 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,708 Using dependency gawk version 4.1.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,708 Using dependency parallel version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,708 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,710 Using dependency blast+ version 2.2.28 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,710 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,710 Using dependency tophat2 version 2.0.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,712 Using dependency sputnik version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,713 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,715 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,715 Using dependency galaxy-ops version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,716 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,716 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,718 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,718 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,718 Using dependency yacca version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,718 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,719 Using dependency cutadapt version 1.8 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,719 Dependency cutadapt not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,721 Using dependency hisat version 2.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,721 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,721 Dependency hisat2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,722 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,723 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,725 Using dependency blast+ version 2.2.26+ of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,725 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,726 Using dependency imagemagick version 6.9.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,726 Using dependency meme version 4.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,728 Dependency perl not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,728 Dependency python not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,730 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,730 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,731 Using dependency trimmomatic version 0.32 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,733 Using dependency SICER version 1.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,734 Dependency gnuplot-py not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,735 Using dependency datamash version 1.0.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,738 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,739 Using dependency taxonomy version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,742 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,743 Using dependency gb_taxonomy version 8d245994d7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,744 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,746 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,747 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,747 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,747 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,749 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,751 Using dependency bowtie2 version 2.2.5 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,751 Using dependency tophat version 2.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,752 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,752 Using dependency gtools version 3.4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,754 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,755 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:45:25,757 Using dependency quasitools version 0.2.2 of type conda | |
| 94.125.130.125 - - [20/Mar/2018:11:45:24 +0000] "GET /admin/manage_tool_dependencies HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:45:26 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin/manage_tool_dependencies" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 11:45:44,384 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@0.1.1 refseq_masher=0.1.1 | |
| 127.0.0.1 - - [20/Mar/2018:11:46:07 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:46:07 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher 0.1.1* -> python 3.6* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 11:46:12,737 Removing failed conda install of [CondaTarget[refseq_masher,version=0.1.1]] | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 11:46:12,737 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@0.1.1 refseq_masher=0.1.1 | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher 0.1.1* -> python 3.5* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 11:46:25,357 Removing failed conda install of refseq_masher, version '0.1.1' | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 11:46:25,357 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@_uv_ refseq_masher | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher -> python 3.5* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 11:46:38,166 Removing failed conda install of [CondaTarget[refseq_masher,unversioned]] | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 11:46:38,167 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@_uv_ refseq_masher | |
| 127.0.0.1 - - [20/Mar/2018:11:47:13 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:47:13 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher -> python 3.5* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 11:47:16,645 Removing failed conda install of refseq_masher, version 'None' | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,837 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,840 Dependency galaxy_sequence_utils not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,843 Using dependency vcflib version 586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,847 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,848 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,848 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,848 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,851 Using dependency fastx_toolkit version 0.0.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,854 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,854 Using dependency biopython version 1.61 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,856 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,856 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,860 Using dependency cutadapt version 1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,860 Using dependency fastqc version 0.11.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,861 Dependency amplicon_analysis_pipeline not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,861 Using dependency sickle version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,861 Using dependency bioawk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,861 Using dependency pandaseq version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,861 Using dependency spades version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,861 Using dependency qiime version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,862 Using dependency blast version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,862 Dependency fasta-splitter not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,862 Dependency rdp-classifier not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,862 Dependency r-base not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,862 Using dependency vsearch version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,862 Dependency microbiomeutil not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,862 Dependency fasta_number not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,866 Using dependency cd-hit-auxtools version 0.5-2012-03-07-fix-dan-gh-0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,869 Using dependency ucsc-fatotwobit version 324 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,872 Using dependency anaconda version 2.3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,875 Using dependency kraken version 0.10.6-eaf8fb68 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,875 Using dependency kraken version 0.10.6_eaf8fb68 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,878 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,878 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,882 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,882 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,885 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,885 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,885 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,889 Using dependency bwa version 0.5.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,892 Using dependency R version 3.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,892 Using dependency vegan version 2.3-0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,895 Using dependency mafft version 7.221 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,897 Dependency kraken not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,900 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,901 Dependency tabix not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,904 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,904 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,904 Using dependency kernlab version 0.1-4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,904 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,905 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,908 Using dependency unicycler version 0.4.4 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,911 Using dependency gatk version 1.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,911 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,914 Using dependency galaxy_sequence_utils version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,917 Using dependency R version 3.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,917 Using dependency deseq2 version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,918 Using dependency diffbind version 1.8.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,921 Using dependency snpEff version 4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,923 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,924 Using dependency limma version 3.25.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,924 Using dependency biopython version 1.65 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,927 Using dependency lastz version 1.02.00 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,930 Using dependency spades version 3.11.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,935 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,936 Dependency ucsc-fatotwobit not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,936 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,940 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,940 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,945 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,945 Using dependency RHmm version 1.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,950 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,950 Using dependency htslib version 1.3.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,950 Using dependency vcftools version 0.1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,953 Using dependency velvet version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,956 Using dependency snpEff version 4.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,959 Using dependency spades version 3.9.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,962 Using dependency galaxy_sequence_utils version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,965 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,966 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,968 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,971 Using dependency freebayes version 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,971 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,975 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,975 Dependency openbabel not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,978 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,981 Using dependency package_r_for_gatk_3_4_0 version 3.1.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,981 Using dependency gatk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,984 Dependency annovar not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,987 Using dependency sailfish version 0.7.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,990 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,991 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,994 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,994 Using dependency cummeRbund version 2.8.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:16,997 Dependency refseq_masher not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,000 Using dependency MINE version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,003 Using dependency freebayes version 0_9_20_b040236 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,004 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,007 Using dependency diamond version 0.6.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,010 Using dependency python version 2.7.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,010 Using dependency deeptools version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,013 Using dependency velvet version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,016 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,019 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,022 Using dependency blast version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,025 Using dependency prokka version 1.12 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,030 Using dependency macs version 1.3.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,030 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,030 Dependency rpy2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,033 Using dependency bamtools version 2.4.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,034 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,035 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,035 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,035 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,035 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,036 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,036 Using dependency bcftools version 1.5 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,039 Using dependency clustalw2 version 2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,039 Dependency gnuplot not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,043 Using dependency fontconfig version 2.11.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,043 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,043 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,046 Using dependency krona version 2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,049 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,052 Using dependency varscan version 2.3.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,055 Dependency deeptools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,060 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,060 Using dependency bioc_qvalue version 1.34.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,062 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,062 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,062 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,062 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,062 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,065 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,068 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,068 Dependency htslib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,071 Using dependency bwa version 0.7.15 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,071 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,072 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,072 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,072 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,075 Using dependency abyss version 2.0.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,078 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,081 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,082 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,085 Dependency biopython not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,087 Using dependency stringtie version 1.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,091 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,091 Using dependency bioc_hilbertvis version 1.18.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,093 Using dependency sra-tools version 2.8.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,096 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,097 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,100 Dependency quast not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,103 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,103 Using dependency tabix version 0.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,106 Using dependency htseq version 0.6.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,106 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,106 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,107 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,111 Using dependency bedtools version 2.22 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,114 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,117 Using dependency snippy version 3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,120 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,120 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,124 Using dependency FastQC version 0.11.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,127 Using dependency hisat version 2.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,129 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,130 Using dependency pyBamParser version 0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,130 Using dependency pyBamTools version 0.0.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,133 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,133 Dependency bowtie not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,136 Using dependency vsearch version 1.9.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,139 Using dependency pear version 0.9.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,141 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,141 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,141 Using dependency gawk version 4.1.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,142 Using dependency parallel version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,142 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,145 Using dependency blast+ version 2.2.28 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,146 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,146 Using dependency tophat2 version 2.0.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,149 Using dependency sputnik version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,154 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,157 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,157 Using dependency galaxy-ops version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,158 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,158 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,162 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,162 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,162 Using dependency yacca version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,162 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,165 Using dependency cutadapt version 1.8 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,165 Dependency cutadapt not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,168 Using dependency hisat version 2.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,168 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,168 Dependency hisat2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,169 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,173 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,178 Using dependency blast+ version 2.2.26+ of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,178 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,181 Using dependency imagemagick version 6.9.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,182 Using dependency meme version 4.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,185 Dependency perl not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,185 Dependency python not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,188 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,188 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,191 Using dependency trimmomatic version 0.32 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,194 Using dependency SICER version 1.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,195 Dependency gnuplot-py not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,198 Using dependency datamash version 1.0.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,201 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,208 Using dependency taxonomy version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,215 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,216 Using dependency gb_taxonomy version 8d245994d7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,223 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,231 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,235 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,235 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,235 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,239 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,247 Using dependency bowtie2 version 2.2.5 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,247 Using dependency tophat version 2.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,254 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,255 Using dependency gtools version 3.4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,263 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,264 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,269 Using dependency quasitools version 0.2.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,400 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,406 Dependency galaxy_sequence_utils not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,409 Using dependency vcflib version 586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,413 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,413 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,413 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,414 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,418 Using dependency fastx_toolkit version 0.0.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,422 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,422 Using dependency biopython version 1.61 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,426 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,427 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,431 Using dependency cutadapt version 1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,431 Using dependency fastqc version 0.11.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,431 Dependency amplicon_analysis_pipeline not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,431 Using dependency sickle version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,431 Using dependency bioawk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,432 Using dependency pandaseq version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,432 Using dependency spades version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,432 Using dependency qiime version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,432 Using dependency blast version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,432 Dependency fasta-splitter not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,432 Dependency rdp-classifier not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,432 Dependency r-base not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,432 Using dependency vsearch version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,433 Dependency microbiomeutil not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,433 Dependency fasta_number not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,435 Using dependency cd-hit-auxtools version 0.5-2012-03-07-fix-dan-gh-0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,436 Using dependency ucsc-fatotwobit version 324 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,439 Using dependency anaconda version 2.3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,441 Using dependency kraken version 0.10.6-eaf8fb68 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,441 Using dependency kraken version 0.10.6_eaf8fb68 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,443 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,443 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,444 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,445 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,446 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,446 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,446 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,449 Using dependency bwa version 0.5.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,450 Using dependency R version 3.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,451 Using dependency vegan version 2.3-0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,452 Using dependency mafft version 7.221 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,453 Dependency kraken not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,454 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,455 Dependency tabix not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,458 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,461 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,461 Using dependency kernlab version 0.1-4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,461 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,462 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,469 Using dependency unicycler version 0.4.4 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,473 Using dependency gatk version 1.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,473 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,475 Using dependency galaxy_sequence_utils version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,478 Using dependency R version 3.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,478 Using dependency deseq2 version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,478 Using dependency diffbind version 1.8.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,480 Using dependency snpEff version 4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,481 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,481 Using dependency limma version 3.25.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,481 Using dependency biopython version 1.65 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,483 Using dependency lastz version 1.02.00 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,487 Using dependency spades version 3.11.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,491 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,492 Dependency ucsc-fatotwobit not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,492 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,493 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,494 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,495 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,495 Using dependency RHmm version 1.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,497 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,497 Using dependency htslib version 1.3.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,497 Using dependency vcftools version 0.1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,498 Using dependency velvet version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,501 Using dependency snpEff version 4.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,504 Using dependency spades version 3.9.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,505 Using dependency galaxy_sequence_utils version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,507 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,507 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,508 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,510 Using dependency freebayes version 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,510 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,511 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,512 Dependency openbabel not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,513 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,514 Using dependency package_r_for_gatk_3_4_0 version 3.1.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,515 Using dependency gatk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,518 Dependency annovar not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,519 Using dependency sailfish version 0.7.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,521 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,521 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,522 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,522 Using dependency cummeRbund version 2.8.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,524 Dependency refseq_masher not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,525 Using dependency MINE version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,527 Using dependency freebayes version 0_9_20_b040236 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,527 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,528 Using dependency diamond version 0.6.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,530 Using dependency python version 2.7.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,530 Using dependency deeptools version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,531 Using dependency velvet version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,533 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,534 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,536 Using dependency blast version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,537 Using dependency prokka version 1.12 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,539 Using dependency macs version 1.3.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,539 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,539 Dependency rpy2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,541 Using dependency bamtools version 2.4.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,541 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,543 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,543 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,543 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,543 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,543 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,543 Using dependency bcftools version 1.5 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,545 Using dependency clustalw2 version 2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,545 Dependency gnuplot not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,547 Using dependency fontconfig version 2.11.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,547 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,547 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,548 Using dependency krona version 2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,551 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,555 Using dependency varscan version 2.3.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,556 Dependency deeptools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,558 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,558 Using dependency bioc_qvalue version 1.34.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,559 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,559 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,560 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,560 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,560 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,562 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,567 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,567 Dependency htslib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,571 Using dependency bwa version 0.7.15 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,573 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,575 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,576 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,576 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,581 Using dependency abyss version 2.0.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,585 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,590 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,590 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,596 Dependency biopython not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,598 Using dependency stringtie version 1.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,600 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,600 Using dependency bioc_hilbertvis version 1.18.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,601 Using dependency sra-tools version 2.8.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,602 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,603 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,604 Dependency quast not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,606 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,606 Using dependency tabix version 0.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,607 Using dependency htseq version 0.6.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,607 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,608 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,608 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,609 Using dependency bedtools version 2.22 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,611 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,612 Using dependency snippy version 3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,613 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,614 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,615 Using dependency FastQC version 0.11.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,617 Using dependency hisat version 2.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,618 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,618 Using dependency pyBamParser version 0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,618 Using dependency pyBamTools version 0.0.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,620 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,620 Dependency bowtie not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,622 Using dependency vsearch version 1.9.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,623 Using dependency pear version 0.9.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,625 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,625 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,625 Using dependency gawk version 4.1.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,625 Using dependency parallel version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,626 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,627 Using dependency blast+ version 2.2.28 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,627 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,628 Using dependency tophat2 version 2.0.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,629 Using dependency sputnik version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,631 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,632 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,632 Using dependency galaxy-ops version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,633 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,633 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,635 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,635 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,635 Using dependency yacca version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,635 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,637 Using dependency cutadapt version 1.8 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,637 Dependency cutadapt not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,638 Using dependency hisat version 2.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,638 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,639 Dependency hisat2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,639 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,640 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,642 Using dependency blast+ version 2.2.26+ of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,642 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,643 Using dependency imagemagick version 6.9.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,644 Using dependency meme version 4.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,645 Dependency perl not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,646 Dependency python not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,647 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,647 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,649 Using dependency trimmomatic version 0.32 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,650 Using dependency SICER version 1.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,651 Dependency gnuplot-py not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,652 Using dependency datamash version 1.0.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,654 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,655 Using dependency taxonomy version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,659 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,660 Using dependency gb_taxonomy version 8d245994d7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,664 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,668 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,669 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,669 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,669 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,671 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,672 Using dependency bowtie2 version 2.2.5 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,673 Using dependency tophat version 2.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,674 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,674 Using dependency gtools version 3.4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,676 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,677 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:47:17,678 Using dependency quasitools version 0.2.2 of type conda | |
| 94.125.130.125 - - [20/Mar/2018:11:45:44 +0000] "GET /admin/manage_tool_dependencies?selected_tool_ids=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&install_dependencies=Install+checked+dependencies+using+Conda HTTP/1.0" 200 - "http://52.54.147.188/admin/manage_tool_dependencies" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:17 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin/manage_tool_dependencies?selected_tool_ids=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&install_dependencies=Install+checked+dependencies+using+Conda" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:44 +0000] "GET / HTTP/1.0" 200 - "-" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:45 +0000] "GET /api/webhooks/history-menu/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:45 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:45 +0000] "GET /api/webhooks/masthead/all HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:45 +0000] "GET /api/datatypes?extension_only=False HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:45 +0000] "GET /api/genomes HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:45 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:45 +0000] "GET /welcome HTTP/1.0" 302 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:45 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:45 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:46 +0000] "GET /api/histories/cbbbf59e8f08c98c?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:47 +0000] "PUT /api/histories/cbbbf59e8f08c98c/contents/datasets/255f6b16db8a3b32 HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:48 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:50 +0000] "GET /api/tools?q=ref HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:51 +0000] "GET /api/tools?q=refs HTTP/1.0" 200 - "http://52.54.147.188/" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:55 +0000] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_matches/0.1.1/build?version=0.1.1&__identifer=pujszbs1dg&tool_version=0.1.1 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_matches%2F0.1.1&version=0.1.1&__identifer=pujszbs1dg" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:55 +0000] "GET /api/webhooks/tool-menu/all HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_matches%2F0.1.1&version=0.1.1&__identifer=pujszbs1dg" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:55 +0000] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_matches/0.1.1/citations HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_matches%2F0.1.1&version=0.1.1&__identifer=pujszbs1dg" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:57 +0000] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1/build?version=0.1.1&__identifer=espwm0zzeja&tool_version=0.1.1 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:57 +0000] "GET /api/webhooks/tool-menu/all HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:57 +0000] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1/citations HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:47:59 +0000] "POST /api/tools/toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1/build HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:02 +0000] "POST /api/tools/toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1/build HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:04 +0000] "POST /api/tools/toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1/build HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.tools DEBUG 2018-03-20 11:48:05,673 Validated and populated state for tool request (20.770 ms) | |
| galaxy.tools.actions INFO 2018-03-20 11:48:05,710 Handled output named output_path_tab for tool toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1 (12.780 ms) | |
| galaxy.tools.actions INFO 2018-03-20 11:48:05,715 Added output datasets to history (4.980 ms) | |
| galaxy.tools.actions INFO 2018-03-20 11:48:05,738 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1] (14.377 ms) | |
| galaxy.tools.actions INFO 2018-03-20 11:48:05,739 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1] complete, ready to flush (23.644 ms) | |
| galaxy.tools.actions INFO 2018-03-20 11:48:05,756 Flushed transaction for job Job[id=5438,tool_id=toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1] (17.428 ms) | |
| galaxy.tools.execute DEBUG 2018-03-20 11:48:05,756 Tool [toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1] created job [5438] (68.055 ms) | |
| galaxy.tools.execute DEBUG 2018-03-20 11:48:05,763 Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_contains/0.1.1 request: (89.673 ms) | |
| 94.125.130.125 - - [20/Mar/2018:11:48:05 +0000] "POST /api/tools HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:05 +0000] "GET /api/webhooks/tool HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:05 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T11%3A52%3A00.275Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:06 +0000] "GET /api/histories/cbbbf59e8f08c98c?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.jobs DEBUG 2018-03-20 11:48:06,267 (5438) Working directory for job is: /mnt/galaxy/tmp/job_working_directory/005/5438 | |
| galaxy.jobs.handler DEBUG 2018-03-20 11:48:06,271 (5438) Dispatching to slurm runner | |
| galaxy.jobs DEBUG 2018-03-20 11:48:06,295 (5438) Persisting job destination (destination id: slurm_cluster) | |
| galaxy.jobs.runners DEBUG 2018-03-20 11:48:06,301 Job [5438] queued (29.259 ms) | |
| galaxy.jobs.handler INFO 2018-03-20 11:48:06,315 (5438) Job dispatched | |
| 52.1.11.160 - - [20/Mar/2018:11:48:06 +0000] "GET / HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:06 +0000] "GET /datasets/error?dataset_id=255f6b16db8a3b32&__identifer=0ssou692cw9n HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:06 +0000] "GET /admin/center?message=&status=done HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:06 +0000] "GET /admin_toolshed/deactivate_or_uninstall_repository?id=44015a2f24f1f430 HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:06 +0000] "GET /admin_toolshed/browse_repositories?status=done&message=The+repository+named+%3Cb%3Erefseq_masher%3C%2Fb%3E+has+been+uninstalled HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:06 +0000] "GET /admin_toolshed/browse_tool_sheds HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:06 +0000] "GET /admin_toolshed/browse_repositories HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:06 +0000] "GET /datasets/255f6b16db8a3b32/show_params HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /root/login?redirect=%2Fdatasets%2Ferror HTTP/1.0" 200 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=1w1zjfjy2tb HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /root/login?redirect=%2F HTTP/1.0" 200 - "-" "Mozilla/5.0 (compatible)" | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 11:48:07,273 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@0.1.1 refseq_masher=0.1.1 | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /admin_toolshed/prepare_for_install?changeset_revisions=26df66c32861&repository_ids=df2fa11538368649&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /root/login?redirect=%2Fadmin%2Fcenter HTTP/1.0" 200 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /admin_toolshed/prepare_for_install HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /root/login?redirect=%2Fdatasets%2F255f6b16db8a3b32%2Fshow_params HTTP/1.0" 200 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /root/login?redirect=%2Fadmin_toolshed%2Fbrowse_repositories HTTP/1.0" 200 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /root/login?redirect=%2Fadmin_toolshed%2Fdeactivate_or_uninstall_repository HTTP/1.0" 200 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /root/login?redirect=%2Fadmin_toolshed%2Fbrowse_tool_sheds HTTP/1.0" 200 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&f-deleted=False&f-free-text-search=refseq HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /admin_toolshed/monitor_repository_installation?installing_repository_ids=44015a2f24f1f430 HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /admin_toolshed/browse_repositories?status=ok&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Erefseq_masher%3C%2Fb%3E HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /admin HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| galaxy.webapps.galaxy.controllers.user WARNING 2018-03-20 11:48:07,999 Redirect URL is outside of Galaxy, will redirect to Galaxy root instead: | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /history/view_multiple HTTP/1.0" 302 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:07 +0000] "GET /user/login?use_panels=True HTTP/1.0" 200 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:08 +0000] "GET /root/login?redirect=%2Fadmin_toolshed%2Fmonitor_repository_installation HTTP/1.0" 200 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:08 +0000] "GET /root/login?redirect=%2Fhistory%2Fview_multiple HTTP/1.0" 200 - "-" "Mozilla/5.0 (compatible)" | |
| 52.1.11.160 - - [20/Mar/2018:11:48:08 +0000] "GET /root/login?redirect=%2Fadmin HTTP/1.0" 200 - "-" "Mozilla/5.0 (compatible)" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:10 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T11%3A48%3A05.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:14 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T11%3A48%3A10.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:48:18 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:48:18 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:18 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T11%3A48%3A14.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher 0.1.1* -> python 3.5* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 11:48:20,632 Removing failed conda install of [CondaTarget[refseq_masher,version=0.1.1]] | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 11:48:20,633 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@0.1.1 refseq_masher=0.1.1 | |
| 52.1.11.160 - - [20/Mar/2018:11:48:20 +0000] "GET /root/login?redirect=%2Fadmin_toolshed%2Fprepare_for_install HTTP/1.0" 200 - "-" "Mozilla/5.0 (compatible)" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:22 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T11%3A48%3A18.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:27 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T11%3A48%3A23.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:31 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T11%3A48%3A27.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher 0.1.1* -> python 3.5* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 11:48:33,354 Removing failed conda install of refseq_masher, version '0.1.1' | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 11:48:33,354 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@_uv_ refseq_masher | |
| 94.125.130.125 - - [20/Mar/2018:11:48:35 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:35 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:35 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:36 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:36 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:36 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:37 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:37 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:37 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:37 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:38 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:38 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:38 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:38 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:39 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:39 +0000] "GET /api/histories/null/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 400 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:39 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:39 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:41 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:42 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:42 +0000] "GET /history/current_history_json HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:42 +0000] "GET /api/users/1cd8e2f6b131e891 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:42 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:45 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher -> python 3.6* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 11:48:47,114 Removing failed conda install of [CondaTarget[refseq_masher,unversioned]] | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-20 11:48:47,114 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __refseq_masher@_uv_ refseq_masher | |
| 94.125.130.125 - - [20/Mar/2018:11:48:47 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T11%3A52%3A57.383Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:51 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T11%3A48%3A47.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:55 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T11%3A48%3A51.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:48:59 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T11%3A48%3A55.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| Fetching package metadata ................... | |
| Solving package specifications: . | |
| UnsatisfiableError: The following specifications were found to be in conflict: | |
| - python 2.7* | |
| - refseq_masher -> python 3.6* | |
| Use "conda info " to see the dependencies for each package. | |
| galaxy.tools.deps.resolvers.conda DEBUG 2018-03-20 11:48:59,986 Removing failed conda install of refseq_masher, version 'None' | |
| galaxy.jobs.command_factory INFO 2018-03-20 11:49:00,012 Built script [/mnt/galaxy/tmp/job_working_directory/005/5438/tool_script.sh] for tool command [ln -s "/mnt/galaxy/files/000/dataset_864.dat" "718138_S1_L001_R1_001.fastq_1.fastq" && ln -s "/mnt/galaxy/files/000/dataset_853.dat" "718138_S1_L001_R2_001.fastq_2.fastq" && refseq_masher -vv contains --output refseq_masher-contains.tab --output-type tab --top-n-results 0 --parallelism "${GALAXY_SLOTS:-1}" --min-identity 0.9 --max-pvalue 0.01 "718138_S1_L001_R1_001.fastq_1.fastq" "718138_S1_L001_R2_001.fastq_2.fastq"] | |
| galaxy.tools.deps DEBUG 2018-03-20 11:49:00,099 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:49:00,100 Using dependency bcftools version 1.5 of type conda | |
| galaxy.jobs.runners DEBUG 2018-03-20 11:49:00,105 (5438) command is: rm -rf working; mkdir -p working; cd working; /mnt/galaxy/tmp/job_working_directory/005/5438/tool_script.sh; return_code=$?; if [ -f /mnt/galaxy/tmp/job_working_directory/005/5438/working/refseq_masher-contains.tab ] ; then cp /mnt/galaxy/tmp/job_working_directory/005/5438/working/refseq_masher-contains.tab /mnt/galaxy/files/008/dataset_8240.dat ; fi; cd '/mnt/galaxy/tmp/job_working_directory/005/5438'; | |
| [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True | |
| export PATH=$PATH:'/mnt/galaxy/tool_dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; export PATH=$PATH:'/mnt/galaxy/tool_dependencies/_conda/envs/mulled-v1-eb2018fd3ce0fcbcee48a4bf89c57219add691c16729281b6c46b30f08339397/bin' ; python "/mnt/galaxy/tmp/job_working_directory/005/5438/set_metadata_uz07xE.py" "/mnt/galaxy/tmp/job_working_directory/005/5438/registry.xml" "/mnt/galaxy/tmp/job_working_directory/005/5438/working/galaxy.json" "/mnt/galaxy/tmp/job_working_directory/005/5438/metadata_in_HistoryDatasetAssociation_8823_aJgBKa,/mnt/galaxy/tmp/job_working_directory/005/5438/metadata_kwds_HistoryDatasetAssociation_8823_7kUAzn,/mnt/galaxy/tmp/job_working_directory/005/5438/metadata_out_HistoryDatasetAssociation_8823_Nx4qcv,/mnt/galaxy/tmp/job_working_directory/005/5438/metadata_results_HistoryDatasetAssociation_8823_e1GtI4,/mnt/galaxy/files/008/dataset_8240.dat,/mnt/galaxy/tmp/job_working_directory/005/5438/metadata_override_HistoryDatasetAssociation_8823_Vqq7hg" 5242880; sh -c "exit $return_code" | |
| galaxy.jobs.runners.drmaa DEBUG 2018-03-20 11:49:00,132 (5438) submitting file /mnt/galaxy/tmp/job_working_directory/005/5438/galaxy_5438.sh | |
| galaxy.jobs.runners.drmaa INFO 2018-03-20 11:49:00,133 (5438) queued as 3 | |
| galaxy.jobs DEBUG 2018-03-20 11:49:00,134 (5438) Persisting job destination (destination id: slurm_cluster) | |
| galaxy.jobs.runners.drmaa DEBUG 2018-03-20 11:49:01,014 (5438/3) state change: job is running | |
| galaxy.jobs.runners.drmaa DEBUG 2018-03-20 11:49:03,108 (5438/3) state change: job finished normally | |
| galaxy.jobs.output_checker INFO 2018-03-20 11:49:03,142 Job 5438: Fatal error: Exit code 127 () | |
| galaxy.jobs.output_checker DEBUG 2018-03-20 11:49:03,142 Tool exit code indicates an error, failing job. | |
| galaxy.jobs DEBUG 2018-03-20 11:49:03,198 (5438) setting dataset 8240 state to ERROR | |
| galaxy.jobs INFO 2018-03-20 11:49:03,298 Collecting metrics for Job 5438 | |
| galaxy.jobs DEBUG 2018-03-20 11:49:03,308 job 5438 ended (finish() executed in (170.527 ms)) | |
| galaxy.tools.error_reports DEBUG 2018-03-20 11:49:03,323 Bug report plugin generated response None | |
| 94.125.130.125 - - [20/Mar/2018:11:49:03 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-20T11%3A48%3A59.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:49:03 +0000] "GET /api/histories/cbbbf59e8f08c98c?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:49:23 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:49:23 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| 94.125.130.125 - - [20/Mar/2018:11:49:30 +0000] "GET /api/tools?q=meta HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:49:31 +0000] "GET /api/histories/cbbbf59e8f08c98c/contents/datasets/41b1376cab30e402 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:49:38 +0000] "GET /api/tools?q=metaspades HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Frefseq_masher%2Frefseq_masher_contains%2F0.1.1&version=0.1.1&__identifer=espwm0zzeja" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:49:40 +0000] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.9.0/build?version=3.9.0&__identifer=lg3osb9orx&tool_version=3.9.0 HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fmetaspades%2Fmetaspades%2F3.9.0&version=3.9.0&__identifer=lg3osb9orx" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:49:40 +0000] "GET /api/webhooks/tool-menu/all HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fmetaspades%2Fmetaspades%2F3.9.0&version=3.9.0&__identifer=lg3osb9orx" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:49:40 +0000] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.9.0/citations HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fmetaspades%2Fmetaspades%2F3.9.0&version=3.9.0&__identifer=lg3osb9orx" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:49:53 +0000] "GET /api/tools?q=prokka HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fmetaspades%2Fmetaspades%2F3.9.0&version=3.9.0&__identifer=lg3osb9orx" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:49:58 +0000] "GET /admin HTTP/1.0" 200 - "http://52.54.147.188/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fmetaspades%2Fmetaspades%2F3.9.0&version=3.9.0&__identifer=lg3osb9orx" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:49:58 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:49:58 +0000] "GET /api/webhooks/masthead/all HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:49:59 +0000] "GET /admin/center?message=&status=done HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:49:59 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin/center?message=&status=done" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:50:04 +0000] "GET /admin_toolshed/browse_tool_sheds HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:50:04 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,259 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,263 Dependency galaxy_sequence_utils not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,269 Using dependency vcflib version 586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,276 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,277 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,277 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,277 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,286 Using dependency fastx_toolkit version 0.0.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,293 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,293 Using dependency biopython version 1.61 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,298 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,298 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,307 Using dependency cutadapt version 1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,308 Using dependency fastqc version 0.11.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,310 Dependency amplicon_analysis_pipeline not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,310 Using dependency sickle version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,310 Using dependency bioawk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,310 Using dependency pandaseq version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,311 Using dependency spades version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,311 Using dependency qiime version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,311 Using dependency blast version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,312 Dependency fasta-splitter not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,312 Dependency rdp-classifier not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,312 Dependency r-base not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,313 Using dependency vsearch version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,313 Dependency microbiomeutil not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,313 Dependency fasta_number not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,322 Using dependency cd-hit-auxtools version 0.5-2012-03-07-fix-dan-gh-0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,326 Using dependency ucsc-fatotwobit version 324 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,328 Using dependency anaconda version 2.3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,331 Using dependency kraken version 0.10.6-eaf8fb68 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,332 Using dependency kraken version 0.10.6_eaf8fb68 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,335 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,335 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,338 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,338 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,343 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,344 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,344 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,350 Using dependency bwa version 0.5.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,354 Using dependency R version 3.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,354 Using dependency vegan version 2.3-0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,357 Using dependency mafft version 7.221 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,359 Dependency kraken not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,362 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,363 Dependency tabix not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,366 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,366 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,366 Using dependency kernlab version 0.1-4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,366 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,366 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,369 Using dependency unicycler version 0.4.4 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,372 Using dependency gatk version 1.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,373 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,376 Using dependency galaxy_sequence_utils version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,379 Using dependency R version 3.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,379 Using dependency deseq2 version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,379 Using dependency diffbind version 1.8.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,382 Using dependency snpEff version 4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,388 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,389 Using dependency limma version 3.25.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,390 Using dependency biopython version 1.65 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,396 Using dependency lastz version 1.02.00 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,399 Using dependency spades version 3.11.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,402 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,403 Dependency ucsc-fatotwobit not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,403 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,406 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,406 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,409 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,409 Using dependency RHmm version 1.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,413 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,413 Using dependency htslib version 1.3.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,413 Using dependency vcftools version 0.1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,417 Using dependency velvet version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,420 Using dependency snpEff version 4.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,423 Using dependency spades version 3.9.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,427 Using dependency galaxy_sequence_utils version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,431 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,431 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,433 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,436 Using dependency freebayes version 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,437 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,440 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,440 Dependency openbabel not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,443 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,446 Using dependency package_r_for_gatk_3_4_0 version 3.1.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,447 Using dependency gatk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,450 Dependency annovar not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,453 Using dependency sailfish version 0.7.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,456 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,456 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,459 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,459 Using dependency cummeRbund version 2.8.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,462 Dependency refseq_masher not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,465 Using dependency MINE version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,468 Using dependency freebayes version 0_9_20_b040236 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,468 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,471 Using dependency diamond version 0.6.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,475 Using dependency python version 2.7.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,475 Using dependency deeptools version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,478 Using dependency velvet version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,481 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,484 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,487 Using dependency blast version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,490 Using dependency prokka version 1.12 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,493 Using dependency macs version 1.3.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,493 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,494 Dependency rpy2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,497 Using dependency bamtools version 2.4.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,497 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,498 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,499 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,499 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,499 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,499 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,499 Using dependency bcftools version 1.5 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,502 Using dependency clustalw2 version 2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,503 Dependency gnuplot not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,506 Using dependency fontconfig version 2.11.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,506 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,507 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,509 Using dependency krona version 2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,513 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,516 Using dependency varscan version 2.3.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,519 Dependency deeptools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,522 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,522 Using dependency bioc_qvalue version 1.34.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,524 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,524 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,524 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,524 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,524 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,528 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,530 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,531 Dependency htslib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,534 Using dependency bwa version 0.7.15 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,534 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,535 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,535 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,535 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,538 Using dependency abyss version 2.0.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,541 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,544 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,545 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,548 Dependency biopython not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,551 Using dependency stringtie version 1.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,554 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,554 Using dependency bioc_hilbertvis version 1.18.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,556 Using dependency sra-tools version 2.8.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,559 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,559 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,563 Dependency quast not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,566 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,567 Using dependency tabix version 0.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,569 Using dependency htseq version 0.6.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,570 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,570 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,570 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,573 Using dependency bedtools version 2.22 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,576 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,579 Using dependency snippy version 3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,582 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,582 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,585 Using dependency FastQC version 0.11.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,588 Using dependency hisat version 2.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,591 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,591 Using dependency pyBamParser version 0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,592 Using dependency pyBamTools version 0.0.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,595 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,596 Dependency bowtie not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,599 Using dependency vsearch version 1.9.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,602 Using dependency pear version 0.9.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,603 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,604 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,604 Using dependency gawk version 4.1.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,604 Using dependency parallel version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,604 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,607 Using dependency blast+ version 2.2.28 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,608 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,608 Using dependency tophat2 version 2.0.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,611 Using dependency sputnik version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,614 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,617 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,617 Using dependency galaxy-ops version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,618 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,618 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,621 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,622 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,622 Using dependency yacca version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,622 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,625 Using dependency cutadapt version 1.8 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,625 Dependency cutadapt not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,628 Using dependency hisat version 2.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,628 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,629 Dependency hisat2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,629 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,632 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,635 Using dependency blast+ version 2.2.26+ of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,635 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,638 Using dependency imagemagick version 6.9.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,639 Using dependency meme version 4.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,642 Dependency perl not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,642 Dependency python not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,645 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,646 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,648 Using dependency trimmomatic version 0.32 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,652 Using dependency SICER version 1.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,653 Dependency gnuplot-py not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,656 Using dependency datamash version 1.0.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,659 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,662 Using dependency taxonomy version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,665 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,665 Using dependency gb_taxonomy version 8d245994d7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,668 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,671 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,673 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,673 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,673 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,674 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,677 Using dependency bowtie2 version 2.2.5 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,678 Using dependency tophat version 2.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,682 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,682 Using dependency gtools version 3.4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,685 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,686 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,689 Using dependency quasitools version 0.2.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,747 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,748 Dependency galaxy_sequence_utils not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,749 Using dependency vcflib version 586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,751 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,751 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,751 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,751 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,753 Using dependency fastx_toolkit version 0.0.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,754 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,754 Using dependency biopython version 1.61 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,755 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,756 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,758 Using dependency cutadapt version 1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,758 Using dependency fastqc version 0.11.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,759 Dependency amplicon_analysis_pipeline not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,759 Using dependency sickle version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,759 Using dependency bioawk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,759 Using dependency pandaseq version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,759 Using dependency spades version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,759 Using dependency qiime version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,759 Using dependency blast version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,759 Dependency fasta-splitter not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,759 Dependency rdp-classifier not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,760 Dependency r-base not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,760 Using dependency vsearch version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,760 Dependency microbiomeutil not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,760 Dependency fasta_number not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,762 Using dependency cd-hit-auxtools version 0.5-2012-03-07-fix-dan-gh-0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,763 Using dependency ucsc-fatotwobit version 324 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,765 Using dependency anaconda version 2.3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,766 Using dependency kraken version 0.10.6-eaf8fb68 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,766 Using dependency kraken version 0.10.6_eaf8fb68 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,768 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,768 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,770 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,770 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,771 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,771 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,772 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,773 Using dependency bwa version 0.5.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,775 Using dependency R version 3.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,775 Using dependency vegan version 2.3-0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,777 Using dependency mafft version 7.221 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,778 Dependency kraken not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,780 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,780 Dependency tabix not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,782 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,782 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,782 Using dependency kernlab version 0.1-4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,782 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,782 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,784 Using dependency unicycler version 0.4.4 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,785 Using dependency gatk version 1.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,785 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,787 Using dependency galaxy_sequence_utils version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,788 Using dependency R version 3.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,789 Using dependency deseq2 version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,789 Using dependency diffbind version 1.8.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,790 Using dependency snpEff version 4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,791 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,791 Using dependency limma version 3.25.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,792 Using dependency biopython version 1.65 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,793 Using dependency lastz version 1.02.00 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,794 Using dependency spades version 3.11.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,796 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,797 Dependency ucsc-fatotwobit not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,797 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,798 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,798 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,800 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,800 Using dependency RHmm version 1.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,802 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,802 Using dependency htslib version 1.3.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,802 Using dependency vcftools version 0.1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,803 Using dependency velvet version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,805 Using dependency snpEff version 4.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,806 Using dependency spades version 3.9.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,808 Using dependency galaxy_sequence_utils version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,809 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,809 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,810 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,812 Using dependency freebayes version 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,812 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,814 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,814 Dependency openbabel not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,815 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,817 Using dependency package_r_for_gatk_3_4_0 version 3.1.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,817 Using dependency gatk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,819 Dependency annovar not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,820 Using dependency sailfish version 0.7.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,821 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,822 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,823 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,823 Using dependency cummeRbund version 2.8.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,825 Dependency refseq_masher not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,827 Using dependency MINE version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,833 Using dependency freebayes version 0_9_20_b040236 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,840 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,843 Using dependency diamond version 0.6.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,846 Using dependency python version 2.7.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,847 Using dependency deeptools version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,850 Using dependency velvet version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,853 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,857 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,862 Using dependency blast version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,865 Using dependency prokka version 1.12 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,869 Using dependency macs version 1.3.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,870 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,874 Dependency rpy2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,878 Using dependency bamtools version 2.4.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,879 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,883 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,884 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,885 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,885 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,886 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,886 Using dependency bcftools version 1.5 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,887 Using dependency clustalw2 version 2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,888 Dependency gnuplot not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,891 Using dependency fontconfig version 2.11.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,891 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,892 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,893 Using dependency krona version 2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,894 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,897 Using dependency varscan version 2.3.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,900 Dependency deeptools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,902 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,902 Using dependency bioc_qvalue version 1.34.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,904 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,904 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,904 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,904 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,904 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,906 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,907 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,907 Dependency htslib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,909 Using dependency bwa version 0.7.15 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,909 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,910 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,910 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,910 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,912 Using dependency abyss version 2.0.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,913 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,915 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,915 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,916 Dependency biopython not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,918 Using dependency stringtie version 1.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,919 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,919 Using dependency bioc_hilbertvis version 1.18.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,920 Using dependency sra-tools version 2.8.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,922 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,922 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,923 Dependency quast not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,925 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,925 Using dependency tabix version 0.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,926 Using dependency htseq version 0.6.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,927 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,927 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,927 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,928 Using dependency bedtools version 2.22 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,930 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,931 Using dependency snippy version 3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,933 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,933 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,934 Using dependency FastQC version 0.11.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,936 Using dependency hisat version 2.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,937 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,937 Using dependency pyBamParser version 0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,937 Using dependency pyBamTools version 0.0.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,941 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,942 Dependency bowtie not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,943 Using dependency vsearch version 1.9.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,945 Using dependency pear version 0.9.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,947 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,947 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,947 Using dependency gawk version 4.1.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,947 Using dependency parallel version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,947 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,949 Using dependency blast+ version 2.2.28 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,949 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,949 Using dependency tophat2 version 2.0.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,951 Using dependency sputnik version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,952 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,954 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,954 Using dependency galaxy-ops version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,955 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,955 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,956 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,956 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,957 Using dependency yacca version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,957 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,960 Using dependency cutadapt version 1.8 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,960 Dependency cutadapt not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,961 Using dependency hisat version 2.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,962 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,962 Dependency hisat2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,962 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,964 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,965 Using dependency blast+ version 2.2.26+ of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,965 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,967 Using dependency imagemagick version 6.9.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,967 Using dependency meme version 4.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,969 Dependency perl not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,969 Dependency python not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,970 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,971 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,972 Using dependency trimmomatic version 0.32 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,973 Using dependency SICER version 1.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,974 Dependency gnuplot-py not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,975 Using dependency datamash version 1.0.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,977 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,978 Using dependency taxonomy version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,980 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,980 Using dependency gb_taxonomy version 8d245994d7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,981 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,983 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,984 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,985 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,985 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,986 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,988 Using dependency bowtie2 version 2.2.5 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,988 Using dependency tophat version 2.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,989 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,989 Using dependency gtools version 3.4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,991 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,993 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:07,994 Using dependency quasitools version 0.2.2 of type conda | |
| 94.125.130.125 - - [20/Mar/2018:11:50:07 +0000] "GET /admin/manage_tool_dependencies HTTP/1.0" 200 - "http://52.54.147.188/admin" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:50:08 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin/manage_tool_dependencies" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,127 Using dependency prokka version 1.12 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,364 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,367 Dependency galaxy_sequence_utils not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,370 Using dependency vcflib version 586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,373 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,373 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,373 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,373 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,377 Using dependency fastx_toolkit version 0.0.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,380 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,380 Using dependency biopython version 1.61 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,382 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,382 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,386 Using dependency cutadapt version 1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,387 Using dependency fastqc version 0.11.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,387 Dependency amplicon_analysis_pipeline not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,387 Using dependency sickle version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,387 Using dependency bioawk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,387 Using dependency pandaseq version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,387 Using dependency spades version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,388 Using dependency qiime version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,388 Using dependency blast version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,388 Dependency fasta-splitter not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,388 Dependency rdp-classifier not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,388 Dependency r-base not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,388 Using dependency vsearch version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,388 Dependency microbiomeutil not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,388 Dependency fasta_number not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,392 Using dependency cd-hit-auxtools version 0.5-2012-03-07-fix-dan-gh-0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,395 Using dependency ucsc-fatotwobit version 324 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,399 Using dependency anaconda version 2.3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,408 Using dependency kraken version 0.10.6-eaf8fb68 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,409 Using dependency kraken version 0.10.6_eaf8fb68 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,417 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,417 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,424 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,425 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,434 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,434 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,434 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,445 Using dependency bwa version 0.5.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,453 Using dependency R version 3.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,454 Using dependency vegan version 2.3-0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,460 Using dependency mafft version 7.221 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,466 Dependency kraken not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,469 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,469 Dependency tabix not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,472 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,472 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,473 Using dependency kernlab version 0.1-4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,473 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,473 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,476 Using dependency unicycler version 0.4.4 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,479 Using dependency gatk version 1.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,479 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,483 Using dependency galaxy_sequence_utils version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,485 Using dependency R version 3.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,486 Using dependency deseq2 version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,486 Using dependency diffbind version 1.8.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,489 Using dependency snpEff version 4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,492 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,492 Using dependency limma version 3.25.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,492 Using dependency biopython version 1.65 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,495 Using dependency lastz version 1.02.00 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,498 Using dependency spades version 3.11.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,501 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,502 Dependency ucsc-fatotwobit not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,502 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,505 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,505 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,508 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,508 Using dependency RHmm version 1.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,512 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,512 Using dependency htslib version 1.3.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,512 Using dependency vcftools version 0.1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,515 Using dependency velvet version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,518 Using dependency snpEff version 4.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,521 Using dependency spades version 3.9.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,524 Using dependency galaxy_sequence_utils version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,527 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,527 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,530 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,533 Using dependency freebayes version 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,533 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,536 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,537 Dependency openbabel not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,540 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,543 Using dependency package_r_for_gatk_3_4_0 version 3.1.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,543 Using dependency gatk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,547 Dependency annovar not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,550 Using dependency sailfish version 0.7.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,553 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,553 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,556 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,556 Using dependency cummeRbund version 2.8.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,559 Dependency refseq_masher not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,562 Using dependency MINE version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,565 Using dependency freebayes version 0_9_20_b040236 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,566 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,568 Using dependency diamond version 0.6.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,572 Using dependency python version 2.7.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,572 Using dependency deeptools version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,575 Using dependency velvet version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,578 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,581 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,584 Using dependency blast version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,587 Using dependency prokka version 1.12 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,591 Using dependency macs version 1.3.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,591 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,592 Dependency rpy2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,595 Using dependency bamtools version 2.4.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,595 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,596 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,596 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,597 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,597 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,597 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,597 Using dependency bcftools version 1.5 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,600 Using dependency clustalw2 version 2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,601 Dependency gnuplot not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,604 Using dependency fontconfig version 2.11.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,604 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,604 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,607 Using dependency krona version 2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,610 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,613 Using dependency varscan version 2.3.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,616 Dependency deeptools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,619 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,620 Using dependency bioc_qvalue version 1.34.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,621 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,621 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,621 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,622 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,622 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,625 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,627 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,627 Dependency htslib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,631 Using dependency bwa version 0.7.15 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,631 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,631 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,632 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,632 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,635 Using dependency abyss version 2.0.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,638 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,641 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,641 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,644 Dependency biopython not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,647 Using dependency stringtie version 1.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,650 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,650 Using dependency bioc_hilbertvis version 1.18.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,653 Using dependency sra-tools version 2.8.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,656 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,656 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,659 Dependency quast not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,662 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,662 Using dependency tabix version 0.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,665 Using dependency htseq version 0.6.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,665 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,665 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,666 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,669 Using dependency bedtools version 2.22 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,672 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,675 Using dependency snippy version 3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,678 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,678 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,681 Using dependency FastQC version 0.11.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,684 Using dependency hisat version 2.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,687 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,687 Using dependency pyBamParser version 0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,687 Using dependency pyBamTools version 0.0.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,690 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,691 Dependency bowtie not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,696 Using dependency vsearch version 1.9.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,699 Using dependency pear version 0.9.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,701 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,701 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,701 Using dependency gawk version 4.1.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,701 Using dependency parallel version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,702 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,705 Using dependency blast+ version 2.2.28 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,705 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,705 Using dependency tophat2 version 2.0.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,708 Using dependency sputnik version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,711 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,714 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,715 Using dependency galaxy-ops version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,715 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,716 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,719 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,719 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,719 Using dependency yacca version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,719 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,723 Using dependency cutadapt version 1.8 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,723 Dependency cutadapt not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,726 Using dependency hisat version 2.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,726 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,726 Dependency hisat2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,727 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,730 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,733 Using dependency blast+ version 2.2.26+ of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,733 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,736 Using dependency imagemagick version 6.9.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,736 Using dependency meme version 4.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,739 Dependency perl not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,740 Dependency python not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,743 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,743 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,746 Using dependency trimmomatic version 0.32 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,749 Using dependency SICER version 1.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,750 Dependency gnuplot-py not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,752 Using dependency datamash version 1.0.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,756 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,759 Using dependency taxonomy version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,762 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,762 Using dependency gb_taxonomy version 8d245994d7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,765 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,768 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,769 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,769 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,770 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,771 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,775 Using dependency bowtie2 version 2.2.5 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,776 Using dependency tophat version 2.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,779 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,779 Using dependency gtools version 3.4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,782 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,783 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,786 Using dependency quasitools version 0.2.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,849 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,851 Dependency galaxy_sequence_utils not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,851 Using dependency vcflib version 586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,853 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,853 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,853 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,853 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,855 Using dependency fastx_toolkit version 0.0.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,856 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,856 Using dependency biopython version 1.61 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,858 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,858 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,861 Using dependency cutadapt version 1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,861 Using dependency fastqc version 0.11.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,861 Dependency amplicon_analysis_pipeline not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,861 Using dependency sickle version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,861 Using dependency bioawk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,861 Using dependency pandaseq version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,862 Using dependency spades version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,862 Using dependency qiime version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,862 Using dependency blast version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,862 Dependency fasta-splitter not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,862 Dependency rdp-classifier not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,862 Dependency r-base not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,862 Using dependency vsearch version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,862 Dependency microbiomeutil not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,862 Dependency fasta_number not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,864 Using dependency cd-hit-auxtools version 0.5-2012-03-07-fix-dan-gh-0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,866 Using dependency ucsc-fatotwobit version 324 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,867 Using dependency anaconda version 2.3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,869 Using dependency kraken version 0.10.6-eaf8fb68 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,869 Using dependency kraken version 0.10.6_eaf8fb68 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,871 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,871 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,872 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,872 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,874 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,874 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,874 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,876 Using dependency bwa version 0.5.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,877 Using dependency R version 3.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,877 Using dependency vegan version 2.3-0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,879 Using dependency mafft version 7.221 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,880 Dependency kraken not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,881 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,881 Dependency tabix not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,883 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,883 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,883 Using dependency kernlab version 0.1-4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,883 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,883 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,885 Using dependency unicycler version 0.4.4 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,887 Using dependency gatk version 1.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,887 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,888 Using dependency galaxy_sequence_utils version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,890 Using dependency R version 3.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,890 Using dependency deseq2 version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,890 Using dependency diffbind version 1.8.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,891 Using dependency snpEff version 4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,893 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,893 Using dependency limma version 3.25.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,893 Using dependency biopython version 1.65 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,894 Using dependency lastz version 1.02.00 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,896 Using dependency spades version 3.11.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,897 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,898 Dependency ucsc-fatotwobit not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,898 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,900 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,900 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,901 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,901 Using dependency RHmm version 1.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,903 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,903 Using dependency htslib version 1.3.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,903 Using dependency vcftools version 0.1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,905 Using dependency velvet version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,906 Using dependency snpEff version 4.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,907 Using dependency spades version 3.9.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,909 Using dependency galaxy_sequence_utils version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,912 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,912 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,913 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,914 Using dependency freebayes version 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,914 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,916 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,916 Dependency openbabel not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,918 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,919 Using dependency package_r_for_gatk_3_4_0 version 3.1.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,919 Using dependency gatk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,921 Dependency annovar not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,922 Using dependency sailfish version 0.7.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,924 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,924 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,925 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,925 Using dependency cummeRbund version 2.8.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,927 Dependency refseq_masher not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,928 Using dependency MINE version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,930 Using dependency freebayes version 0_9_20_b040236 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,930 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,931 Using dependency diamond version 0.6.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,933 Using dependency python version 2.7.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,933 Using dependency deeptools version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,934 Using dependency velvet version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,936 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,937 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,939 Using dependency blast version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,941 Using dependency prokka version 1.12 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,942 Using dependency macs version 1.3.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,942 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,943 Dependency rpy2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,945 Using dependency bamtools version 2.4.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,945 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,946 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,946 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,946 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,947 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,947 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,947 Using dependency bcftools version 1.5 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,949 Using dependency clustalw2 version 2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,949 Dependency gnuplot not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,951 Using dependency fontconfig version 2.11.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,951 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,951 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,952 Using dependency krona version 2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,954 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,955 Using dependency varscan version 2.3.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,957 Dependency deeptools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,958 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,958 Using dependency bioc_qvalue version 1.34.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,960 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,960 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,960 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,960 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,960 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,962 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,963 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,963 Dependency htslib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,965 Using dependency bwa version 0.7.15 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,965 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,966 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,966 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,966 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,968 Using dependency abyss version 2.0.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,969 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,971 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,971 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,972 Dependency biopython not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,974 Using dependency stringtie version 1.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,975 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,975 Using dependency bioc_hilbertvis version 1.18.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,976 Using dependency sra-tools version 2.8.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,978 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,978 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,979 Dependency quast not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,981 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,981 Using dependency tabix version 0.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,982 Using dependency htseq version 0.6.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,982 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,982 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,983 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,984 Using dependency bedtools version 2.22 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,986 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,987 Using dependency snippy version 3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,988 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,988 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,990 Using dependency FastQC version 0.11.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,992 Using dependency hisat version 2.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,994 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,994 Using dependency pyBamParser version 0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,994 Using dependency pyBamTools version 0.0.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,995 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,996 Dependency bowtie not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,998 Using dependency vsearch version 1.9.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:25,999 Using dependency pear version 0.9.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,001 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,001 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,001 Using dependency gawk version 4.1.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,001 Using dependency parallel version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,002 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,003 Using dependency blast+ version 2.2.28 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,003 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,003 Using dependency tophat2 version 2.0.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,005 Using dependency sputnik version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,006 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,008 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,008 Using dependency galaxy-ops version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,009 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,009 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,011 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,011 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,011 Using dependency yacca version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,011 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,013 Using dependency cutadapt version 1.8 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,013 Dependency cutadapt not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,015 Using dependency hisat version 2.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,015 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,015 Dependency hisat2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,015 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,017 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,018 Using dependency blast+ version 2.2.26+ of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,018 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,020 Using dependency imagemagick version 6.9.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,020 Using dependency meme version 4.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,022 Dependency perl not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,022 Dependency python not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,023 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,024 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,025 Using dependency trimmomatic version 0.32 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,026 Using dependency SICER version 1.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,027 Dependency gnuplot-py not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,028 Using dependency datamash version 1.0.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,030 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,031 Using dependency taxonomy version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,033 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,033 Using dependency gb_taxonomy version 8d245994d7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,035 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,036 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,038 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,038 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,038 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,039 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,041 Using dependency bowtie2 version 2.2.5 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,041 Using dependency tophat version 2.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,042 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,042 Using dependency gtools version 3.4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,047 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,050 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:26,052 Using dependency quasitools version 0.2.2 of type conda | |
| 94.125.130.125 - - [20/Mar/2018:11:50:25 +0000] "GET /admin/manage_tool_dependencies?selected_tool_ids=toolshed.g2.bx.psu.edu%2Frepos%2Fcrs4%2Fprokka%2Fprokka%2F1.12.0&install_dependencies=Install+checked+dependencies+using+Conda HTTP/1.0" 200 - "http://52.54.147.188/admin/manage_tool_dependencies" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:50:26 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin/manage_tool_dependencies?selected_tool_ids=toolshed.g2.bx.psu.edu%2Frepos%2Fcrs4%2Fprokka%2Fprokka%2F1.12.0&install_dependencies=Install+checked+dependencies+using+Conda" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 127.0.0.1 - - [20/Mar/2018:11:50:29 +0000] "GET / HTTP/1.1" 302 - "-" "Python-urllib/2.7" | |
| 127.0.0.1 - - [20/Mar/2018:11:50:29 +0000] "GET /root/login?redirect=%2F HTTP/1.1" 200 - "-" "Python-urllib/2.7" | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,719 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,722 Dependency galaxy_sequence_utils not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,725 Using dependency vcflib version 586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,728 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,728 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,728 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,728 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,731 Using dependency fastx_toolkit version 0.0.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,734 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,735 Using dependency biopython version 1.61 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,736 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,736 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,740 Using dependency cutadapt version 1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,741 Using dependency fastqc version 0.11.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,741 Dependency amplicon_analysis_pipeline not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,741 Using dependency sickle version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,741 Using dependency bioawk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,741 Using dependency pandaseq version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,741 Using dependency spades version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,742 Using dependency qiime version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,742 Using dependency blast version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,742 Dependency fasta-splitter not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,742 Dependency rdp-classifier not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,742 Dependency r-base not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,742 Using dependency vsearch version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,742 Dependency microbiomeutil not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,742 Dependency fasta_number not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,746 Using dependency cd-hit-auxtools version 0.5-2012-03-07-fix-dan-gh-0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,749 Using dependency ucsc-fatotwobit version 324 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,752 Using dependency anaconda version 2.3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,755 Using dependency kraken version 0.10.6-eaf8fb68 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,755 Using dependency kraken version 0.10.6_eaf8fb68 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,758 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,758 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,763 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,763 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,766 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,766 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,767 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,770 Using dependency bwa version 0.5.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,773 Using dependency R version 3.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,773 Using dependency vegan version 2.3-0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,776 Using dependency mafft version 7.221 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,778 Dependency kraken not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,781 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,782 Dependency tabix not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,785 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,785 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,785 Using dependency kernlab version 0.1-4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,785 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,785 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,788 Using dependency unicycler version 0.4.4 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,792 Using dependency gatk version 1.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,792 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,795 Using dependency galaxy_sequence_utils version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,798 Using dependency R version 3.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,798 Using dependency deseq2 version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,798 Using dependency diffbind version 1.8.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,801 Using dependency snpEff version 4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,804 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,804 Using dependency limma version 3.25.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,805 Using dependency biopython version 1.65 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,808 Using dependency lastz version 1.02.00 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,811 Using dependency spades version 3.11.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,815 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,816 Dependency ucsc-fatotwobit not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,816 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,819 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,819 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,823 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,823 Using dependency RHmm version 1.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,826 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,826 Using dependency htslib version 1.3.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,826 Using dependency vcftools version 0.1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,829 Using dependency velvet version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,832 Using dependency snpEff version 4.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,835 Using dependency spades version 3.9.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,838 Using dependency galaxy_sequence_utils version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,841 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,841 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,844 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,847 Using dependency freebayes version 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,847 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,851 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,852 Dependency openbabel not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,855 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,858 Using dependency package_r_for_gatk_3_4_0 version 3.1.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,858 Using dependency gatk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,861 Dependency annovar not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,864 Using dependency sailfish version 0.7.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,870 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,870 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,873 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,873 Using dependency cummeRbund version 2.8.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,876 Dependency refseq_masher not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,879 Using dependency MINE version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,883 Using dependency freebayes version 0_9_20_b040236 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,883 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,886 Using dependency diamond version 0.6.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,888 Using dependency python version 2.7.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,889 Using dependency deeptools version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,892 Using dependency velvet version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,895 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,898 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,901 Using dependency blast version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,904 Using dependency prokka version 1.12 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,907 Using dependency macs version 1.3.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,907 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,908 Dependency rpy2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,911 Using dependency bamtools version 2.4.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,911 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,913 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,913 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,913 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,913 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,914 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,914 Using dependency bcftools version 1.5 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,917 Using dependency clustalw2 version 2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,917 Dependency gnuplot not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,921 Using dependency fontconfig version 2.11.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,921 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,921 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,924 Using dependency krona version 2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,927 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,930 Using dependency varscan version 2.3.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,933 Dependency deeptools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,936 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,937 Using dependency bioc_qvalue version 1.34.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,938 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,938 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,938 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,938 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,938 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,942 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,944 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,944 Dependency htslib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,948 Using dependency bwa version 0.7.15 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,948 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,948 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,949 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,949 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,953 Using dependency abyss version 2.0.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,956 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,959 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,959 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,962 Dependency biopython not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,966 Using dependency stringtie version 1.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,969 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,969 Using dependency bioc_hilbertvis version 1.18.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,972 Using dependency sra-tools version 2.8.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,975 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,976 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,979 Dependency quast not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,982 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,982 Using dependency tabix version 0.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,985 Using dependency htseq version 0.6.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,985 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,985 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,985 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,988 Using dependency bedtools version 2.22 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,992 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,994 Using dependency snippy version 3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,997 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:39,998 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,001 Using dependency FastQC version 0.11.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,005 Using dependency hisat version 2.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,008 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,008 Using dependency pyBamParser version 0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,008 Using dependency pyBamTools version 0.0.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,011 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,012 Dependency bowtie not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,015 Using dependency vsearch version 1.9.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,018 Using dependency pear version 0.9.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,020 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,020 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,020 Using dependency gawk version 4.1.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,020 Using dependency parallel version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,021 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,026 Using dependency blast+ version 2.2.28 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,027 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,027 Using dependency tophat2 version 2.0.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,030 Using dependency sputnik version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,033 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,036 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,036 Using dependency galaxy-ops version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,037 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,037 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,040 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,040 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,040 Using dependency yacca version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,041 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,043 Using dependency cutadapt version 1.8 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,044 Dependency cutadapt not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,047 Using dependency hisat version 2.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,047 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,047 Dependency hisat2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,048 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,051 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,054 Using dependency blast+ version 2.2.26+ of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,054 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,057 Using dependency imagemagick version 6.9.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,058 Using dependency meme version 4.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,061 Dependency perl not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,061 Dependency python not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,064 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,064 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,067 Using dependency trimmomatic version 0.32 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,070 Using dependency SICER version 1.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,071 Dependency gnuplot-py not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,074 Using dependency datamash version 1.0.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,079 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,085 Using dependency taxonomy version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,088 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,088 Using dependency gb_taxonomy version 8d245994d7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,091 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,094 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,096 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,096 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,096 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,097 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,100 Using dependency bowtie2 version 2.2.5 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,100 Using dependency tophat version 2.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,103 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,103 Using dependency gtools version 3.4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,108 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,109 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,112 Using dependency quasitools version 0.2.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,164 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,166 Dependency galaxy_sequence_utils not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,167 Using dependency vcflib version 586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,168 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,168 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,169 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,169 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,171 Using dependency fastx_toolkit version 0.0.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,172 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,172 Using dependency biopython version 1.61 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,174 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,174 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,176 Using dependency cutadapt version 1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,177 Using dependency fastqc version 0.11.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,177 Dependency amplicon_analysis_pipeline not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,177 Using dependency sickle version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,177 Using dependency bioawk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,177 Using dependency pandaseq version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,177 Using dependency spades version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,177 Using dependency qiime version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,178 Using dependency blast version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,178 Dependency fasta-splitter not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,178 Dependency rdp-classifier not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,178 Dependency r-base not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,178 Using dependency vsearch version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,178 Dependency microbiomeutil not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,178 Dependency fasta_number not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,180 Using dependency cd-hit-auxtools version 0.5-2012-03-07-fix-dan-gh-0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,182 Using dependency ucsc-fatotwobit version 324 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,183 Using dependency anaconda version 2.3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,185 Using dependency kraken version 0.10.6-eaf8fb68 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,185 Using dependency kraken version 0.10.6_eaf8fb68 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,186 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,186 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,189 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,190 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,191 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,191 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,191 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,196 Using dependency bwa version 0.5.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,199 Using dependency R version 3.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,199 Using dependency vegan version 2.3-0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,201 Using dependency mafft version 7.221 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,202 Dependency kraken not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,203 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,203 Dependency tabix not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,205 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,205 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,205 Using dependency kernlab version 0.1-4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,205 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,205 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,207 Using dependency unicycler version 0.4.4 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,209 Using dependency gatk version 1.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,209 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,210 Using dependency galaxy_sequence_utils version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,212 Using dependency R version 3.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,212 Using dependency deseq2 version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,212 Using dependency diffbind version 1.8.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,214 Using dependency snpEff version 4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,215 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,215 Using dependency limma version 3.25.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,215 Using dependency biopython version 1.65 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,217 Using dependency lastz version 1.02.00 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,218 Using dependency spades version 3.11.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,220 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,220 Dependency ucsc-fatotwobit not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,220 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,222 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,222 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,223 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,223 Using dependency RHmm version 1.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,225 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,226 Using dependency htslib version 1.3.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,226 Using dependency vcftools version 0.1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,227 Using dependency velvet version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,228 Using dependency snpEff version 4.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,230 Using dependency spades version 3.9.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,231 Using dependency galaxy_sequence_utils version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,233 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,233 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,234 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,236 Using dependency freebayes version 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,236 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,237 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,237 Dependency openbabel not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,239 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,240 Using dependency package_r_for_gatk_3_4_0 version 3.1.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,240 Using dependency gatk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,242 Dependency annovar not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,243 Using dependency sailfish version 0.7.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,245 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,245 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,247 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,247 Using dependency cummeRbund version 2.8.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,248 Dependency refseq_masher not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,250 Using dependency MINE version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,252 Using dependency freebayes version 0_9_20_b040236 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,252 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,254 Using dependency diamond version 0.6.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,256 Using dependency python version 2.7.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,256 Using dependency deeptools version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,260 Using dependency velvet version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,266 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,272 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,277 Using dependency blast version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,281 Using dependency prokka version 1.12 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,288 Using dependency macs version 1.3.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,288 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,289 Dependency rpy2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,290 Using dependency bamtools version 2.4.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,290 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,292 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,292 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,292 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,292 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,293 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,293 Using dependency bcftools version 1.5 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,294 Using dependency clustalw2 version 2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,295 Dependency gnuplot not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,296 Using dependency fontconfig version 2.11.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,296 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,297 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,298 Using dependency krona version 2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,299 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,301 Using dependency varscan version 2.3.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,303 Dependency deeptools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,304 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,304 Using dependency bioc_qvalue version 1.34.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,306 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,306 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,306 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,306 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,306 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,308 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,309 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,309 Dependency htslib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,311 Using dependency bwa version 0.7.15 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,311 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,312 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,312 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,312 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,314 Using dependency abyss version 2.0.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,315 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,317 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,317 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,319 Dependency biopython not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,320 Using dependency stringtie version 1.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,322 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,322 Using dependency bioc_hilbertvis version 1.18.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,323 Using dependency sra-tools version 2.8.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,324 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,325 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,326 Dependency quast not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,328 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,328 Using dependency tabix version 0.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,329 Using dependency htseq version 0.6.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,329 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,329 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,329 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,331 Using dependency bedtools version 2.22 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,332 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,334 Using dependency snippy version 3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,335 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,335 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,337 Using dependency FastQC version 0.11.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,338 Using dependency hisat version 2.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,340 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,340 Using dependency pyBamParser version 0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,340 Using dependency pyBamTools version 0.0.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,342 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,342 Dependency bowtie not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,343 Using dependency vsearch version 1.9.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,345 Using dependency pear version 0.9.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,347 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,347 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,347 Using dependency gawk version 4.1.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,347 Using dependency parallel version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,347 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,349 Using dependency blast+ version 2.2.28 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,349 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,349 Using dependency tophat2 version 2.0.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,351 Using dependency sputnik version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,354 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,356 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,356 Using dependency galaxy-ops version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,357 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,357 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,358 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,359 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,359 Using dependency yacca version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,359 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,360 Using dependency cutadapt version 1.8 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,360 Dependency cutadapt not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,362 Using dependency hisat version 2.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,362 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,362 Dependency hisat2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,363 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,364 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,366 Using dependency blast+ version 2.2.26+ of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,366 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,367 Using dependency imagemagick version 6.9.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,367 Using dependency meme version 4.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,369 Dependency perl not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,369 Dependency python not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,371 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,371 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,372 Using dependency trimmomatic version 0.32 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,374 Using dependency SICER version 1.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,374 Dependency gnuplot-py not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,376 Using dependency datamash version 1.0.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,377 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,379 Using dependency taxonomy version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,380 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,381 Using dependency gb_taxonomy version 8d245994d7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,382 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,384 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,385 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,385 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,385 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,387 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,388 Using dependency bowtie2 version 2.2.5 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,388 Using dependency tophat version 2.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,390 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,390 Using dependency gtools version 3.4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,391 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,393 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:40,394 Using dependency quasitools version 0.2.2 of type conda | |
| 94.125.130.125 - - [20/Mar/2018:11:50:39 +0000] "GET /admin/manage_tool_dependencies?viewkey=Switch+to+tool-centric+view HTTP/1.0" 200 - "http://52.54.147.188/admin/manage_tool_dependencies?selected_tool_ids=toolshed.g2.bx.psu.edu%2Frepos%2Fcrs4%2Fprokka%2Fprokka%2F1.12.0&install_dependencies=Install+checked+dependencies+using+Conda" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| 94.125.130.125 - - [20/Mar/2018:11:50:41 +0000] "GET /api/webhooks/onload/all HTTP/1.0" 200 - "http://52.54.147.188/admin/manage_tool_dependencies?viewkey=Switch+to+tool-centric+view" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/64.0.3282.186 Safari/537.36" | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,279 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,283 Dependency galaxy_sequence_utils not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,285 Using dependency vcflib version 586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,288 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,288 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,288 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,289 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,292 Using dependency fastx_toolkit version 0.0.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,295 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,295 Using dependency biopython version 1.61 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,297 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,297 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,301 Using dependency cutadapt version 1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,301 Using dependency fastqc version 0.11.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,301 Dependency amplicon_analysis_pipeline not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,301 Using dependency sickle version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,302 Using dependency bioawk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,302 Using dependency pandaseq version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,302 Using dependency spades version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,302 Using dependency qiime version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,302 Using dependency blast version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,302 Dependency fasta-splitter not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,302 Dependency rdp-classifier not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,302 Dependency r-base not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,302 Using dependency vsearch version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,303 Dependency microbiomeutil not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,303 Dependency fasta_number not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,306 Using dependency cd-hit-auxtools version 0.5-2012-03-07-fix-dan-gh-0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,309 Using dependency ucsc-fatotwobit version 324 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,312 Using dependency anaconda version 2.3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,315 Using dependency kraken version 0.10.6-eaf8fb68 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,315 Using dependency kraken version 0.10.6_eaf8fb68 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,319 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,319 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,322 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,322 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,325 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,325 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,325 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,329 Using dependency bwa version 0.5.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,334 Using dependency R version 3.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,334 Using dependency vegan version 2.3-0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,341 Using dependency mafft version 7.221 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,350 Dependency kraken not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,353 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,354 Dependency tabix not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,357 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,357 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,357 Using dependency kernlab version 0.1-4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,357 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,357 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,360 Using dependency unicycler version 0.4.4 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,363 Using dependency gatk version 1.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,364 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,367 Using dependency galaxy_sequence_utils version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,370 Using dependency R version 3.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,370 Using dependency deseq2 version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,370 Using dependency diffbind version 1.8.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,373 Using dependency snpEff version 4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,376 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,376 Using dependency limma version 3.25.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,376 Using dependency biopython version 1.65 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,379 Using dependency lastz version 1.02.00 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,382 Using dependency spades version 3.11.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,387 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,388 Dependency ucsc-fatotwobit not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,388 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,391 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,391 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,394 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,394 Using dependency RHmm version 1.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,397 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,397 Using dependency htslib version 1.3.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,397 Using dependency vcftools version 0.1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,401 Using dependency velvet version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,403 Using dependency snpEff version 4.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,406 Using dependency spades version 3.9.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,409 Using dependency galaxy_sequence_utils version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,412 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,413 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,415 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,418 Using dependency freebayes version 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,418 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,421 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,422 Dependency openbabel not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,426 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,429 Using dependency package_r_for_gatk_3_4_0 version 3.1.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,429 Using dependency gatk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,432 Dependency annovar not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,435 Using dependency sailfish version 0.7.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,439 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,439 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,443 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,443 Using dependency cummeRbund version 2.8.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,446 Dependency refseq_masher not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,451 Using dependency MINE version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,454 Using dependency freebayes version 0_9_20_b040236 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,455 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,458 Using dependency diamond version 0.6.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,460 Using dependency python version 2.7.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,461 Using dependency deeptools version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,464 Using dependency velvet version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,467 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,470 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,473 Using dependency blast version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,476 Using dependency prokka version 1.12 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,479 Using dependency macs version 1.3.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,479 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,479 Dependency rpy2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,483 Using dependency bamtools version 2.4.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,483 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,484 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,484 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,484 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,484 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,485 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,485 Using dependency bcftools version 1.5 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,488 Using dependency clustalw2 version 2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,489 Dependency gnuplot not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,492 Using dependency fontconfig version 2.11.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,492 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,492 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,495 Using dependency krona version 2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,498 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,501 Using dependency varscan version 2.3.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,504 Dependency deeptools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,507 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,508 Using dependency bioc_qvalue version 1.34.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,509 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,509 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,509 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,509 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,509 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,513 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,515 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,516 Dependency htslib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,519 Using dependency bwa version 0.7.15 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,519 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,520 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,520 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,520 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,523 Using dependency abyss version 2.0.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,526 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,529 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,529 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,532 Dependency biopython not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,535 Using dependency stringtie version 1.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,538 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,538 Using dependency bioc_hilbertvis version 1.18.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,542 Using dependency sra-tools version 2.8.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,545 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,546 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,549 Dependency quast not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,552 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,552 Using dependency tabix version 0.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,555 Using dependency htseq version 0.6.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,555 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,555 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,555 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,558 Using dependency bedtools version 2.22 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,561 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,564 Using dependency snippy version 3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,567 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,568 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,577 Using dependency FastQC version 0.11.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,581 Using dependency hisat version 2.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,585 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,585 Using dependency pyBamParser version 0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,585 Using dependency pyBamTools version 0.0.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,590 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,591 Dependency bowtie not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,598 Using dependency vsearch version 1.9.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,601 Using dependency pear version 0.9.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,603 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,603 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,603 Using dependency gawk version 4.1.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,603 Using dependency parallel version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,604 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,607 Using dependency blast+ version 2.2.28 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,607 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,607 Using dependency tophat2 version 2.0.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,610 Using dependency sputnik version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,613 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,617 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,617 Using dependency galaxy-ops version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,618 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,618 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,621 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,621 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,621 Using dependency yacca version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,621 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,624 Using dependency cutadapt version 1.8 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,625 Dependency cutadapt not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,628 Using dependency hisat version 2.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,628 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,628 Dependency hisat2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,629 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,632 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,635 Using dependency blast+ version 2.2.26+ of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,635 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,638 Using dependency imagemagick version 6.9.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,638 Using dependency meme version 4.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,641 Dependency perl not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,641 Dependency python not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,649 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,649 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,657 Using dependency trimmomatic version 0.32 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,665 Using dependency SICER version 1.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,667 Dependency gnuplot-py not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,674 Using dependency datamash version 1.0.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,682 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,690 Using dependency taxonomy version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,697 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,698 Using dependency gb_taxonomy version 8d245994d7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,705 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,711 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,713 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,713 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,713 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,714 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,717 Using dependency bowtie2 version 2.2.5 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,718 Using dependency tophat version 2.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,720 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,720 Using dependency gtools version 3.4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,724 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,725 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,728 Using dependency quasitools version 0.2.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,848 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,853 Dependency galaxy_sequence_utils not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,857 Using dependency vcflib version 586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,861 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,861 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,864 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,864 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,868 Using dependency fastx_toolkit version 0.0.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,872 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,872 Using dependency biopython version 1.61 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,877 Using dependency picard version 1.136 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,877 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,882 Using dependency cutadapt version 1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,882 Using dependency fastqc version 0.11.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,883 Dependency amplicon_analysis_pipeline not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,883 Using dependency sickle version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,883 Using dependency bioawk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,883 Using dependency pandaseq version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,883 Using dependency spades version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,883 Using dependency qiime version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,883 Using dependency blast version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,884 Dependency fasta-splitter not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,884 Dependency rdp-classifier not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,884 Dependency r-base not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,884 Using dependency vsearch version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,884 Dependency microbiomeutil not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,884 Dependency fasta_number not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,888 Using dependency cd-hit-auxtools version 0.5-2012-03-07-fix-dan-gh-0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,890 Using dependency ucsc-fatotwobit version 324 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,893 Using dependency anaconda version 2.3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,895 Using dependency kraken version 0.10.6-eaf8fb68 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,895 Using dependency kraken version 0.10.6_eaf8fb68 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,896 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,896 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,898 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,898 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,900 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,900 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,900 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,902 Using dependency bwa version 0.5.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,904 Using dependency R version 3.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,904 Using dependency vegan version 2.3-0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,905 Using dependency mafft version 7.221 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,906 Dependency kraken not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,908 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,908 Dependency tabix not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,909 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,910 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,910 Using dependency kernlab version 0.1-4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,910 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,910 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,911 Using dependency unicycler version 0.4.4 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,913 Using dependency gatk version 1.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,913 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,915 Using dependency galaxy_sequence_utils version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,916 Using dependency R version 3.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,916 Using dependency deseq2 version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,916 Using dependency diffbind version 1.8.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,918 Using dependency snpEff version 4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,920 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,920 Using dependency limma version 3.25.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,921 Using dependency biopython version 1.65 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,922 Using dependency lastz version 1.02.00 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,923 Using dependency spades version 3.11.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,925 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,926 Dependency ucsc-fatotwobit not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,926 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,927 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,927 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,929 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,929 Using dependency RHmm version 1.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,931 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,931 Using dependency htslib version 1.3.2 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,931 Using dependency vcftools version 0.1.11 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,932 Using dependency velvet version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,934 Using dependency snpEff version 4.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,935 Using dependency spades version 3.9.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,937 Using dependency galaxy_sequence_utils version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,938 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,938 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,939 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,941 Using dependency freebayes version 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,941 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,942 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,943 Dependency openbabel not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,946 Using dependency bamtools version 2.3.0_2d7685d2ae of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,949 Using dependency package_r_for_gatk_3_4_0 version 3.1.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,950 Using dependency gatk version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,951 Dependency annovar not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,953 Using dependency sailfish version 0.7.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,954 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,954 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,956 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,956 Using dependency cummeRbund version 2.8.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,958 Dependency refseq_masher not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,959 Using dependency MINE version 1.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,961 Using dependency freebayes version 0_9_20_b040236 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,961 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,962 Using dependency diamond version 0.6.13 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,963 Using dependency python version 2.7.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,963 Using dependency deeptools version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,965 Using dependency velvet version 1.2.10 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,966 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,968 Using dependency samtools version 0.1.16 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,969 Using dependency blast version 2.5.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,971 Using dependency prokka version 1.12 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,972 Using dependency macs version 1.3.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,972 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,973 Dependency rpy2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,975 Using dependency bamtools version 2.4.0 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,975 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,976 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,976 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,976 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,976 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,977 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,977 Using dependency bcftools version 1.5 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,979 Using dependency clustalw2 version 2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,979 Dependency gnuplot not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,980 Using dependency fontconfig version 2.11.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,981 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,981 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,982 Using dependency krona version 2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,984 Using dependency cufflinks version 2.2.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,985 Using dependency varscan version 2.3.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,987 Dependency deeptools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,988 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,988 Using dependency bioc_qvalue version 1.34.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,990 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,990 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,990 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,990 Using dependency R version 3.1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,990 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,992 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,993 Dependency vcflib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,993 Dependency htslib not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,995 Using dependency bwa version 0.7.15 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,995 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,996 Using dependency samtools version 1.3.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,996 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,996 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,997 Using dependency abyss version 2.0.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:48,999 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,001 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,001 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,002 Dependency biopython not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,005 Using dependency stringtie version 1.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,009 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,009 Using dependency bioc_hilbertvis version 1.18.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,010 Using dependency sra-tools version 2.8.1 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,012 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,012 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,013 Dependency quast not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,015 Using dependency vcflib version 8a5602bf07 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,015 Using dependency tabix version 0.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,016 Using dependency htseq version 0.6.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,016 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,017 Using dependency samtools version 0.1.19 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,017 Using dependency pysam version 0.7.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,018 Using dependency bedtools version 2.22 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,020 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,021 Using dependency snippy version 3.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,022 Using dependency bwa version 0.7.12 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,023 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,024 Using dependency FastQC version 0.11.4 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,026 Using dependency hisat version 2.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,027 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,027 Using dependency pyBamParser version 0.0.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,027 Using dependency pyBamTools version 0.0.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,029 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,029 Dependency bowtie not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,031 Using dependency vsearch version 1.9.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,032 Using dependency pear version 0.9.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,034 Using dependency freebayes version 1.1.0.46 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,034 Using dependency samtools version 0.1.19 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,034 Using dependency gawk version 4.1.3 of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,034 Using dependency parallel version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,035 Using dependency samtools version None of type conda | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,036 Using dependency blast+ version 2.2.28 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,036 Using dependency bowtie version 0.12.7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,036 Using dependency tophat2 version 2.0.9 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,038 Using dependency sputnik version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,039 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,041 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,041 Using dependency galaxy-ops version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,042 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,042 Dependency bedtools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,044 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,044 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,044 Using dependency yacca version 1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,044 Using dependency rpy version 1.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,045 Using dependency cutadapt version 1.8 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,045 Dependency cutadapt not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,047 Using dependency hisat version 2.0.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,047 Using dependency samtools version 1.2 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,047 Dependency hisat2 not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,048 Dependency ucsc_tools not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,049 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,053 Using dependency blast+ version 2.2.26+ of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,053 Using dependency bx-python version 0.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,054 Using dependency imagemagick version 6.9.3 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,054 Using dependency meme version 4.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,056 Dependency perl not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,057 Dependency python not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,058 Using dependency samtools version 0.1.18 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,058 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,060 Using dependency trimmomatic version 0.32 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,062 Using dependency SICER version 1.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,062 Dependency gnuplot-py not found. | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,064 Using dependency datamash version 1.0.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,065 Using dependency vcftools version 0.1.11 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,067 Using dependency taxonomy version 1.0.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,068 Using dependency gnu_awk version 4.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,068 Using dependency gb_taxonomy version 8d245994d7 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,070 Using dependency bowtie2 version 2.2.6 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,071 Using dependency picard version 1.56.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,073 Using dependency macs2 version 2.1.0.20151222 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,073 Using dependency numpy version 1.7.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,073 Using dependency scipy version 0.12.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,074 Using dependency bedtools version 2.24 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,076 Using dependency bowtie2 version 2.2.5 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,076 Using dependency tophat version 2.1.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,077 Using dependency R version 2.15.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,077 Using dependency gtools version 3.4.1 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,079 Using dependency R version 2.11.0 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,080 Using dependency glimmer version 3.02b of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-20 11:50:49,082 Using |
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