Created
May 7, 2020 10:15
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Initial issues with kombu on certain uwsgi processes that might explain lack of later tool sync
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| Wed May 6 22:55:43 2020 - *** Starting uWSGI 2.0.18 (64bit) on [Wed May 6 22:55:43 2020] *** | |
| Wed May 6 22:55:43 2020 - compiled with version: 8.2.1 20180905 (Red Hat 8.2.1-3) on 17 April 2019 16:51:59 | |
| Wed May 6 22:55:43 2020 - os: Linux-3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 | |
| Wed May 6 22:55:43 2020 - nodename: ******** | |
| Wed May 6 22:55:43 2020 - machine: x86_64 | |
| Wed May 6 22:55:43 2020 - clock source: unix | |
| Wed May 6 22:55:43 2020 - pcre jit disabled | |
| Wed May 6 22:55:43 2020 - detected number of CPU cores: 32 | |
| Wed May 6 22:55:43 2020 - current working directory: *******/galaxy/server/galaxy-20.01 | |
| Wed May 6 22:55:43 2020 - detected binary path: /usr/bin/python3.6 | |
| Wed May 6 22:55:43 2020 - writing pidfile to *******/galaxy/server/galaxy-20.01/galaxy_web.pid | |
| Wed May 6 22:55:43 2020 - your processes number limit is 65535 | |
| Wed May 6 22:55:43 2020 - your memory page size is 4096 bytes | |
| Wed May 6 22:55:43 2020 - detected max file descriptor number: 65535 | |
| Wed May 6 22:55:43 2020 - building mime-types dictionary from file /etc/mime.types...Wed May 6 22:55:43 2020 - 1060 entry found | |
| Wed May 6 22:55:43 2020 - lock engine: pthread robust mutexes | |
| Wed May 6 22:55:43 2020 - thunder lock: enabled | |
| Wed May 6 22:55:43 2020 - uwsgi socket 0 bound to UNIX address /tmp/galaxy_gxa_uwsgi.sock fd 3 | |
| Wed May 6 22:55:43 2020 - Python version: 3.6.8 (default, Apr 2 2020, 13:34:55) [GCC 4.8.5 20150623 (Red Hat 4.8.5-39)] | |
| Wed May 6 22:55:43 2020 - --- Python VM already initialized --- | |
| Wed May 6 22:55:43 2020 - Python main interpreter initialized at 0x1aaa700 | |
| Wed May 6 22:55:43 2020 - python threads support enabled | |
| Wed May 6 22:55:43 2020 - your server socket listen backlog is limited to 100 connections | |
| Wed May 6 22:55:43 2020 - your mercy for graceful operations on workers is 60 seconds | |
| Wed May 6 22:55:43 2020 - mapped 425960 bytes (415 KB) for 4 cores | |
| Wed May 6 22:55:43 2020 - *** Operational MODE: preforking *** | |
| Wed May 6 22:55:43 2020 - added lib/ to pythonpath. | |
| Wed May 6 22:55:43 2020 - added lib/ to pythonpath. | |
| DEBUG:galaxy.app:python path is: lib/, lib/, ., , *******/galaxy/server/venv_20.01/bin, /usr/lib64/python36.zip, /usr/lib64/python3.6, /usr/lib64/python3.6/lib-dynload, *******/galaxy/server/venv_20.01/lib64/python3.6/site-packages, *******/galaxy/server/venv_20.01/lib/python3.6/site-packages | |
| WARNING:galaxy.config:No Galaxy config file found, running from current working directory: *******/galaxy/server/galaxy-20.01 | |
| DEBUG:galaxy.config:Configuration directory is *******/galaxy/server/galaxy-20.01/config | |
| DEBUG:galaxy.config:Data directory is *******/galaxy/server/galaxy-20.01/database | |
| DEBUG:galaxy.config:Mutable config directory is *******/galaxy/server/galaxy-20.01/config | |
| DEBUG:galaxy.containers:config file '*******/galaxy/server/galaxy-20.01/config/containers_conf.yml' does not exist, running with default config | |
| galaxy.web_stack DEBUG 2020-05-06 22:55:55,160 [p:23723,w:0,m:0] [MainThread] UWSGIApplicationStack initialized | |
| galaxy.queue_worker INFO 2020-05-06 22:55:55,160 [p:23723,w:0,m:0] [MainThread] Initializing main Galaxy Queue Worker on sqlalchemy+postgresql://galaxy:********@******/galaxydev?client_encoding=utf8 | |
| galaxy.tool_shed.tool_shed_registry DEBUG 2020-05-06 22:55:55,192 [p:23723,w:0,m:0] [MainThread] Loading references to tool sheds from *******/galaxy/server/galaxy-20.01/config/tool_sheds_conf.xml.sample | |
| galaxy.tool_shed.tool_shed_registry DEBUG 2020-05-06 22:55:55,192 [p:23723,w:0,m:0] [MainThread] Loaded reference to tool shed: Galaxy Main Tool Shed | |
| migrate.versioning.repository DEBUG 2020-05-06 22:55:55,264 [p:23723,w:0,m:0] [MainThread] Loading repository lib/galaxy/model/migrate... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,265 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,265 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,265 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,266 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,266 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,266 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,266 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,266 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,266 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,266 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,266 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,266 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,266 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,266 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,267 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,267 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,267 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0009_request_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,267 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,267 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,267 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,267 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,267 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,267 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0012_user_address.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,267 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,267 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,267 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,268 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0014_pages.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,268 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,268 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0015_tagging.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,268 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,268 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,268 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,268 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,268 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,268 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,268 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,268 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,269 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0019_request_library_folder.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,269 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0020_library_upload_job.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,269 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0020_library_upload_job.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,269 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0021_user_prefs.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,269 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0021_user_prefs.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,270 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0022_visualization_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,270 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0022_visualization_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,270 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,270 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,270 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,271 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,271 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0025_user_info.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,271 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0025_user_info.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,271 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0026_cloud_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,271 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0026_cloud_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,271 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0027_request_events.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,272 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0027_request_events.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,272 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,272 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,272 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0029_user_actions.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,272 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0029_user_actions.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,273 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0030_history_slug_column.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,273 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0030_history_slug_column.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,273 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,273 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,273 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,273 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,274 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,274 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,274 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0034_page_user_share_association.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,274 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0034_page_user_share_association.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,274 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,275 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,275 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,275 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,275 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0037_samples_library.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,275 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0037_samples_library.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,276 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,276 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,276 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,276 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,276 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0040_page_annotations.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,277 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0040_page_annotations.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,277 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0041_workflow_invocation.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,277 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0041_workflow_invocation.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,277 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,277 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,277 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,278 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,278 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,278 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,278 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,278 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,278 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0046_post_job_actions.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,279 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0046_post_job_actions.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,279 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,279 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,279 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,279 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,280 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0049_api_keys_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,280 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0049_api_keys_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,280 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,280 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,281 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,281 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,281 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,281 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,281 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0053_item_ratings.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,282 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0053_item_ratings.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,282 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,282 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,282 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,282 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,282 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0056_workflow_outputs.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,283 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0056_workflow_outputs.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,283 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0057_request_notify.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,283 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0057_request_notify.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,283 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0058_history_import_export.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,283 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0058_history_import_export.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,283 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,284 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,284 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0060_history_archive_import.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,284 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0060_history_archive_import.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,284 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0061_tasks.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,284 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0061_tasks.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,284 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0062_user_openid_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,285 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0062_user_openid_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,285 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0063_sequencer_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,285 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0063_sequencer_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,285 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,286 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,286 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,286 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,286 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,286 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,286 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,287 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,287 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,287 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,287 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,288 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,288 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,288 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,288 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,288 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,289 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,289 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,289 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,289 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,290 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,290 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,290 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,290 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,290 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,291 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,291 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,291 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,291 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,291 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,291 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,292 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,292 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0080_quota_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,292 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0080_quota_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,292 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,293 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,293 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,293 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,293 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,293 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,293 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,294 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,294 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0085_add_task_info.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,294 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0085_add_task_info.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,294 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,294 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,294 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,294 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,295 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,295 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,295 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,295 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,295 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,295 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,295 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,295 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,295 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,295 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,296 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0093_add_job_params_col.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,296 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0093_add_job_params_col.py loaded successfully | |
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| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,296 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,296 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0095_hda_subsets.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,297 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0095_hda_subsets.py loaded successfully | |
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| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,297 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py loaded successfully | |
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| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,298 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py loaded successfully | |
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| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,298 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,298 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,298 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,298 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,298 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,298 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,298 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,298 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,299 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,299 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,299 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,299 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,299 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,299 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,299 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,300 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,300 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,300 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,300 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,301 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,301 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,301 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,301 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,301 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,301 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,302 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,302 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,302 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,302 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,302 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,302 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,303 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,303 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,303 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,303 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,303 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,303 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,303 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,304 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0119_job_metrics.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,304 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0119_job_metrics.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,304 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0120_dataset_collections.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,304 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0120_dataset_collections.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,304 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,305 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,305 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,305 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,305 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,305 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,306 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,306 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,306 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,306 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,307 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,307 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,307 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,307 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,307 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,308 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,308 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,308 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,308 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,308 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,308 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,309 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,309 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,309 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,309 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,310 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,310 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,310 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,310 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0135_add_library_tags.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,310 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0135_add_library_tags.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,310 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,311 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,311 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,311 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,311 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0138_add_hda_version.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,312 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0138_add_hda_version.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,312 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,312 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,312 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,312 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,312 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,313 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,313 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,313 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,313 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,313 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py loaded successfully | |
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| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,314 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,314 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,314 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py loaded successfully | |
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| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,315 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0147_job_messages.py loaded successfully | |
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| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,316 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0151_add_worker_process.py... | |
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| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,317 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0152_add_metadata_file_uuid.py loaded successfully | |
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| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,318 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0156_add_interactivetools.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,319 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0156_add_interactivetools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,319 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0157_rework_dataset_validation.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,319 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0157_rework_dataset_validation.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,319 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0158_workflow_reports.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,319 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0158_workflow_reports.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,320 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0159_add_job_external_id_index.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,320 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0159_add_job_external_id_index.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,320 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0160_hda_set_deleted_if_purged_again.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,320 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0160_hda_set_deleted_if_purged_again.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,320 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0161_add_workflow_invocation_output_table.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,321 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0161_add_workflow_invocation_output_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,321 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0162_job_only_pjas.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,321 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0162_job_only_pjas.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,321 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0163_worker_process_pid.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,321 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0163_worker_process_pid.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,321 [p:23723,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0164_page_format.py... | |
| migrate.versioning.script.base DEBUG 2020-05-06 22:55:55,322 [p:23723,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0164_page_format.py loaded successfully | |
| migrate.versioning.repository DEBUG 2020-05-06 22:55:55,322 [p:23723,w:0,m:0] [MainThread] Repository lib/galaxy/model/migrate loaded successfully | |
| migrate.versioning.repository DEBUG 2020-05-06 22:55:55,322 [p:23723,w:0,m:0] [MainThread] Config: OrderedDict([('db_settings', OrderedDict([('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) | |
| galaxy.model.migrate.check INFO 2020-05-06 22:55:55,694 [p:23723,w:0,m:0] [MainThread] At database version 164 | |
| galaxy.config INFO 2020-05-06 22:55:55,696 [p:23723,w:0,m:0] [MainThread] Install database targetting Galaxy's database configuration. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,753 [p:23723,w:0,m:0] [MainThread] Loading datatypes from *******/galaxy/server/galaxy-20.01/config/datatypes_conf.xml.sample | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,753 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,760 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,772 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,772 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,772 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,772 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioContigsDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,772 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,773 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioGenomesDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,773 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioPanDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,773 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,773 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioProfileDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,773 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioSamplesDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,773 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,773 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioStructureDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,774 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,774 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,774 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:Paf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,774 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,774 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,774 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,774 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,775 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,775 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,775 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,775 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:BamInputSorted from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,775 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:BamQuerynameSorted from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,775 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:BamNative from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,775 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:ProBam from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,775 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,775 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,776 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,776 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,776 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,776 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,776 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:ProBed from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,791 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,792 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:DAA from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,792 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:RMA6 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,792 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:DMND from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,792 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Idat from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,792 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,792 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,792 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,792 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,793 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,793 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,793 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,793 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,799 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,799 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,799 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,799 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,799 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,799 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,800 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:ImgtJson from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,800 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:GeoJson from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,800 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,800 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,800 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,800 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,800 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastg from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,801 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,801 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,801 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,802 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,802 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,802 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,802 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,802 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,803 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,803 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,803 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,803 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,803 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,803 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,804 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,804 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,804 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,804 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Loom from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,804 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Anndata from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,804 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,804 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,805 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,805 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Cool from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,805 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:MCool from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,805 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:55,805 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,329 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaTab from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,330 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaJson from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,330 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,330 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,330 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,331 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,331 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,331 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,331 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,331 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,332 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,332 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,332 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,332 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,332 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,333 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,333 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,333 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,333 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,333 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,334 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,334 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,334 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,334 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,334 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,334 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,334 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,335 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,335 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,335 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,335 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,335 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,335 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,335 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,335 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,336 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,336 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,336 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,336 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,339 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,340 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,340 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,340 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,340 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,340 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,341 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,341 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,341 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,341 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,341 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,341 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,342 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,342 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,342 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:BafTar from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,342 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:YepTar from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,342 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:TdfTar from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,342 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:MassHunterTar from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,342 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:MassLynxTar from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,343 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:WiffTar from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,343 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,343 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:NmrML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,343 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,343 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,343 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,343 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,343 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,344 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,344 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,344 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,344 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,344 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,344 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,344 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,344 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,345 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,345 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:BlibSQlite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,345 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:DlibSQlite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,345 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:ElibSQlite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,345 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,345 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,345 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,345 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,346 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,346 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:PostgresqlArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,346 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,346 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,346 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,346 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,347 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,347 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,347 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,347 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,347 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,348 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,348 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Analyze75 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,348 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,348 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,348 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,349 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,349 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,349 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,349 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,349 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,349 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,349 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:MatrixMarket from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,349 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,350 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,350 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,350 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,350 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,350 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,350 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,350 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,351 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,351 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,351 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,351 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,351 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,351 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,351 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,359 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.gis:Shapefile from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,359 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,360 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,360 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,360 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,360 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,360 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,360 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,361 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,361 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,361 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,361 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,361 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,362 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,362 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:CuffDiffSQlite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,362 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:GAFASQLite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,362 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,362 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,362 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,362 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,363 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,363 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,363 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,363 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,363 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,363 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,363 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,364 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,364 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,364 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,364 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,364 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,365 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,365 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,365 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,365 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,365 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,366 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,366 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,366 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,366 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,366 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,366 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,367 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:IQTree from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,378 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,386 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,386 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,386 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,386 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,386 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,387 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,387 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,387 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,387 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,387 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,387 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,388 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,388 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,388 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,388 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,388 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,388 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,388 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,388 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,389 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,389 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:ExpressionJson from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,401 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,401 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,413 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,414 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,414 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,414 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,414 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,414 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,414 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,414 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,415 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,415 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,415 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,415 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,415 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,416 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,416 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,416 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,416 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,416 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,416 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,417 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,417 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,417 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,417 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,417 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,418 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,418 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,418 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,418 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,418 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,419 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,419 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,419 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,419 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,419 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,420 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,420 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,420 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,420 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,420 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,420 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,421 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,421 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,421 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,421 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,422 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,422 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,422 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,422 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,422 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,422 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,423 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,423 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,423 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,423 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,423 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,424 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,424 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,424 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,424 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,424 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,425 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,425 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,425 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,425 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,425 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,426 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,426 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,426 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,426 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,426 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,427 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,427 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,427 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,427 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,427 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,427 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,428 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,428 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,428 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,428 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,429 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,429 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,429 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,429 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,429 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,429 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,430 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,430 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,430 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,439 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.phylip:Phylip from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,439 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,439 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,439 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,439 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,440 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,440 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,440 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,440 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,441 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,441 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,441 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,441 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,441 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,447 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,447 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,447 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:ICM from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,464 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.msa:InfernalCM from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,465 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,465 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,465 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,465 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,470 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Cel from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,471 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gpr from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,471 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gal from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,471 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,471 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,471 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,471 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,472 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,472 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,472 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,472 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,472 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,475 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,475 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,475 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,475 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,475 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,476 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,476 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,476 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:MashSketch from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,476 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,485 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,485 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,485 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,485 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,485 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,485 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,486 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,486 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,486 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,486 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,486 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,486 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,486 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:PQR from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,486 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Trr from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,487 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Dcd from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,487 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,487 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,487 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,487 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,488 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,488 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Xtc from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,488 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Cpt from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,488 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Edr from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,488 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,489 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Vel from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,489 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,489 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,489 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,489 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,489 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,489 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,490 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,490 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,490 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,490 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,490 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,491 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,491 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,491 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,491 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,491 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,491 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,492 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,492 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,492 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,492 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,492 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,492 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,492 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,493 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,493 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,493 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,493 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,493 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,494 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,494 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,494 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,494 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,494 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,494 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,495 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,495 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,495 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,495 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,502 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,502 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDBzip from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,503 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,508 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,508 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,508 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,509 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,509 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,509 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,509 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,515 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,515 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,515 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenotypeMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,515 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,515 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,516 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,516 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,516 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:DataIn from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,516 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:MarkerMap from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,517 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,517 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,517 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:AllegroLOD from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,517 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.genetics:IdeasPre from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,517 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.xml:Sbml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,526 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnNuclDb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,526 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnProtDb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,527 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,527 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,527 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,527 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,527 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,528 [p:23723,w:0,m:0] [MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,528 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,528 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,528 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,528 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,528 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,529 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,529 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,529 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,529 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,529 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,529 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,529 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,529 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,529 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,529 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,530 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,530 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,530 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,530 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,530 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,530 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,530 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,530 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,530 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,530 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,531 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ElibSQlite' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,531 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DlibSQlite' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,531 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BlibSQlite' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,531 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CuffDiffSQlite' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,531 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GAFASQLite' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,531 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,531 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cool' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,531 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MCool' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,532 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Loom' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,532 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Anndata' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,532 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,532 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,532 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,532 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamQuerynameSorted' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,532 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamNative' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,532 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,532 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,533 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,533 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,533 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DAA' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,533 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RMA6' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,533 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,533 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BafTar' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,533 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TdfTar' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,533 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassHunterTar' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,533 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassLynxTar' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,534 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:YepTar' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,534 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:WiffTar' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,534 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,534 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,534 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,534 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PostgresqlArchive' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,534 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ICM' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,534 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Idat' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,534 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Trr' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,535 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Dcd' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,535 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xtc' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,535 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cpt' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,535 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Edr' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,535 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Vel' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,535 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,535 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,535 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,535 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,536 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,536 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Sbml' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,536 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,536 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:NmrML' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,536 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,536 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,536 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,536 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,537 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,537 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,537 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,537 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,537 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,537 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,537 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,537 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,538 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,538 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,538 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,538 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,538 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,538 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,538 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,538 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,539 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,539 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,539 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastg' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,539 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,539 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,539 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,539 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,539 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,540 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,540 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,540 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,540 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PQR' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,540 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.phylip:Phylip' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,540 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,540 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqCSSanger' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,540 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,541 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,541 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,541 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Html' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,541 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,541 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,541 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,541 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,542 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,542 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,542 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,542 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,542 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,542 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Paf' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,542 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,542 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,543 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,543 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,543 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:IQTree' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,543 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,543 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,543 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,543 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,544 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:ImgtJson' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,544 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:GeoJson' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,544 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Json' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,544 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:GenotypeMatrix' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,544 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:DataIn' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,544 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:MarkerMap' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,545 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:AllegroLOD' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,545 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,545 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,545 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,545 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,545 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,546 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:MatrixMarket' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,546 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,546 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,546 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,546 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,546 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:InfernalCM' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,546 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,547 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Cel' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,547 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gpr' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,547 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gal' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,547 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,547 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,547 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Png' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,547 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,548 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,548 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,548 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Im' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,548 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,548 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,548 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,548 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,549 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,549 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,549 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,549 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,549 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,549 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,549 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,550 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,550 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,550 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,550 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,550 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,550 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,551 [p:23723,w:0,m:0] [MainThread] Loaded sniffer for datatype 'galaxy.datatypes.neo4j:Neo4jDBzip' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,561 [p:23723,w:0,m:0] [MainThread] Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,562 [p:23723,w:0,m:0] [MainThread] Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,564 [p:23723,w:0,m:0] [MainThread] Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'] | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,565 [p:23723,w:0,m:0] [MainThread] Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,565 [p:23723,w:0,m:0] [MainThread] Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,566 [p:23723,w:0,m:0] [MainThread] Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,566 [p:23723,w:0,m:0] [MainThread] Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,568 [p:23723,w:0,m:0] [MainThread] Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:55:56,568 [p:23723,w:0,m:0] [MainThread] Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,593 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/all_fasta.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,594 [p:23723,w:0,m:0] [MainThread] Loaded 0 lines from '*******/galaxy/server/galaxy-20.01/tool-data/all_fasta.loc.sample' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,595 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'all_fasta' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,595 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/bfast_indexes.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,596 [p:23723,w:0,m:0] [MainThread] Loaded 0 lines from '*******/galaxy/server/galaxy-20.01/tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,596 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'bfast_indexes' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,597 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/blastdb.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,598 [p:23723,w:0,m:0] [MainThread] Loaded 0 lines from '*******/galaxy/server/galaxy-20.01/tool-data/blastdb.loc.sample' for 'blastdb' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,598 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'blastdb' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,599 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/blastdb_p.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,599 [p:23723,w:0,m:0] [MainThread] Loaded 0 lines from '*******/galaxy/server/galaxy-20.01/tool-data/blastdb_p.loc.sample' for 'blastdb_p' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,599 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'blastdb_p' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,600 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/blastdb_d.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,601 [p:23723,w:0,m:0] [MainThread] Loaded 0 lines from '*******/galaxy/server/galaxy-20.01/tool-data/blastdb_d.loc.sample' for 'blastdb_d' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,601 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'blastdb_d' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data WARNING 2020-05-06 22:55:56,602 [p:23723,w:0,m:0] [MainThread] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,602 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'bwa_indexes' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data WARNING 2020-05-06 22:55:56,603 [p:23723,w:0,m:0] [MainThread] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,603 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'bwa_indexes_color' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,604 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/maf_index.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,605 [p:23723,w:0,m:0] [MainThread] Loaded 0 lines from '*******/galaxy/server/galaxy-20.01/tool-data/maf_index.loc.sample' for 'indexed_maf_files' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,605 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'indexed_maf_files' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,606 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/ngs_sim_fasta.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,606 [p:23723,w:0,m:0] [MainThread] Loaded 0 lines from '*******/galaxy/server/galaxy-20.01/tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,607 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'ngs_sim_fasta' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,607 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/perm_base_index.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,608 [p:23723,w:0,m:0] [MainThread] Loaded 0 lines from '*******/galaxy/server/galaxy-20.01/tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,608 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'perm_base_indexes' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,609 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/perm_color_index.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,610 [p:23723,w:0,m:0] [MainThread] Loaded 0 lines from '*******/galaxy/server/galaxy-20.01/tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,610 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'perm_color_indexes' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,611 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/picard_index.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,611 [p:23723,w:0,m:0] [MainThread] Loaded 0 lines from '*******/galaxy/server/galaxy-20.01/tool-data/picard_index.loc.sample' for 'picard_indexes' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,611 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'picard_indexes' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,612 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/picard_index.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,612 [p:23723,w:0,m:0] [MainThread] Loaded 0 lines from '*******/galaxy/server/galaxy-20.01/tool-data/picard_index.loc.sample' for 'srma_indexes' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,613 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'srma_indexes' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,613 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/mosaik_index.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,614 [p:23723,w:0,m:0] [MainThread] Loaded 0 lines from '*******/galaxy/server/galaxy-20.01/tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,614 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'mosaik_indexes' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,615 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/twobit.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,616 [p:23723,w:0,m:0] [MainThread] Loaded 0 lines from '*******/galaxy/server/galaxy-20.01/tool-data/twobit.loc.sample' for 'twobit' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,616 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'twobit' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| urllib3.connectionpool DEBUG 2020-05-06 22:55:56,623 [p:23723,w:0,m:0] [MainThread] Starting new HTTP connection (1): igv.broadinstitute.org:80 | |
| urllib3.connectionpool DEBUG 2020-05-06 22:55:56,887 [p:23723,w:0,m:0] [MainThread] http://igv.broadinstitute.org:80 "GET /genomes/genomes.txt HTTP/1.1" 200 15787 | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,965 [p:23723,w:0,m:0] [MainThread] Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "*******/galaxy/shared/galaxy_wd/tmp/TTDT_URL_igv_broad_genomes-baambrzz". | |
| galaxy.tools.data WARNING 2020-05-06 22:55:56,967 [p:23723,w:0,m:0] [MainThread] Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields): | |
| <Server-Side Genome List> | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,970 [p:23723,w:0,m:0] [MainThread] Loaded 156 lines from '*******/galaxy/shared/galaxy_wd/tmp/TTDT_URL_igv_broad_genomes-baambrzz' for 'igv_broad_genomes' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,971 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'igv_broad_genomes' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,972 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/liftOver.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,973 [p:23723,w:0,m:0] [MainThread] Loaded 0 lines from '*******/galaxy/server/galaxy-20.01/tool-data/liftOver.loc.sample' for 'liftOver' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,973 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'liftOver' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,974 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/bam_iobio.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,975 [p:23723,w:0,m:0] [MainThread] Loaded 1 lines from '*******/galaxy/server/galaxy-20.01/tool-data/bam_iobio.loc.sample' for 'bam_iobio' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,976 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'bam_iobio' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,976 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/vcf_iobio.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,977 [p:23723,w:0,m:0] [MainThread] Loaded 1 lines from '*******/galaxy/server/galaxy-20.01/tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,977 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'vcf_iobio' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,978 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/biom_simple_display.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,979 [p:23723,w:0,m:0] [MainThread] Loaded 1 lines from '*******/galaxy/server/galaxy-20.01/tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,979 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'biom_simple_display' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,980 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/intermine_simple_display.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,981 [p:23723,w:0,m:0] [MainThread] Loaded 1 lines from '*******/galaxy/server/galaxy-20.01/tool-data/intermine_simple_display.loc.sample' for 'intermine_simple_display' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,981 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'intermine_simple_display' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2020-05-06 22:55:56,981 [p:23723,w:0,m:0] [MainThread] Could not find tool data *******/galaxy/server/galaxy-20.01/tool-data/icn3d_simple_display.loc, reading sample | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,982 [p:23723,w:0,m:0] [MainThread] Loaded 1 lines from '*******/galaxy/server/galaxy-20.01/tool-data/icn3d_simple_display.loc.sample' for 'icn3d_simple_display' | |
| galaxy.tools.data DEBUG 2020-05-06 22:55:56,982 [p:23723,w:0,m:0] [MainThread] Loaded tool data table 'icn3d_simple_display' from file '*******/galaxy/server/galaxy-20.01/config/tool_data_table_conf.xml.sample' | |
| galaxy.jobs DEBUG 2020-05-06 22:55:57,243 [p:23723,w:0,m:0] [MainThread] Loading job configuration from *******/galaxy/server/config_20.01/job_conf.xml | |
| galaxy.jobs INFO 2020-05-06 22:55:57,244 [p:23723,w:0,m:0] [MainThread] Job handler assignment methods set to: db-skip-locked | |
| galaxy.web_stack.handlers DEBUG 2020-05-06 22:55:57,245 [p:23723,w:0,m:0] [MainThread] default set to child with id or tag 'cluster' | |
| galaxy.jobs DEBUG 2020-05-06 22:55:57,246 [p:23723,w:0,m:0] [MainThread] Done loading job configuration | |
| galaxy.tools WARNING 2020-05-06 22:55:57,513 [p:23723,w:0,m:0] [MainThread] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 22:55:57,514 [p:23723,w:0,m:0] [MainThread] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,669 [p:23723,w:0,m:0] [MainThread] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,681 [p:23723,w:0,m:0] [MainThread] Loaded tool id: upload1, version: 1.1.6 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,683 [p:23723,w:0,m:0] [MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,685 [p:23723,w:0,m:0] [MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,688 [p:23723,w:0,m:0] [MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,690 [p:23723,w:0,m:0] [MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,692 [p:23723,w:0,m:0] [MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,695 [p:23723,w:0,m:0] [MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,697 [p:23723,w:0,m:0] [MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,700 [p:23723,w:0,m:0] [MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,702 [p:23723,w:0,m:0] [MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,704 [p:23723,w:0,m:0] [MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,706 [p:23723,w:0,m:0] [MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,709 [p:23723,w:0,m:0] [MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,711 [p:23723,w:0,m:0] [MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,713 [p:23723,w:0,m:0] [MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,715 [p:23723,w:0,m:0] [MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,718 [p:23723,w:0,m:0] [MainThread] Loaded tool id: send_to_cloud, version: 0.1.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,721 [p:23723,w:0,m:0] [MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,723 [p:23723,w:0,m:0] [MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,725 [p:23723,w:0,m:0] [MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,727 [p:23723,w:0,m:0] [MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,729 [p:23723,w:0,m:0] [MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,739 [p:23723,w:0,m:0] [MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,741 [p:23723,w:0,m:0] [MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,744 [p:23723,w:0,m:0] [MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,746 [p:23723,w:0,m:0] [MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,748 [p:23723,w:0,m:0] [MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,751 [p:23723,w:0,m:0] [MainThread] Loaded tool id: __APPLY_RULES__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,753 [p:23723,w:0,m:0] [MainThread] Loaded tool id: __BUILD_LIST__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,756 [p:23723,w:0,m:0] [MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,759 [p:23723,w:0,m:0] [MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,762 [p:23723,w:0,m:0] [MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,764 [p:23723,w:0,m:0] [MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,766 [p:23723,w:0,m:0] [MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,769 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,771 [p:23723,w:0,m:0] [MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,775 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,776 [p:23723,w:0,m:0] [MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,777 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,779 [p:23723,w:0,m:0] [MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,781 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,783 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,785 [p:23723,w:0,m:0] [MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,787 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,789 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Show tail1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,792 [p:23723,w:0,m:0] [MainThread] Loaded tool id: trimmer, version: 0.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,794 [p:23723,w:0,m:0] [MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,797 [p:23723,w:0,m:0] [MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,799 [p:23723,w:0,m:0] [MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,801 [p:23723,w:0,m:0] [MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,805 [p:23723,w:0,m:0] [MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,809 [p:23723,w:0,m:0] [MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,811 [p:23723,w:0,m:0] [MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,814 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,816 [p:23723,w:0,m:0] [MainThread] Loaded tool id: wig_to_bigWig, version: 1.1.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,818 [p:23723,w:0,m:0] [MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,821 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Filter1, version: 1.1.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,824 [p:23723,w:0,m:0] [MainThread] Loaded tool id: sort1, version: 1.1.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,826 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Grep1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,829 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,831 [p:23723,w:0,m:0] [MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,833 [p:23723,w:0,m:0] [MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,835 [p:23723,w:0,m:0] [MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,839 [p:23723,w:0,m:0] [MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,841 [p:23723,w:0,m:0] [MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,844 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,847 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,850 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,853 [p:23723,w:0,m:0] [MainThread] Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,856 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,859 [p:23723,w:0,m:0] [MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,862 [p:23723,w:0,m:0] [MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,864 [p:23723,w:0,m:0] [MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,867 [p:23723,w:0,m:0] [MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,870 [p:23723,w:0,m:0] [MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,872 [p:23723,w:0,m:0] [MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,875 [p:23723,w:0,m:0] [MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,879 [p:23723,w:0,m:0] [MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,881 [p:23723,w:0,m:0] [MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,883 [p:23723,w:0,m:0] [MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,885 [p:23723,w:0,m:0] [MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,887 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,889 [p:23723,w:0,m:0] [MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,893 [p:23723,w:0,m:0] [MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 22:55:57,895 [p:23723,w:0,m:0] [MainThread] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 22:55:57,897 [p:23723,w:0,m:0] [MainThread] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 22:55:57,898 [p:23723,w:0,m:0] [MainThread] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,901 [p:23723,w:0,m:0] [MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,907 [p:23723,w:0,m:0] [MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,908 [p:23723,w:0,m:0] [MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,910 [p:23723,w:0,m:0] [MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. | |
| galaxy.tools WARNING 2020-05-06 22:55:57,910 [p:23723,w:0,m:0] [MainThread] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 22:55:57,911 [p:23723,w:0,m:0] [MainThread] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,911 [p:23723,w:0,m:0] [MainThread] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-06 22:55:57,912 [p:23723,w:0,m:0] [MainThread] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 22:55:57,912 [p:23723,w:0,m:0] [MainThread] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,912 [p:23723,w:0,m:0] [MainThread] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools WARNING 2020-05-06 22:55:57,912 [p:23723,w:0,m:0] [MainThread] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 22:55:57,913 [p:23723,w:0,m:0] [MainThread] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,913 [p:23723,w:0,m:0] [MainThread] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 22:55:57,913 [p:23723,w:0,m:0] [MainThread] Reading tools from config files finished (401.535 ms) | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-06 22:55:57,915 [p:23723,w:0,m:0] [MainThread] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.tools.search DEBUG 2020-05-06 22:57:54,942 [p:23723,w:0,m:0] [MainThread] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-06 22:57:55,538 [p:23723,w:0,m:0] [MainThread] Toolbox index finished (595.092 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,541 [p:23723,w:0,m:0] [MainThread] Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,542 [p:23723,w:0,m:0] [MainThread] Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,550 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igv_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,551 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igb_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,552 [p:23723,w:0,m:0] [MainThread] Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,553 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igb_bed' for datatype 'bed', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,554 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,555 [p:23723,w:0,m:0] [MainThread] Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,556 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,557 [p:23723,w:0,m:0] [MainThread] Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,558 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,559 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,560 [p:23723,w:0,m:0] [MainThread] Loaded display application 'intermine_simple' for datatype 'intermine_tabular', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,565 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,567 [p:23723,w:0,m:0] [MainThread] Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,572 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igv_gff' for datatype 'gff', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,573 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,575 [p:23723,w:0,m:0] [MainThread] Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,577 [p:23723,w:0,m:0] [MainThread] Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,578 [p:23723,w:0,m:0] [MainThread] Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,585 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,586 [p:23723,w:0,m:0] [MainThread] Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,587 [p:23723,w:0,m:0] [MainThread] Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. | |
| galaxy.datatypes.display_applications.application ERROR 2020-05-06 22:57:55,589 [p:23723,w:0,m:0] [MainThread] Error loading a set of Dynamic Display Application links: A format or a metadata can be defined for a DisplayApplicationParameter, but not both. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,590 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,591 [p:23723,w:0,m:0] [MainThread] Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,592 [p:23723,w:0,m:0] [MainThread] Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,593 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igb_wig' for datatype 'wig', inherit=False. | |
| galaxy.datatypes.display_applications.application ERROR 2020-05-06 22:57:55,594 [p:23723,w:0,m:0] [MainThread] Error loading a set of Dynamic Display Application links: A format or a metadata can be defined for a DisplayApplicationParameter, but not both. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,594 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,601 [p:23723,w:0,m:0] [MainThread] Loaded display application 'igv_genbank' for datatype 'genbank', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,602 [p:23723,w:0,m:0] [MainThread] Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,602 [p:23723,w:0,m:0] [MainThread] Loaded display application 'icn3d_simple' for datatype 'sdf', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,603 [p:23723,w:0,m:0] [MainThread] Loaded display application 'icn3d_simple' for datatype 'mol2', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,604 [p:23723,w:0,m:0] [MainThread] Loaded display application 'icn3d_simple' for datatype 'pdb', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,604 [p:23723,w:0,m:0] [MainThread] Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,610 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,610 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,610 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,610 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,610 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,610 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,610 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,610 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,610 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,610 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,611 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,611 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,611 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed6' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,611 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,611 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed6' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,611 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,611 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed12' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,611 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,611 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed12' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,611 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,612 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_interval' to datatype 'probed' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,612 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'probed' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,612 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'rviewer_interval' to datatype 'probed' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,612 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'probed' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,613 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_interval' to datatype 'chrint' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,613 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,613 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'rviewer_interval' to datatype 'chrint' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,613 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,616 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_fasta' to datatype 'fasta.gz' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,620 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,620 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,620 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.gz' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,620 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.gz' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,621 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.bz2' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,621 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.bz2' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,622 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gtf' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,622 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_gff' to datatype 'gtf' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,642 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,642 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,642 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,642 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,644 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_fasta' to datatype 'sequences' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,687 [p:23723,w:0,m:0] [MainThread] Adding inherited display application 'igv_fasta' to datatype 'mothur.align' | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,698 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_Bam_Bai_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,699 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,700 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,702 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,703 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,704 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,706 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_cram_to_bam_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,707 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_to_gff_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,708 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,710 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,712 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,713 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_to_fli_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,714 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bedgraph_to_bigwig | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,716 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_len_to_linecount | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,718 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,719 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,721 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,722 [p:23723,w:0,m:0] [MainThread] Loaded converter: csv_to_tabular | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,724 [p:23723,w:0,m:0] [MainThread] Loaded converter: tabular_to_csv | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,725 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fasta_to_tabular | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,727 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_base_index | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,729 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_color_index | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,730 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fasta_to_2bit | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,732 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fasta_to_len | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,734 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fasta_to_fai | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,736 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,737 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,739 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,740 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,742 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,743 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,744 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,746 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,747 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,749 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,750 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,751 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,753 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,754 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,755 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,757 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,758 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gff_to_bed_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,760 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,761 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,763 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gff_to_fli_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,764 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gff_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,766 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,768 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,769 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,771 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,772 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bed_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,773 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bedstrict_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,775 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bed6_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,776 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bed12_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,778 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,779 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,781 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,783 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_picard_interval_list_to_bed6 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,784 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_tar_to_directory | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,786 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_maf_to_fasta_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,787 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_maf_to_interval_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,789 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_encodepeak_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,791 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_encodepeak_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,792 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,794 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,795 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,797 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_sam_to_unsorted_bam | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,799 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,800 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,802 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_sam_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,803 [p:23723,w:0,m:0] [MainThread] Loaded converter: tabular_to_dbnsfp | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,805 [p:23723,w:0,m:0] [MainThread] Loaded converter: tabular_to_csv | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,806 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,808 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_vcf_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,809 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,811 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_vcf_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,813 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,814 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bcf_to_bcf_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,816 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,818 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_wig_to_bigwig | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,820 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_wiggle_to_interval_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,821 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,823 [p:23723,w:0,m:0] [MainThread] Loaded converter: lped2fpedconvert | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,824 [p:23723,w:0,m:0] [MainThread] Loaded converter: lped2pbedconvert | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,826 [p:23723,w:0,m:0] [MainThread] Loaded converter: pbed2lpedconvert | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,827 [p:23723,w:0,m:0] [MainThread] Loaded converter: pbed2ldindepconvert | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,829 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,830 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_biom1_to_biom2 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,832 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_biom2_to_biom1 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,834 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_SMILES_to_sdf | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,836 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_SMILES_to_inchi | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,837 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_SMILES_to_cml | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,839 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_SMILES_to_MOL | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,841 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_SMILES_to_MOL2 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,844 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_smiles_to_smiles | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,845 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_sdf_to_smiles | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,847 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_sdf_to_inchi | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,849 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_sdf_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,850 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_sdf_to_cml | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,852 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_inchi_to_smi | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,853 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_inchi_to_sdf | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,855 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_inchi_to_mol | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,857 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_inchi_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,859 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_inchi_to_cml | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,861 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol_to_smi | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,863 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,864 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,866 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol_to_cml | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,868 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol2_to_smi | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,869 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol2_to_sdf | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,871 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol2_to_inchi | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,872 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol2_to_mol | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,874 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol2_to_cml | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,876 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_cml_to_smiles | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,878 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_cml_to_inchi | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,879 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_cml_to_sdf | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,881 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_cml_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,883 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_ref_to_seq_taxomony | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,884 [p:23723,w:0,m:0] [MainThread] Loaded converter: CONVERTER_neostorezip_to_neostore | |
| galaxy.datatypes.registry DEBUG 2020-05-06 22:57:55,894 [p:23723,w:0,m:0] [MainThread] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 22:57:55,914 [p:23723,w:0,m:0] [MainThread] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 22:57:55,916 [p:23723,w:0,m:0] [MainThread] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 22:57:55,918 [p:23723,w:0,m:0] [MainThread] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:55,931 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: aequatus | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:55,936 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: annotate_image | |
| galaxy.visualization.plugins.config_parser INFO 2020-05-06 22:57:55,960 [p:23723,w:0,m:0] [MainThread] Visualizations plugin disabled: Circster. Skipping... | |
| galaxy.visualization.plugins.config_parser INFO 2020-05-06 22:57:55,964 [p:23723,w:0,m:0] [MainThread] template syntax is deprecated: use entry_point instead | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:55,965 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: csg | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:55,971 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: cytoscape | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:55,976 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: drawrna | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:55,982 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: example | |
| galaxy.visualization.plugins.config_parser INFO 2020-05-06 22:57:55,986 [p:23723,w:0,m:0] [MainThread] template syntax is deprecated: use entry_point instead | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,006 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: graphviz | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,021 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,031 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: heatmap_default | |
| galaxy.visualization.plugins.config_parser INFO 2020-05-06 22:57:56,033 [p:23723,w:0,m:0] [MainThread] template syntax is deprecated: use entry_point instead | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,034 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: hivtrace | |
| galaxy.visualization.plugins.config_parser INFO 2020-05-06 22:57:56,037 [p:23723,w:0,m:0] [MainThread] template syntax is deprecated: use entry_point instead | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,038 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: hyphyvision | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,059 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,069 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: jqplot_box | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,078 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,087 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: jqplot_line | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,096 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,099 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: msa | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,105 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: ngl | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,120 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,131 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,140 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,149 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,159 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,168 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,178 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_line | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,345 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,348 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,356 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,363 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,370 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,377 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,379 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: openlayers | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,382 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: phylocanvas | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,384 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: phyloviz | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,386 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: pv | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,388 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: scatterplot | |
| galaxy.visualization.plugins.config_parser INFO 2020-05-06 22:57:56,390 [p:23723,w:0,m:0] [MainThread] Visualizations plugin disabled: Sweepster. Skipping... | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,392 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: trackster | |
| galaxy.visualization.plugins.config_parser INFO 2020-05-06 22:57:56,393 [p:23723,w:0,m:0] [MainThread] template syntax is deprecated: use entry_point instead | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,393 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: unipept | |
| galaxy.visualization.plugins.registry INFO 2020-05-06 22:57:56,396 [p:23723,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: venn | |
| galaxy.tours INFO 2020-05-06 22:57:56,442 [p:23723,w:0,m:0] [MainThread] Loaded tour 'core.galaxy_ui' | |
| galaxy.tours INFO 2020-05-06 22:57:56,472 [p:23723,w:0,m:0] [MainThread] Loaded tour 'core.history' | |
| galaxy.tours INFO 2020-05-06 22:57:56,488 [p:23723,w:0,m:0] [MainThread] Loaded tour 'core.scratchbook' | |
| galaxy.workflow.scheduling_manager INFO 2020-05-06 22:57:56,621 [p:23723,w:0,m:0] [MainThread] No workflow schedulers plugin config file defined, using default scheduler. | |
| galaxy.app INFO 2020-05-06 22:57:56,630 [p:23723,w:0,m:0] [MainThread] Galaxy app startup finished (122936.916 ms) | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:56,729 [p:23723,w:0,m:0] [MainThread] Enabling 'admin' controller, class: AdminGalaxy | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,076 [p:23723,w:0,m:0] [MainThread] Enabling 'admin_toolshed' controller, class: AdminGalaxy | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,076 [p:23723,w:0,m:0] [MainThread] Enabling 'admin_toolshed' controller, class: AdminToolshed | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,078 [p:23723,w:0,m:0] [MainThread] Enabling 'async' controller, class: ASync | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,081 [p:23723,w:0,m:0] [MainThread] Enabling 'authnz' controller, class: JSAppLauncher | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,081 [p:23723,w:0,m:0] [MainThread] Enabling 'authnz' controller, class: OIDC | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,085 [p:23723,w:0,m:0] [MainThread] Enabling 'data_manager' controller, class: DataManager | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,088 [p:23723,w:0,m:0] [MainThread] Enabling 'dataset' controller, class: DatasetInterface | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,097 [p:23723,w:0,m:0] [MainThread] Enabling 'error' controller, class: Error | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,100 [p:23723,w:0,m:0] [MainThread] Enabling 'forms' controller, class: Forms | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,105 [p:23723,w:0,m:0] [MainThread] Enabling 'history' controller, class: HistoryController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,107 [p:23723,w:0,m:0] [MainThread] Enabling 'interactive_environments' controller, class: InteractiveEnvironmentsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,109 [p:23723,w:0,m:0] [MainThread] Enabling 'interactivetool' controller, class: InteractiveTool | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,110 [p:23723,w:0,m:0] [MainThread] Enabling 'library' controller, class: Library | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,236 [p:23723,w:0,m:0] [MainThread] Enabling 'openid' controller, class: OpenID | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,310 [p:23723,w:0,m:0] [MainThread] Enabling 'page' controller, class: PageController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,313 [p:23723,w:0,m:0] [MainThread] Enabling 'root' controller, class: RootController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,314 [p:23723,w:0,m:0] [MainThread] Enabling 'shed_tool_static' controller, class: ShedToolStatic | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,321 [p:23723,w:0,m:0] [MainThread] Enabling 'tag' controller, class: TagsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,323 [p:23723,w:0,m:0] [MainThread] Enabling 'tool_runner' controller, class: ToolRunner | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,325 [p:23723,w:0,m:0] [MainThread] Enabling 'user' controller, class: User | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,326 [p:23723,w:0,m:0] [MainThread] Enabling 'userskeys' controller, class: User | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,330 [p:23723,w:0,m:0] [MainThread] Enabling 'visualization' controller, class: VisualizationController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,424 [p:23723,w:0,m:0] [MainThread] Enabling 'workflow' controller, class: WorkflowController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,437 [p:23723,w:0,m:0] [MainThread] Enabling 'history_annotations' API controller, class: HistoryAnnotationsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,437 [p:23723,w:0,m:0] [MainThread] Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,437 [p:23723,w:0,m:0] [MainThread] Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,448 [p:23723,w:0,m:0] [MainThread] Enabling 'authenticate' API controller, class: AuthenticationController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,507 [p:23723,w:0,m:0] [MainThread] Enabling 'cloud' API controller, class: CloudController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,524 [p:23723,w:0,m:0] [MainThread] Enabling 'cloudauthz' API controller, class: CloudAuthzController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,526 [p:23723,w:0,m:0] [MainThread] Enabling 'configuration' API controller, class: ConfigurationController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,528 [p:23723,w:0,m:0] [MainThread] Enabling 'container_resolution' API controller, class: ContainerResolutionAPIController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,531 [p:23723,w:0,m:0] [MainThread] Enabling 'dataset_collections' API controller, class: DatasetCollectionsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,534 [p:23723,w:0,m:0] [MainThread] Enabling 'datasets' API controller, class: DatasetsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,543 [p:23723,w:0,m:0] [MainThread] Enabling 'datatypes' API controller, class: DatatypesController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,545 [p:23723,w:0,m:0] [MainThread] Enabling 'display_applications' API controller, class: DisplayApplicationsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,547 [p:23723,w:0,m:0] [MainThread] Enabling 'dynamic_tools' API controller, class: DynamicToolsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,549 [p:23723,w:0,m:0] [MainThread] Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,549 [p:23723,w:0,m:0] [MainThread] Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,552 [p:23723,w:0,m:0] [MainThread] Enabling 'folder_contents' API controller, class: FolderContentsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,558 [p:23723,w:0,m:0] [MainThread] Enabling 'folders' API controller, class: FoldersController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,578 [p:23723,w:0,m:0] [MainThread] Enabling 'forms' API controller, class: FormDefinitionAPIController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,582 [p:23723,w:0,m:0] [MainThread] Enabling 'genomes' API controller, class: GenomesController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,584 [p:23723,w:0,m:0] [MainThread] Enabling 'group_roles' API controller, class: GroupRolesAPIController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,587 [p:23723,w:0,m:0] [MainThread] Enabling 'group_users' API controller, class: GroupUsersAPIController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,589 [p:23723,w:0,m:0] [MainThread] Enabling 'groups' API controller, class: GroupAPIController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,593 [p:23723,w:0,m:0] [MainThread] Enabling 'histories' API controller, class: HistoriesController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,607 [p:23723,w:0,m:0] [MainThread] Enabling 'history_contents' API controller, class: HistoryContentsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,610 [p:23723,w:0,m:0] [MainThread] Enabling 'history_content_tags' API controller, class: HistoryContentTagsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,610 [p:23723,w:0,m:0] [MainThread] Enabling 'history_tags' API controller, class: HistoryTagsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,610 [p:23723,w:0,m:0] [MainThread] Enabling 'workflow_tags' API controller, class: WorkflowTagsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,612 [p:23723,w:0,m:0] [MainThread] Enabling 'job_files' API controller, class: JobFilesAPIController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,652 [p:23723,w:0,m:0] [MainThread] Enabling 'job_ports' API controller, class: JobPortsAPIController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,655 [p:23723,w:0,m:0] [MainThread] Enabling 'jobs' API controller, class: JobController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,657 [p:23723,w:0,m:0] [MainThread] Enabling 'libraries' API controller, class: LibrariesController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,668 [p:23723,w:0,m:0] [MainThread] Enabling 'library_contents' API controller, class: LibraryContentsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,673 [p:23723,w:0,m:0] [MainThread] Enabling 'library_datasets' API controller, class: LibraryDatasetsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,674 [p:23723,w:0,m:0] [MainThread] Enabling 'metrics' API controller, class: MetricsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,676 [p:23723,w:0,m:0] [MainThread] Enabling 'page_revisions' API controller, class: PageRevisionsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,679 [p:23723,w:0,m:0] [MainThread] Enabling 'pages' API controller, class: PagesController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,681 [p:23723,w:0,m:0] [MainThread] Enabling 'plugins' API controller, class: PluginsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,683 [p:23723,w:0,m:0] [MainThread] Enabling 'history_content_provenance' API controller, class: HDAProvenanceController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,683 [p:23723,w:0,m:0] [MainThread] Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,685 [p:23723,w:0,m:0] [MainThread] Enabling 'quotas' API controller, class: QuotaAPIController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,697 [p:23723,w:0,m:0] [MainThread] Enabling 'remote_files' API controller, class: RemoteFilesAPIController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,720 [p:23723,w:0,m:0] [MainThread] Enabling 'roles' API controller, class: RoleAPIController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,797 [p:23723,w:0,m:0] [MainThread] Enabling 'search' API controller, class: SearchController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,799 [p:23723,w:0,m:0] [MainThread] Enabling 'tags' API controller, class: TagsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,801 [p:23723,w:0,m:0] [MainThread] Enabling 'tool_data' API controller, class: ToolData | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,803 [p:23723,w:0,m:0] [MainThread] Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,805 [p:23723,w:0,m:0] [MainThread] Enabling 'tool_entry_points' API controller, class: ToolEntryPointsAPIController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,807 [p:23723,w:0,m:0] [MainThread] Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,812 [p:23723,w:0,m:0] [MainThread] Enabling 'tools' API controller, class: ToolsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,814 [p:23723,w:0,m:0] [MainThread] Enabling 'toolshed' API controller, class: ToolShedController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,815 [p:23723,w:0,m:0] [MainThread] Enabling 'tours' API controller, class: ToursController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,825 [p:23723,w:0,m:0] [MainThread] Enabling 'uploads' API controller, class: UploadsAPIController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,840 [p:23723,w:0,m:0] [MainThread] Enabling 'users' API controller, class: UserAPIController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,842 [p:23723,w:0,m:0] [MainThread] Enabling 'visualizations' API controller, class: VisualizationsController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,844 [p:23723,w:0,m:0] [MainThread] Enabling 'webhooks' API controller, class: WebhooksController | |
| galaxy.web.framework.base DEBUG 2020-05-06 22:57:57,850 [p:23723,w:0,m:0] [MainThread] Enabling 'workflows' API controller, class: WorkflowsAPIController | |
| galaxy.webapps.util DEBUG 2020-05-06 22:57:58,322 [p:23723,w:0,m:0] [MainThread] Enabling 'paste.httpexceptions' middleware | |
| galaxy.webapps.util DEBUG 2020-05-06 22:57:58,325 [p:23723,w:0,m:0] [MainThread] Enabling 'RecursiveMiddleware' middleware | |
| galaxy.webapps.util DEBUG 2020-05-06 22:57:58,325 [p:23723,w:0,m:0] [MainThread] Enabling 'ErrorMiddleware' middleware | |
| galaxy.webapps.util DEBUG 2020-05-06 22:57:58,337 [p:23723,w:0,m:0] [MainThread] Enabling 'TransLogger' middleware | |
| galaxy.webapps.util DEBUG 2020-05-06 22:57:58,337 [p:23723,w:0,m:0] [MainThread] Enabling 'XForwardedHostMiddleware' middleware | |
| galaxy.webapps.util DEBUG 2020-05-06 22:57:58,337 [p:23723,w:0,m:0] [MainThread] Enabling 'RequestIDMiddleware' middleware | |
| galaxy.webapps.util DEBUG 2020-05-06 22:57:58,337 [p:23723,w:0,m:0] [MainThread] Enabling 'BatchMiddleware' middleware | |
| galaxy.webapps.util WARNING 2020-05-06 22:57:58,337 [p:23723,w:0,m:0] [MainThread] 'wrap_in_static' is enabled in your configuration but the uWSGI application stack does not support it, this middleware has been disabled | |
| galaxy.webapps.galaxy.buildapp DEBUG 2020-05-06 22:57:58,338 [p:23723,w:0,m:0] [MainThread] Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 140280905905984)> is alive. | |
| Wed May 6 22:57:58 2020 - WSGI app 0 (mountpoint='') ready in 135 seconds on interpreter 0x1aaa700 pid: 23723 (default app) | |
| Wed May 6 22:57:58 2020 - *** uWSGI is running in multiple interpreter mode *** | |
| Wed May 6 22:57:58 2020 - spawned uWSGI master process (pid: 23723) | |
| Wed May 6 22:57:58 2020 - spawned uWSGI worker 1 (pid: 28737, cores: 1) | |
| Wed May 6 22:57:58 2020 - spawned 1 offload threads for uWSGI worker 1 | |
| Wed May 6 22:57:58 2020 - spawned uWSGI worker 2 (pid: 28739, cores: 1) | |
| Wed May 6 22:57:58 2020 - spawned 1 offload threads for uWSGI worker 2 | |
| Wed May 6 22:57:58 2020 - spawned uWSGI worker 3 (pid: 28741, cores: 1) | |
| Wed May 6 22:57:58 2020 - spawned 1 offload threads for uWSGI worker 3 | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,346 [p:28737,w:1,m:0] [MainThread] Calling postfork function: <bound method ApplicationStack.set_postfork_server_name of <galaxy.web_stack.UWSGIApplicationStack object at 0x7f95b18486a0>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,348 [p:28739,w:2,m:0] [MainThread] Calling postfork function: <bound method ApplicationStack.set_postfork_server_name of <galaxy.web_stack.UWSGIApplicationStack object at 0x7f95b18486a0>> | |
| Wed May 6 22:57:58 2020 - spawned uWSGI worker 4 (pid: 28743, cores: 1) | |
| Wed May 6 22:57:58 2020 - *** Stats server enabled on 127.0.0.1:9191 fd: 16 *** | |
| Wed May 6 22:57:58 2020 - running "unix_signal:2 gracefully_kill_them_all" (master-start)... | |
| Wed May 6 22:57:58 2020 - running "unix_signal:15 gracefully_kill_them_all" (master-start)... | |
| Wed May 6 22:57:58 2020 - spawned 1 offload threads for uWSGI worker 4 | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,350 [p:28741,w:3,m:0] [MainThread] Calling postfork function: <bound method ApplicationStack.set_postfork_server_name of <galaxy.web_stack.UWSGIApplicationStack object at 0x7f95b18486a0>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,355 [p:28737,w:1,m:0] [MainThread] server_name set to: main.web.1 | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,355 [p:28739,w:2,m:0] [MainThread] server_name set to: main.web.2 | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,355 [p:28737,w:1,m:0] [MainThread] Calling postfork function: <bound method JobManager.start of <galaxy.jobs.manager.JobManager object at 0x7f958d988630>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,355 [p:28739,w:2,m:0] [MainThread] Calling postfork function: <bound method JobManager.start of <galaxy.jobs.manager.JobManager object at 0x7f958d988630>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,355 [p:28737,w:1,m:0] [MainThread] Calling postfork function: <bound method DatabaseHeartbeat.start of <galaxy.model.database_heartbeat.DatabaseHeartbeat object at 0x7f958d9904e0>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,355 [p:28739,w:2,m:0] [MainThread] Calling postfork function: <bound method DatabaseHeartbeat.start of <galaxy.model.database_heartbeat.DatabaseHeartbeat object at 0x7f958d9904e0>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,357 [p:28741,w:3,m:0] [MainThread] server_name set to: main.web.3 | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,353 [p:28743,w:4,m:0] [MainThread] Calling postfork function: <bound method ApplicationStack.set_postfork_server_name of <galaxy.web_stack.UWSGIApplicationStack object at 0x7f95b18486a0>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,357 [p:28741,w:3,m:0] [MainThread] Calling postfork function: <bound method JobManager.start of <galaxy.jobs.manager.JobManager object at 0x7f958d988630>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,357 [p:28741,w:3,m:0] [MainThread] Calling postfork function: <bound method DatabaseHeartbeat.start of <galaxy.model.database_heartbeat.DatabaseHeartbeat object at 0x7f958d9904e0>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,361 [p:28739,w:2,m:0] [MainThread] Calling postfork function: <bound method UWSGIApplicationStack.start of <galaxy.web_stack.UWSGIApplicationStack object at 0x7f95b18486a0>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,361 [p:28737,w:1,m:0] [MainThread] Calling postfork function: <bound method UWSGIApplicationStack.start of <galaxy.web_stack.UWSGIApplicationStack object at 0x7f95b18486a0>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,362 [p:28743,w:4,m:0] [MainThread] server_name set to: main.web.4 | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,362 [p:28743,w:4,m:0] [MainThread] Calling postfork function: <bound method JobManager.start of <galaxy.jobs.manager.JobManager object at 0x7f958d988630>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,362 [p:28743,w:4,m:0] [MainThread] Calling postfork function: <bound method DatabaseHeartbeat.start of <galaxy.model.database_heartbeat.DatabaseHeartbeat object at 0x7f958d9904e0>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,361 [p:28737,w:1,m:0] [MainThread] Calling postfork function: <built-in function register> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,363 [p:28741,w:3,m:0] [MainThread] Calling postfork function: <bound method UWSGIApplicationStack.start of <galaxy.web_stack.UWSGIApplicationStack object at 0x7f95b18486a0>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,362 [p:28737,w:1,m:0] [MainThread] Calling postfork function: <function postfork_setup at 0x7f9595ef1bf8> | |
| galaxy.queue_worker INFO 2020-05-06 22:57:58,363 [p:28737,w:1,m:0] [MainThread] Binding and starting galaxy control worker for main.web.1 | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,363 [p:28741,w:3,m:0] [MainThread] Calling postfork function: <built-in function register> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,363 [p:28739,w:2,m:0] [MainThread] Calling postfork function: <built-in function register> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,364 [p:28741,w:3,m:0] [MainThread] Calling postfork function: <function postfork_setup at 0x7f9595ef1bf8> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,364 [p:28739,w:2,m:0] [MainThread] Calling postfork function: <function postfork_setup at 0x7f9595ef1bf8> | |
| galaxy.queue_worker INFO 2020-05-06 22:57:58,365 [p:28741,w:3,m:0] [MainThread] Binding and starting galaxy control worker for main.web.3 | |
| galaxy.queue_worker INFO 2020-05-06 22:57:58,365 [p:28739,w:2,m:0] [MainThread] Binding and starting galaxy control worker for main.web.2 | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,367 [p:28743,w:4,m:0] [MainThread] Calling postfork function: <bound method UWSGIApplicationStack.start of <galaxy.web_stack.UWSGIApplicationStack object at 0x7f95b18486a0>> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,368 [p:28743,w:4,m:0] [MainThread] Calling postfork function: <built-in function register> | |
| galaxy.web_stack DEBUG 2020-05-06 22:57:58,369 [p:28743,w:4,m:0] [MainThread] Calling postfork function: <function postfork_setup at 0x7f9595ef1bf8> | |
| galaxy.queue_worker INFO 2020-05-06 22:57:58,370 [p:28743,w:4,m:0] [MainThread] Binding and starting galaxy control worker for main.web.4 | |
| galaxy.web_stack INFO 2020-05-06 22:57:58,374 [p:28741,w:3,m:0] [MainThread] Galaxy server instance 'main.web.3' is running | |
| galaxy.web_stack INFO 2020-05-06 22:57:58,374 [p:28739,w:2,m:0] [MainThread] Galaxy server instance 'main.web.2' is running | |
| galaxy.web_stack INFO 2020-05-06 22:57:58,375 [p:28737,w:1,m:0] [MainThread] Galaxy server instance 'main.web.1' is running | |
| Starting server in PID 23723. | |
| serving on uwsgi:///tmp/galaxy_gxa_uwsgi.sock | |
| galaxy.web_stack INFO 2020-05-06 22:57:58,391 [p:28743,w:4,m:0] [MainThread] Galaxy server instance 'main.web.4' is running | |
| galaxy.model.database_heartbeat DEBUG 2020-05-06 22:57:58,416 [p:28739,w:2,m:0] [database_heartbeart_main.web.2.thread] main.web.2 is config watcher | |
| galaxy.util.watcher DEBUG 2020-05-06 22:57:58,423 [p:28739,w:2,m:0] [database_heartbeart_main.web.2.thread] Watching for changes in directory (recursively): *******/galaxy/server/galaxy-20.01/tool-data | |
| galaxy.model.database_heartbeat DEBUG 2020-05-06 22:57:58,433 [p:28743,w:4,m:0] [database_heartbeart_main.web.4.thread] main.web.4 is config watcher | |
| galaxy.util.watcher DEBUG 2020-05-06 22:57:58,442 [p:28743,w:4,m:0] [database_heartbeart_main.web.4.thread] Watching for changes in directory (recursively): *******/galaxy/server/galaxy-20.01/tool-data | |
| Exception in thread Thread-1: | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1246, in _execute_context | |
| cursor, statement, parameters, context | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/default.py", line 581, in do_execute | |
| cursor.execute(statement, parameters) | |
| psycopg2.errors.DuplicateTable: relation "queue_id_sequence" already exists | |
| The above exception was the direct cause of the following exception: | |
| Traceback (most recent call last): | |
| File "/usr/lib64/python3.6/threading.py", line 916, in _bootstrap_inner | |
| self.run() | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/mixins.py", line 175, in run | |
| for _ in self.consume(limit=None, **kwargs): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/mixins.py", line 191, in consume | |
| with self.consumer_context(**kwargs) as (conn, channel, consumers): | |
| File "/usr/lib64/python3.6/contextlib.py", line 81, in __enter__ | |
| return next(self.gen) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/mixins.py", line 184, in consumer_context | |
| with self.Consumer() as (connection, channel, consumers): | |
| File "/usr/lib64/python3.6/contextlib.py", line 81, in __enter__ | |
| return next(self.gen) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/mixins.py", line 233, in Consumer | |
| with self._consume_from(*self.get_consumers(cls, channel)) as c: | |
| File "lib/galaxy/queue_worker.py", line 374, in get_consumers | |
| accept={'application/json'}) for q in self.control_queues] | |
| File "lib/galaxy/queue_worker.py", line 374, in <listcomp> | |
| accept={'application/json'}) for q in self.control_queues] | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/messaging.py", line 386, in __init__ | |
| self.revive(self.channel) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/messaging.py", line 408, in revive | |
| self.declare() | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/messaging.py", line 421, in declare | |
| queue.declare() | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/entity.py", line 609, in declare | |
| self._create_queue(nowait=nowait, channel=channel) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/entity.py", line 618, in _create_queue | |
| self.queue_declare(nowait=nowait, passive=False, channel=channel) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/entity.py", line 653, in queue_declare | |
| nowait=nowait, | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 531, in queue_declare | |
| self._new_queue(queue, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 82, in _new_queue | |
| self._get_or_create(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 70, in _get_or_create | |
| obj = self.session.query(self.queue_cls) \ | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 65, in session | |
| _, Session = self._open() | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 58, in _open | |
| metadata.create_all(engine) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/schema.py", line 4316, in create_all | |
| ddl.SchemaGenerator, self, checkfirst=checkfirst, tables=tables | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 2049, in _run_visitor | |
| conn._run_visitor(visitorcallable, element, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1618, in _run_visitor | |
| visitorcallable(self.dialect, self, **kwargs).traverse_single(element) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/visitors.py", line 138, in traverse_single | |
| return meth(obj, **kw) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/ddl.py", line 781, in visit_metadata | |
| _is_metadata_operation=True, | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/visitors.py", line 138, in traverse_single | |
| return meth(obj, **kw) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/ddl.py", line 815, in visit_table | |
| self.traverse_single(column.default) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/visitors.py", line 138, in traverse_single | |
| return meth(obj, **kw) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/ddl.py", line 859, in visit_sequence | |
| self.connection.execute(CreateSequence(sequence)) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 982, in execute | |
| return meth(self, multiparams, params) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/ddl.py", line 72, in _execute_on_connection | |
| return connection._execute_ddl(self, multiparams, params) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1044, in _execute_ddl | |
| compiled, | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1250, in _execute_context | |
| e, statement, parameters, cursor, context | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1476, in _handle_dbapi_exception | |
| util.raise_from_cause(sqlalchemy_exception, exc_info) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/util/compat.py", line 398, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/util/compat.py", line 152, in reraise | |
| raise value.with_traceback(tb) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1246, in _execute_context | |
| cursor, statement, parameters, context | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/default.py", line 581, in do_execute | |
| cursor.execute(statement, parameters) | |
| sqlalchemy.exc.ProgrammingError: (psycopg2.errors.DuplicateTable) relation "queue_id_sequence" already exists | |
| [SQL: CREATE SEQUENCE queue_id_sequence] | |
| (Background on this error at: http://sqlalche.me/e/f405) | |
| Exception in thread Thread-1: | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1246, in _execute_context | |
| cursor, statement, parameters, context | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/default.py", line 581, in do_execute | |
| cursor.execute(statement, parameters) | |
| psycopg2.errors.UniqueViolation: duplicate key value violates unique constraint "pg_type_typname_nsp_index" | |
| DETAIL: Key (typname, typnamespace)=(queue_id_sequence, 2200) already exists. | |
| The above exception was the direct cause of the following exception: | |
| Traceback (most recent call last): | |
| File "/usr/lib64/python3.6/threading.py", line 916, in _bootstrap_inner | |
| self.run() | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/mixins.py", line 175, in run | |
| for _ in self.consume(limit=None, **kwargs): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/mixins.py", line 191, in consume | |
| with self.consumer_context(**kwargs) as (conn, channel, consumers): | |
| File "/usr/lib64/python3.6/contextlib.py", line 81, in __enter__ | |
| return next(self.gen) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/mixins.py", line 184, in consumer_context | |
| with self.Consumer() as (connection, channel, consumers): | |
| File "/usr/lib64/python3.6/contextlib.py", line 81, in __enter__ | |
| return next(self.gen) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/mixins.py", line 233, in Consumer | |
| with self._consume_from(*self.get_consumers(cls, channel)) as c: | |
| File "lib/galaxy/queue_worker.py", line 374, in get_consumers | |
| accept={'application/json'}) for q in self.control_queues] | |
| File "lib/galaxy/queue_worker.py", line 374, in <listcomp> | |
| accept={'application/json'}) for q in self.control_queues] | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/messaging.py", line 386, in __init__ | |
| self.revive(self.channel) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/messaging.py", line 408, in revive | |
| self.declare() | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/messaging.py", line 421, in declare | |
| queue.declare() | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/entity.py", line 609, in declare | |
| self._create_queue(nowait=nowait, channel=channel) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/entity.py", line 618, in _create_queue | |
| self.queue_declare(nowait=nowait, passive=False, channel=channel) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/entity.py", line 653, in queue_declare | |
| nowait=nowait, | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 531, in queue_declare | |
| self._new_queue(queue, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 82, in _new_queue | |
| self._get_or_create(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 70, in _get_or_create | |
| obj = self.session.query(self.queue_cls) \ | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 65, in session | |
| _, Session = self._open() | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 58, in _open | |
| metadata.create_all(engine) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/schema.py", line 4316, in create_all | |
| ddl.SchemaGenerator, self, checkfirst=checkfirst, tables=tables | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 2049, in _run_visitor | |
| conn._run_visitor(visitorcallable, element, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1618, in _run_visitor | |
| visitorcallable(self.dialect, self, **kwargs).traverse_single(element) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/visitors.py", line 138, in traverse_single | |
| return meth(obj, **kw) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/ddl.py", line 781, in visit_metadata | |
| _is_metadata_operation=True, | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/visitors.py", line 138, in traverse_single | |
| return meth(obj, **kw) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/ddl.py", line 815, in visit_table | |
| self.traverse_single(column.default) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/visitors.py", line 138, in traverse_single | |
| return meth(obj, **kw) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/ddl.py", line 859, in visit_sequence | |
| self.connection.execute(CreateSequence(sequence)) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 982, in execute | |
| return meth(self, multiparams, params) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/ddl.py", line 72, in _execute_on_connection | |
| return connection._execute_ddl(self, multiparams, params) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1044, in _execute_ddl | |
| compiled, | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1250, in _execute_context | |
| e, statement, parameters, cursor, context | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1476, in _handle_dbapi_exception | |
| util.raise_from_cause(sqlalchemy_exception, exc_info) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/util/compat.py", line 398, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/util/compat.py", line 152, in reraise | |
| raise value.with_traceback(tb) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1246, in _execute_context | |
| cursor, statement, parameters, context | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/default.py", line 581, in do_execute | |
| cursor.execute(statement, parameters) | |
| sqlalchemy.exc.IntegrityError: (psycopg2.errors.UniqueViolation) duplicate key value violates unique constraint "pg_type_typname_nsp_index" | |
| DETAIL: Key (typname, typnamespace)=(queue_id_sequence, 2200) already exists. | |
| [SQL: CREATE SEQUENCE queue_id_sequence] | |
| (Background on this error at: http://sqlalche.me/e/gkpj) | |
| Exception in thread Thread-1: | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1246, in _execute_context | |
| cursor, statement, parameters, context | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/default.py", line 581, in do_execute | |
| cursor.execute(statement, parameters) | |
| psycopg2.errors.UniqueViolation: duplicate key value violates unique constraint "pg_type_typname_nsp_index" | |
| DETAIL: Key (typname, typnamespace)=(kombu_queue, 2200) already exists. | |
| The above exception was the direct cause of the following exception: | |
| Traceback (most recent call last): | |
| File "/usr/lib64/python3.6/threading.py", line 916, in _bootstrap_inner | |
| self.run() | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/mixins.py", line 175, in run | |
| for _ in self.consume(limit=None, **kwargs): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/mixins.py", line 191, in consume | |
| with self.consumer_context(**kwargs) as (conn, channel, consumers): | |
| File "/usr/lib64/python3.6/contextlib.py", line 81, in __enter__ | |
| return next(self.gen) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/mixins.py", line 184, in consumer_context | |
| with self.Consumer() as (connection, channel, consumers): | |
| File "/usr/lib64/python3.6/contextlib.py", line 81, in __enter__ | |
| return next(self.gen) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/mixins.py", line 233, in Consumer | |
| with self._consume_from(*self.get_consumers(cls, channel)) as c: | |
| File "lib/galaxy/queue_worker.py", line 374, in get_consumers | |
| accept={'application/json'}) for q in self.control_queues] | |
| File "lib/galaxy/queue_worker.py", line 374, in <listcomp> | |
| accept={'application/json'}) for q in self.control_queues] | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/messaging.py", line 386, in __init__ | |
| self.revive(self.channel) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/messaging.py", line 408, in revive | |
| self.declare() | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/messaging.py", line 421, in declare | |
| queue.declare() | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/entity.py", line 609, in declare | |
| self._create_queue(nowait=nowait, channel=channel) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/entity.py", line 618, in _create_queue | |
| self.queue_declare(nowait=nowait, passive=False, channel=channel) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/entity.py", line 653, in queue_declare | |
| nowait=nowait, | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 531, in queue_declare | |
| self._new_queue(queue, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 82, in _new_queue | |
| self._get_or_create(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 70, in _get_or_create | |
| obj = self.session.query(self.queue_cls) \ | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 65, in session | |
| _, Session = self._open() | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 58, in _open | |
| metadata.create_all(engine) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/schema.py", line 4316, in create_all | |
| ddl.SchemaGenerator, self, checkfirst=checkfirst, tables=tables | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 2049, in _run_visitor | |
| conn._run_visitor(visitorcallable, element, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1618, in _run_visitor | |
| visitorcallable(self.dialect, self, **kwargs).traverse_single(element) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/visitors.py", line 138, in traverse_single | |
| return meth(obj, **kw) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/ddl.py", line 781, in visit_metadata | |
| _is_metadata_operation=True, | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/visitors.py", line 138, in traverse_single | |
| return meth(obj, **kw) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/ddl.py", line 826, in visit_table | |
| include_foreign_key_constraints, | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 982, in execute | |
| return meth(self, multiparams, params) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/sql/ddl.py", line 72, in _execute_on_connection | |
| return connection._execute_ddl(self, multiparams, params) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1044, in _execute_ddl | |
| compiled, | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1250, in _execute_context | |
| e, statement, parameters, cursor, context | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1476, in _handle_dbapi_exception | |
| util.raise_from_cause(sqlalchemy_exception, exc_info) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/util/compat.py", line 398, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/util/compat.py", line 152, in reraise | |
| raise value.with_traceback(tb) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/base.py", line 1246, in _execute_context | |
| cursor, statement, parameters, context | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/sqlalchemy/engine/default.py", line 581, in do_execute | |
| cursor.execute(statement, parameters) | |
| sqlalchemy.exc.IntegrityError: (psycopg2.errors.UniqueViolation) duplicate key value violates unique constraint "pg_type_typname_nsp_index" | |
| DETAIL: Key (typname, typnamespace)=(kombu_queue, 2200) already exists. | |
| [SQL: | |
| CREATE TABLE kombu_queue ( | |
| id INTEGER NOT NULL, | |
| name VARCHAR(200), | |
| PRIMARY KEY (id), | |
| UNIQUE (name) | |
| ) | |
| ] | |
| (Background on this error at: http://sqlalche.me/e/gkpj) | |
| galaxy.model.database_heartbeat DEBUG 2020-05-06 22:58:58,439 [p:28739,w:2,m:0] [database_heartbeart_main.web.2.thread] main.web.2 is not config watcher | |
| 10.114.180.83 - - [06/May/2020:23:00:32 +0100] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 1/1] 10.114.180.83 () {52 vars in 1377 bytes} [Wed May 6 23:00:32 2020] GET / => generated 101407 bytes in 476 msecs (HTTP/1.1 200) 8 headers in 393 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:00:34 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 1/2] 10.114.180.83 () {52 vars in 1341 bytes} [Wed May 6 23:00:34 2020] GET /api/webhooks => generated 2 bytes in 46 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:00:35 +0100] "GET /api/users/current HTTP/1.1" 400 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 1/3] 10.114.180.83 () {50 vars in 1299 bytes} [Wed May 6 23:00:35 2020] GET /api/users/current => generated 77 bytes in 56 msecs (HTTP/1.1 400) 3 headers in 148 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:00:35 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 1/4] 10.114.180.83 () {50 vars in 1299 bytes} [Wed May 6 23:00:35 2020] GET /api/configuration => generated 2175 bytes in 58 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:00:35 +0100] "GET /scripts/bundled/assets/e417938def579af5c4d237a1cc340445.png HTTP/1.1" 404 227 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 2/5] 10.114.180.83 () {50 vars in 1392 bytes} [Wed May 6 23:00:35 2020] GET /scripts/bundled/assets/e417938def579af5c4d237a1cc340445.png => generated 227 bytes in 2 msecs (HTTP/1.1 404) 2 headers in 87 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:00:35 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 2/6] 10.114.180.83 () {52 vars in 1341 bytes} [Wed May 6 23:00:35 2020] GET /api/webhooks => generated 2 bytes in 22 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:00:35 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 2/7] 10.114.180.83 () {54 vars in 1349 bytes} [Wed May 6 23:00:35 2020] GET /api/genomes => generated 55436 bytes in 21 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:00:35 +0100] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 2/8] 10.114.180.83 () {54 vars in 1394 bytes} [Wed May 6 23:00:35 2020] GET /api/datatypes?extension_only=False => generated 53304 bytes in 21 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:00:35 +0100] "GET /welcome HTTP/1.1" 302 267 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 3/9] 10.114.180.83 () {52 vars in 1410 bytes} [Wed May 6 23:00:35 2020] GET /welcome => generated 267 bytes in 11 msecs (HTTP/1.1 302) 4 headers in 166 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:00:35 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 3/10] 10.114.180.83 () {52 vars in 1373 bytes} [Wed May 6 23:00:35 2020] GET /history/current_history_json => generated 548 bytes in 347 msecs (HTTP/1.1 200) 5 headers in 171 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:00:35 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 3/11] 10.114.180.83 () {52 vars in 1351 bytes} [Wed May 6 23:00:35 2020] GET /api/users/current => generated 82 bytes in 45 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:00:35 +0100] "GET /api/histories/f2db41e1fa331b3e/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 3/12] 10.114.180.83 () {52 vars in 1574 bytes} [Wed May 6 23:00:35 2020] GET /api/histories/f2db41e1fa331b3e/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True => generated 2 bytes in 69 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:00:36 +0100] "GET /api/histories/f2db41e1fa331b3e?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 4/13] 10.114.180.83 () {52 vars in 1494 bytes} [Wed May 6 23:00:36 2020] GET /api/histories/f2db41e1fa331b3e?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 112 bytes in 103 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:00:49 +0100] "GET /api/tools/join1/build?version=2.1.3&__identifer=higvlpfhzes&tool_version=2.1.3 HTTP/1.1" 200 - "http://localhost:60089/?tool_id=join1&version=2.1.3&__identifer=higvlpfhzes" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 4/14] 10.114.180.83 () {54 vars in 1534 bytes} [Wed May 6 23:00:49 2020] GET /api/tools/join1/build?version=2.1.3&__identifer=higvlpfhzes&tool_version=2.1.3 => generated 9470 bytes in 309 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:00:49 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 4/15] 10.114.180.83 () {52 vars in 1341 bytes} [Wed May 6 23:00:49 2020] GET /api/webhooks => generated 2 bytes in 20 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:24:24 +0100] "GET /login HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 4/16] 10.114.180.83 () {54 vars in 1434 bytes} [Wed May 6 23:24:24 2020] GET /login => generated 4554 bytes in 365 msecs (HTTP/1.1 200) 2 headers in 88 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:24:26 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/login" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 5/17] 10.114.180.83 () {50 vars in 1305 bytes} [Wed May 6 23:24:26 2020] GET /api/configuration => generated 2175 bytes in 19 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:24:26 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/login" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 5/18] 10.114.180.83 () {50 vars in 1305 bytes} [Wed May 6 23:24:26 2020] GET /api/users/current => generated 82 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:24:26 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/login" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 5/19] 10.114.180.83 () {52 vars in 1347 bytes} [Wed May 6 23:24:26 2020] GET /api/webhooks => generated 2 bytes in 26 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:10 +0100] "POST /user/create HTTP/1.1" 200 - "http://localhost:60089/login" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 5/20] 10.114.180.83 () {56 vars in 1441 bytes} [Wed May 6 23:25:10 2020] POST /user/create => generated 23 bytes in 335 msecs (HTTP/1.1 200) 4 headers in 332 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:10 +0100] "GET / HTTP/1.1" 200 - "http://localhost:60089/login" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 6/21] 10.114.180.83 () {54 vars in 1429 bytes} [Wed May 6 23:25:10 2020] GET / => generated 125745 bytes in 115 msecs (HTTP/1.1 200) 7 headers in 200 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:12 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 6/22] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:25:12 2020] GET /api/webhooks => generated 2 bytes in 19 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:12 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 6/23] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:25:12 2020] GET /api/configuration => generated 2300 bytes in 20 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:12 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 6/24] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:25:12 2020] GET /api/users/current => generated 271 bytes in 66 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:12 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 7/25] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:25:12 2020] GET /api/webhooks => generated 2 bytes in 20 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:12 +0100] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 7/26] 10.114.180.83 () {54 vars in 1395 bytes} [Wed May 6 23:25:12 2020] GET /api/datatypes?extension_only=False => generated 53304 bytes in 19 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:13 +0100] "GET /welcome HTTP/1.1" 302 267 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 7/27] 10.114.180.83 () {52 vars in 1411 bytes} [Wed May 6 23:25:13 2020] GET /welcome => generated 267 bytes in 17 msecs (HTTP/1.1 302) 4 headers in 166 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:13 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 7/28] 10.114.180.83 () {54 vars in 1350 bytes} [Wed May 6 23:25:13 2020] GET /api/genomes => generated 55436 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:13 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 8/29] 10.114.180.83 () {52 vars in 1374 bytes} [Wed May 6 23:25:13 2020] GET /history/current_history_json => generated 562 bytes in 62 msecs (HTTP/1.1 200) 5 headers in 171 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:13 +0100] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 8/30] 10.114.180.83 () {52 vars in 1575 bytes} [Wed May 6 23:25:13 2020] GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True => generated 2 bytes in 44 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:13 +0100] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 8/31] 10.114.180.83 () {52 vars in 1370 bytes} [Wed May 6 23:25:13 2020] GET /api/users/f2db41e1fa331b3e => generated 271 bytes in 55 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:13 +0100] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 8/32] 10.114.180.83 () {52 vars in 1495 bytes} [Wed May 6 23:25:13 2020] GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 112 bytes in 97 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:23 +0100] "GET /admin HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 9/33] 10.114.180.83 () {54 vars in 1434 bytes} [Wed May 6 23:25:23 2020] GET /admin => generated 125882 bytes in 70 msecs (HTTP/1.1 200) 7 headers in 200 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:25 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 9/34] 10.114.180.83 () {50 vars in 1305 bytes} [Wed May 6 23:25:25 2020] GET /api/users/current => generated 271 bytes in 60 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:25 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 9/35] 10.114.180.83 () {50 vars in 1305 bytes} [Wed May 6 23:25:25 2020] GET /api/configuration => generated 2300 bytes in 15 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:25 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 9/36] 10.114.180.83 () {52 vars in 1347 bytes} [Wed May 6 23:25:25 2020] GET /api/webhooks => generated 2 bytes in 24 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:31 +0100] "GET /user?__identifer=9roprnldcwn HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 10/37] 10.114.180.83 () {56 vars in 1538 bytes} [Wed May 6 23:25:31 2020] GET /user?__identifer=9roprnldcwn => generated 125803 bytes in 64 msecs (HTTP/1.1 200) 7 headers in 200 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:32 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 10/38] 10.114.180.83 () {52 vars in 1370 bytes} [Wed May 6 23:25:32 2020] GET /api/webhooks => generated 2 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:32 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 10/39] 10.114.180.83 () {50 vars in 1328 bytes} [Wed May 6 23:25:32 2020] GET /api/configuration => generated 2300 bytes in 20 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:32 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 10/40] 10.114.180.83 () {50 vars in 1328 bytes} [Wed May 6 23:25:32 2020] GET /api/users/current => generated 271 bytes in 46 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:32 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 11/41] 10.114.180.83 () {52 vars in 1370 bytes} [Wed May 6 23:25:32 2020] GET /api/webhooks => generated 2 bytes in 19 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:32 +0100] "GET /scripts/bundled/assets/e417938def579af5c4d237a1cc340445.png HTTP/1.1" 404 227 "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 11/42] 10.114.180.83 () {50 vars in 1421 bytes} [Wed May 6 23:25:32 2020] GET /scripts/bundled/assets/e417938def579af5c4d237a1cc340445.png => generated 227 bytes in 2 msecs (HTTP/1.1 404) 2 headers in 87 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:32 +0100] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 11/43] 10.114.180.83 () {54 vars in 1423 bytes} [Wed May 6 23:25:32 2020] GET /api/datatypes?extension_only=False => generated 53304 bytes in 20 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:32 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 11/44] 10.114.180.83 () {54 vars in 1378 bytes} [Wed May 6 23:25:32 2020] GET /api/genomes => generated 55436 bytes in 21 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:33 +0100] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 12/45] 10.114.180.83 () {50 vars in 1346 bytes} [Wed May 6 23:25:33 2020] GET /api/users/f2db41e1fa331b3e => generated 271 bytes in 46 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:33 +0100] "GET /scripts/bundled/assets/68f6ead9b879fa12c09aa5ea225584f0.png HTTP/1.1" 404 227 "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 12/46] 10.114.180.83 () {50 vars in 1421 bytes} [Wed May 6 23:25:33 2020] GET /scripts/bundled/assets/68f6ead9b879fa12c09aa5ea225584f0.png => generated 227 bytes in 2 msecs (HTTP/1.1 404) 2 headers in 87 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:33 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 12/47] 10.114.180.83 () {52 vars in 1402 bytes} [Wed May 6 23:25:33 2020] GET /history/current_history_json => generated 562 bytes in 64 msecs (HTTP/1.1 200) 5 headers in 171 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:33 +0100] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 12/48] 10.114.180.83 () {52 vars in 1398 bytes} [Wed May 6 23:25:33 2020] GET /api/users/f2db41e1fa331b3e => generated 271 bytes in 46 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:33 +0100] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 13/49] 10.114.180.83 () {52 vars in 1603 bytes} [Wed May 6 23:25:33 2020] GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True => generated 2 bytes in 49 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:33 +0100] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 13/50] 10.114.180.83 () {52 vars in 1523 bytes} [Wed May 6 23:25:33 2020] GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 112 bytes in 71 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:36 +0100] "GET /user/api_key HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 13/51] 10.114.180.83 () {54 vars in 1476 bytes} [Wed May 6 23:25:36 2020] GET /user/api_key => generated 125745 bytes in 99 msecs (HTTP/1.1 200) 7 headers in 200 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:37 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 13/52] 10.114.180.83 () {52 vars in 1354 bytes} [Wed May 6 23:25:37 2020] GET /api/webhooks => generated 2 bytes in 21 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:37 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 14/53] 10.114.180.83 () {50 vars in 1312 bytes} [Wed May 6 23:25:37 2020] GET /api/users/current => generated 271 bytes in 61 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:37 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 14/54] 10.114.180.83 () {50 vars in 1312 bytes} [Wed May 6 23:25:37 2020] GET /api/configuration => generated 2300 bytes in 16 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:38 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 14/55] 10.114.180.83 () {52 vars in 1354 bytes} [Wed May 6 23:25:38 2020] GET /api/webhooks => generated 2 bytes in 21 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:38 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| 10.114.180.83 - - [06/May/2020:23:25:38 +0100] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 14/56] 10.114.180.83 () {54 vars in 1362 bytes} [Wed May 6 23:25:38 2020] GET /api/genomes => generated 55436 bytes in 21 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| [pid: 28739|app: 0|req: 15/57] 10.114.180.83 () {54 vars in 1407 bytes} [Wed May 6 23:25:38 2020] GET /api/datatypes?extension_only=False => generated 53304 bytes in 21 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:38 +0100] "GET /api/users/f2db41e1fa331b3e/api_key/inputs HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 15/58] 10.114.180.83 () {52 vars in 1369 bytes} [Wed May 6 23:25:38 2020] GET /api/users/f2db41e1fa331b3e/api_key/inputs => generated 340 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:38 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 15/59] 10.114.180.83 () {52 vars in 1386 bytes} [Wed May 6 23:25:38 2020] GET /history/current_history_json => generated 562 bytes in 75 msecs (HTTP/1.1 200) 5 headers in 171 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:38 +0100] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 15/60] 10.114.180.83 () {52 vars in 1382 bytes} [Wed May 6 23:25:38 2020] GET /api/users/f2db41e1fa331b3e => generated 271 bytes in 43 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:38 +0100] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 16/61] 10.114.180.83 () {52 vars in 1587 bytes} [Wed May 6 23:25:38 2020] GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True => generated 2 bytes in 48 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:38 +0100] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 16/62] 10.114.180.83 () {52 vars in 1507 bytes} [Wed May 6 23:25:38 2020] GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 112 bytes in 82 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:25:41 +0100] "PUT /api/users/f2db41e1fa331b3e/api_key/inputs HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 16/63] 10.114.180.83 () {58 vars in 1486 bytes} [Wed May 6 23:25:41 2020] PUT /api/users/f2db41e1fa331b3e/api_key/inputs => generated 386 bytes in 47 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.25.100.188 - - [06/May/2020:23:30:29 +0100] "GET /api/tool_shed_repositories?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28741|app: 0|req: 16/64] 10.25.100.188 () {38 vars in 604 bytes} [Wed May 6 23:30:29 2020] GET /api/tool_shed_repositories?key=ff1fadcdba102650fb96c7f486b45d6b => generated 2 bytes in 35 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:30:30,960 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:32,605 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Flow Text File Tools | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-06 23:30:32,611 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Adding new row for repository 'auto_collapse_pop' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:30:32,623 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:32,623 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:32,648 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Flow Text File Tools | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-06 23:30:32,657 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/immport-devteam/auto_collapse_pop' at 0:7632562ada41 | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:30:44,713 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:30:44,714 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowscore', which is used in the 'format' attribute of parameter 'profile' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:30:45,638 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:30:45,638 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowscore', which is used in the 'format' attribute of parameter 'profile' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:30:45,648 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:30:45,648 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowscore', which is used in the 'format' attribute of parameter 'profile' | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:45,650 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/auto_collapse_pop/auto_collapse_populations/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-06 23:30:45,651 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-06 23:30:45,695 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-06 23:30:46,598 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-06 23:30:46,598 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-06 23:30:56,804 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-06 23:30:56,812 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-06 23:30:57,246 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:30:57,246 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-06 23:30:57,294 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:30:57,294 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,296 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:30:57,315 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:30:57,318 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:30:57,321 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-06 23:30:57,322 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:30:57,322 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,323 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-06 23:30:57,324 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:30:57,324 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,326 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:30:57,329 [p:28737,w:1,m:0] [Thread-1] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:30:57,329 [p:28737,w:1,m:0] [Thread-1] Datatype class not found for extension 'flowscore', which is used in the 'format' attribute of parameter 'profile' | |
| galaxy.tools WARNING 2020-05-06 23:30:57,334 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:30:57,334 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,335 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,335 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (44.844 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,338 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,342 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,342 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,345 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,346 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,346 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,349 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,351 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,352 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,353 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,354 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,356 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,357 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,358 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,358 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,359 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,359 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,359 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,359 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,359 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,360 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,360 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,360 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,360 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,360 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,360 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,360 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,361 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,361 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,361 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,361 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,361 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/auto_collapse_pop/auto_collapse_populations/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,362 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,362 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,362 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:30:57,362 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (24.081 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,362 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_Bam_Bai_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,362 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,362 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,363 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,363 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,363 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,363 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_cram_to_bam_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,363 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bed_to_gff_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,363 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bed_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,364 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bed_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,364 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,364 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bed_to_fli_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,364 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bedgraph_to_bigwig | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,364 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_len_to_linecount | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,364 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,365 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,365 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,365 [p:28737,w:1,m:0] [Thread-1] Loaded converter: csv_to_tabular | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,365 [p:28737,w:1,m:0] [Thread-1] Loaded converter: tabular_to_csv | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,365 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_fasta_to_tabular | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,365 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_base_index | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,365 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_color_index | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,366 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_fasta_to_2bit | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,366 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_fasta_to_len | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,366 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_fasta_to_fai | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,366 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,366 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,366 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,366 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,367 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,367 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,367 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,367 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,368 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,368 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,368 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,368 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,368 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,369 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,369 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,369 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,369 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_gff_to_bed_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,369 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,370 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,370 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_gff_to_fli_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,370 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_gff_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,370 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,370 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,370 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,371 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,371 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_interval_to_bed_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,371 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_interval_to_bedstrict_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,371 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_interval_to_bed6_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,371 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_interval_to_bed12_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,371 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,372 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,372 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_interval_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,372 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_picard_interval_list_to_bed6 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,372 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_tar_to_directory | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,372 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_maf_to_fasta_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,372 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_maf_to_interval_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,372 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_encodepeak_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,372 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_encodepeak_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,373 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,373 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,373 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,373 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_sam_to_unsorted_bam | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,373 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,374 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,374 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_sam_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,374 [p:28737,w:1,m:0] [Thread-1] Loaded converter: tabular_to_dbnsfp | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,374 [p:28737,w:1,m:0] [Thread-1] Loaded converter: tabular_to_csv | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,374 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,374 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_vcf_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,375 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,375 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_vcf_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,375 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,375 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bcf_to_bcf_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,375 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,375 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_wig_to_bigwig | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,376 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_wiggle_to_interval_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,376 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,376 [p:28737,w:1,m:0] [Thread-1] Loaded converter: lped2fpedconvert | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,376 [p:28737,w:1,m:0] [Thread-1] Loaded converter: lped2pbedconvert | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,376 [p:28737,w:1,m:0] [Thread-1] Loaded converter: pbed2lpedconvert | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,376 [p:28737,w:1,m:0] [Thread-1] Loaded converter: pbed2ldindepconvert | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,376 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,376 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_biom1_to_biom2 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,377 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_biom2_to_biom1 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,377 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_SMILES_to_sdf | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,377 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_SMILES_to_inchi | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,377 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_SMILES_to_cml | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,377 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_SMILES_to_MOL | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,377 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_SMILES_to_MOL2 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,377 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_smiles_to_smiles | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,377 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_sdf_to_smiles | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,378 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_sdf_to_inchi | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,378 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_sdf_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,378 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_sdf_to_cml | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,378 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_inchi_to_smi | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,378 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_inchi_to_sdf | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,378 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_inchi_to_mol | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,378 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_inchi_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,378 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_inchi_to_cml | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,379 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_mol_to_smi | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,379 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_mol_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,379 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_mol_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,379 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_mol_to_cml | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,379 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_mol2_to_smi | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,379 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_mol2_to_sdf | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,379 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_mol2_to_inchi | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,380 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_mol2_to_mol | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,380 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_mol2_to_cml | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,380 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_cml_to_smiles | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,380 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_cml_to_inchi | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,380 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_cml_to_sdf | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,380 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_cml_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,380 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_ref_to_seq_taxomony | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,380 [p:28737,w:1,m:0] [Thread-1] Loaded converter: CONVERTER_neostorezip_to_neostore | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:30:57,384 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:30:57,387 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:30:57,390 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:30:57,393 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-06 23:30:57,394 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:30:57,436 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (189.464 ms) | |
| galaxy.queue_worker INFO 2020-05-06 23:30:57,447 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-06 23:30:57,447 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-06 23:30:57,538 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (91.084 ms) | |
| galaxy.config WARNING 2020-05-06 23:31:45,713 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Waiting for toolbox reload timed out after 60 seconds | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:31:45,737 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __pandas@0.17.1 pandas=0.17.1 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_conda/envs/__pandas@0.17.1 | |
| added / updated specs: | |
| - pandas=0.17.1 | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| _libgcc_mutex-0.1 | conda_forge 3 KB conda-forge | |
| _openmp_mutex-4.5 | 1_llvm 5 KB conda-forge | |
| certifi-2019.11.28 | py27_0 149 KB conda-forge | |
| ld_impl_linux-64-2.34 | h53a641e_0 616 KB conda-forge | |
| libblas-3.8.0 | 16_openblas 10 KB conda-forge | |
| libcblas-3.8.0 | 16_openblas 10 KB conda-forge | |
| libffi-3.2.1 | he1b5a44_1007 47 KB conda-forge | |
| libgcc-ng-9.2.0 | h24d8f2e_2 8.2 MB conda-forge | |
| libgfortran-ng-7.3.0 | hdf63c60_5 1.7 MB conda-forge | |
| liblapack-3.8.0 | 16_openblas 10 KB conda-forge | |
| libopenblas-0.3.9 | h5ec1e0e_0 7.8 MB conda-forge | |
| libstdcxx-ng-9.2.0 | hdf63c60_2 4.5 MB conda-forge | |
| llvm-openmp-10.0.0 | hc9558a2_0 2.8 MB conda-forge | |
| ncurses-6.1 | hf484d3e_1002 1.3 MB conda-forge | |
| numpy-1.9.3 |py27he5ce36f_1209 3.3 MB conda-forge | |
| pandas-0.17.1 | np19py27_0 12.2 MB | |
| pip-20.1 | pyh9f0ad1d_0 1.1 MB conda-forge | |
| python-2.7.15 |h5a48372_1011_cpython 12.2 MB conda-forge | |
| python-dateutil-2.8.1 | py_0 220 KB conda-forge | |
| pytz-2020.1 | pyh9f0ad1d_0 227 KB conda-forge | |
| readline-8.0 | hf8c457e_0 441 KB conda-forge | |
| setuptools-44.0.0 | py27_0 663 KB conda-forge | |
| six-1.14.0 | py_1 13 KB conda-forge | |
| sqlite-3.30.1 | hcee41ef_0 2.0 MB conda-forge | |
| tk-8.6.10 | hed695b0_0 3.2 MB conda-forge | |
| wheel-0.34.2 | py_1 24 KB conda-forge | |
| zlib-1.2.11 | h516909a_1006 105 KB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 62.7 MB | |
| The following NEW packages will be INSTALLED: | |
| _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge | |
| _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_llvm | |
| ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0 | |
| certifi conda-forge/linux-64::certifi-2019.11.28-py27_0 | |
| ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 | |
| libblas conda-forge/linux-64::libblas-3.8.0-16_openblas | |
| libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas | |
| libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 | |
| libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2 | |
| libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5 | |
| liblapack conda-forge/linux-64::liblapack-3.8.0-16_openblas | |
| libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0 | |
| libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2 | |
| llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0 | |
| ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002 | |
| numpy conda-forge/linux-64::numpy-1.9.3-py27he5ce36f_1209 | |
| openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_0 | |
| pandas pkgs/free/linux-64::pandas-0.17.1-np19py27_0 | |
| pip conda-forge/noarch::pip-20.1-pyh9f0ad1d_0 | |
| python conda-forge/linux-64::python-2.7.15-h5a48372_1011_cpython | |
| python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0 | |
| pytz conda-forge/noarch::pytz-2020.1-pyh9f0ad1d_0 | |
| readline conda-forge/linux-64::readline-8.0-hf8c457e_0 | |
| setuptools conda-forge/linux-64::setuptools-44.0.0-py27_0 | |
| six conda-forge/noarch::six-1.14.0-py_1 | |
| sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0 | |
| tk conda-forge/linux-64::tk-8.6.10-hed695b0_0 | |
| wheel conda-forge/noarch::wheel-0.34.2-py_1 | |
| zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1006 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:33:59,213 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Using dependency pandas version 0.17.1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:33:59,214 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Using dependency pandas version 0.17.1 of type conda | |
| 10.25.100.188 - - [06/May/2020:23:30:30 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28739|app: 0|req: 17/65] 10.25.100.188 () {42 vars in 751 bytes} [Wed May 6 23:30:30 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 663 bytes in 208936 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:34:00,528 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:02,084 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: FCS File Tools | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-06 23:34:02,091 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Adding new row for repository 'check_fcs_headers' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:34:02,100 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:02,100 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:02,126 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: FCS File Tools | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-06 23:34:02,135 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/immport-devteam/check_fcs_headers' at 0:d3957a51cc51 | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:34:09,542 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:34:10,495 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:34:10,505 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:10,507 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/check_fcs_headers/get_fcs_headers/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-06 23:34:10,508 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-06 23:34:10,531 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-06 23:34:11,342 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-06 23:34:11,342 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-06 23:34:21,484 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-06 23:34:21,489 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-06 23:34:21,654 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:34:21,654 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-06 23:34:21,690 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:34:21,691 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,692 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:34:21,706 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:34:21,708 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:34:21,711 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-06 23:34:21,711 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:34:21,712 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,713 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-06 23:34:21,714 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:34:21,714 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,715 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:34:21,717 [p:28737,w:1,m:0] [Thread-1] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools WARNING 2020-05-06 23:34:21,720 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:34:21,720 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,721 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,721 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (32.171 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,722 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,725 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,726 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,729 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,729 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,729 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,733 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,735 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,735 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,736 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,737 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,740 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,740 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,741 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,741 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,742 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,743 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,743 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,743 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,743 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,743 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,743 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,743 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,744 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,744 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,744 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,744 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,744 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,744 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,744 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,745 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/check_fcs_headers/get_fcs_headers/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,745 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,745 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,746 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,746 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:34:21,746 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (24.426 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:34:21,752 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:34:21,755 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:34:21,757 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:34:21,759 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-06 23:34:21,760 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:34:21,770 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (116.190 ms) | |
| galaxy.queue_worker INFO 2020-05-06 23:34:21,780 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-06 23:34:21,780 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-06 23:34:21,804 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (24.158 ms) | |
| 10.114.180.83 - - [06/May/2020:23:34:57 +0100] "GET /user/api_key HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 17/66] 10.114.180.83 () {56 vars in 1507 bytes} [Wed May 6 23:34:57 2020] GET /user/api_key => generated 129750 bytes in 119 msecs (HTTP/1.1 200) 7 headers in 200 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:34:58 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 17/67] 10.114.180.83 () {52 vars in 1354 bytes} [Wed May 6 23:34:58 2020] GET /api/webhooks => generated 2 bytes in 20 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:34:58 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 18/68] 10.114.180.83 () {50 vars in 1312 bytes} [Wed May 6 23:34:58 2020] GET /api/users/current => generated 271 bytes in 50 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:34:58 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 18/69] 10.114.180.83 () {50 vars in 1312 bytes} [Wed May 6 23:34:58 2020] GET /api/configuration => generated 2300 bytes in 21 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:34:59 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 18/70] 10.114.180.83 () {52 vars in 1354 bytes} [Wed May 6 23:34:59 2020] GET /api/webhooks => generated 2 bytes in 19 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:34:59 +0100] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 19/71] 10.114.180.83 () {54 vars in 1407 bytes} [Wed May 6 23:34:59 2020] GET /api/datatypes?extension_only=False => generated 53304 bytes in 21 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:34:59 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 19/72] 10.114.180.83 () {54 vars in 1362 bytes} [Wed May 6 23:34:59 2020] GET /api/genomes => generated 55436 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:34:59 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 19/73] 10.114.180.83 () {52 vars in 1386 bytes} [Wed May 6 23:34:59 2020] GET /history/current_history_json => generated 562 bytes in 59 msecs (HTTP/1.1 200) 5 headers in 171 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:34:59 +0100] "GET /api/users/f2db41e1fa331b3e/api_key/inputs HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 20/74] 10.114.180.83 () {52 vars in 1369 bytes} [Wed May 6 23:34:59 2020] GET /api/users/f2db41e1fa331b3e/api_key/inputs => generated 358 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:34:59 +0100] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 20/75] 10.114.180.83 () {52 vars in 1382 bytes} [Wed May 6 23:34:59 2020] GET /api/users/f2db41e1fa331b3e => generated 271 bytes in 47 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:34:59 +0100] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 20/76] 10.114.180.83 () {52 vars in 1587 bytes} [Wed May 6 23:34:59 2020] GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True => generated 2 bytes in 55 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:34:59 +0100] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:60089/user/api_key" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 21/77] 10.114.180.83 () {52 vars in 1507 bytes} [Wed May 6 23:34:59 2020] GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 112 bytes in 86 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:35:05 +0100] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/immport-devteam/check_fcs_headers/get_fcs_headers/1.0/build?version=1.0&__identifer=bcu976jjj2m&tool_version=1.0 HTTP/1.1" 200 - "http://localhost:60089/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimmport-devteam%2Fcheck_fcs_headers%2Fget_fcs_headers%2F1.0&version=1.0&__identifer=bcu976jjj2m" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 21/78] 10.114.180.83 () {54 vars in 1766 bytes} [Wed May 6 23:35:05 2020] GET /api/tools/toolshed.g2.bx.psu.edu/repos/immport-devteam/check_fcs_headers/get_fcs_headers/1.0/build?version=1.0&__identifer=bcu976jjj2m&tool_version=1.0 => generated 2666 bytes in 188 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:35:06 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 21/79] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:35:06 2020] GET /api/webhooks => generated 2 bytes in 31 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.config WARNING 2020-05-06 23:35:10,551 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Waiting for toolbox reload timed out after 60 seconds | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:35:10,572 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-1c69867621cc696bf9c174e09a7fa90a91900c4fe7fa6f1c45f9f13758c5da7c r=3.3.0 bioconductor-flowcore=1.38.2 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... failed | |
| PackagesNotFoundError: The following packages are not available from current channels: | |
| - r=3.3.0 | |
| Current channels: | |
| - https://conda.anaconda.org/iuc/linux-64 | |
| - https://conda.anaconda.org/iuc/noarch | |
| - https://conda.anaconda.org/conda-forge/linux-64 | |
| - https://conda.anaconda.org/conda-forge/noarch | |
| - https://conda.anaconda.org/bioconda/linux-64 | |
| - https://conda.anaconda.org/bioconda/noarch | |
| - https://repo.anaconda.com/pkgs/main/linux-64 | |
| - https://repo.anaconda.com/pkgs/main/noarch | |
| - https://repo.anaconda.com/pkgs/free/linux-64 | |
| - https://repo.anaconda.com/pkgs/free/noarch | |
| - https://repo.anaconda.com/pkgs/r/linux-64 | |
| - https://repo.anaconda.com/pkgs/r/noarch | |
| To search for alternate channels that may provide the conda package you're | |
| looking for, navigate to | |
| https://anaconda.org | |
| and use the search bar at the top of the page. | |
| galaxy.tool_util.deps.resolvers.conda DEBUG 2020-05-06 23:35:19,758 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Removing failed conda install of [CondaTarget[r,version=3.3.0], CondaTarget[bioconductor-flowcore,version=1.38.2]] | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:35:19,761 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __r@3.3.0 r=3.3.0 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... failed | |
| PackagesNotFoundError: The following packages are not available from current channels: | |
| - r=3.3.0 | |
| Current channels: | |
| - https://conda.anaconda.org/iuc/linux-64 | |
| - https://conda.anaconda.org/iuc/noarch | |
| - https://conda.anaconda.org/conda-forge/linux-64 | |
| - https://conda.anaconda.org/conda-forge/noarch | |
| - https://conda.anaconda.org/bioconda/linux-64 | |
| - https://conda.anaconda.org/bioconda/noarch | |
| - https://repo.anaconda.com/pkgs/main/linux-64 | |
| - https://repo.anaconda.com/pkgs/main/noarch | |
| - https://repo.anaconda.com/pkgs/free/linux-64 | |
| - https://repo.anaconda.com/pkgs/free/noarch | |
| - https://repo.anaconda.com/pkgs/r/linux-64 | |
| - https://repo.anaconda.com/pkgs/r/noarch | |
| To search for alternate channels that may provide the conda package you're | |
| looking for, navigate to | |
| https://anaconda.org | |
| and use the search bar at the top of the page. | |
| galaxy.tool_util.deps.resolvers.conda DEBUG 2020-05-06 23:35:27,533 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Removing failed conda install of r, version '3.3.0' | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:35:27,535 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __bioconductor-flowcore@1.38.2 bioconductor-flowcore=1.38.2 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... 10.25.100.188 - - [06/May/2020:23:39:00 +0100] "GET /api/tool_shed_repositories?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28739|app: 0|req: 22/80] 10.25.100.188 () {38 vars in 604 bytes} [Wed May 6 23:39:00 2020] GET /api/tool_shed_repositories?key=ff1fadcdba102650fb96c7f486b45d6b => generated 1323 bytes in 16 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:39:02,183 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:06,997 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-06 23:39:07,000 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Adding new row for repository 'dropletutils_read_10x' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:39:07,005 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:07,005 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:07,018 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-06 23:39:07,024 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x' at 2:48c1e7b39675 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:15,507 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.3+galaxy0, version: 1.0.3+galaxy0 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-06 23:39:15,508 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-06 23:39:15,524 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-06 23:39:16,109 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-06 23:39:16,110 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-06 23:39:26,199 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-06 23:39:26,203 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-06 23:39:26,673 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:39:26,673 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-06 23:39:26,695 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:39:26,695 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,696 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:39:26,704 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:39:26,705 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:39:26,706 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-06 23:39:26,707 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:39:26,707 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,708 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-06 23:39:26,708 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:39:26,708 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,709 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools WARNING 2020-05-06 23:39:26,710 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:39:26,710 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,710 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,710 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (16.202 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,710 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,713 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,713 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,715 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,715 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,715 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,717 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,718 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,719 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,719 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,720 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,721 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,722 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,722 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,722 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,723 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,723 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,723 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,723 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,723 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,723 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,723 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,723 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,724 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,724 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,724 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,724 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.3+galaxy0, version: 1.0.3+galaxy0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,724 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,724 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,724 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,724 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,725 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,725 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,725 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,725 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:39:26,725 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (14.748 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:39:26,730 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:39:26,732 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:39:26,733 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:39:26,735 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-06 23:39:26,735 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:39:26,742 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (68.571 ms) | |
| galaxy.config DEBUG 2020-05-06 23:39:26,743 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Finished waiting for toolbox reload (11219.563 ms) | |
| galaxy.queue_worker INFO 2020-05-06 23:39:26,750 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-06 23:39:26,751 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:39:26,764 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __dropletutils-scripts@0.0.4 dropletutils-scripts=0.0.4 | |
| galaxy.tools.search DEBUG 2020-05-06 23:39:26,786 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (35.469 ms) | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| 10.114.180.83 - - [06/May/2020:23:41:14 +0100] "GET / HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 22/81] 10.114.180.83 () {56 vars in 1483 bytes} [Wed May 6 23:41:14 2020] GET / => generated 125745 bytes in 63 msecs (HTTP/1.1 200) 7 headers in 200 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:15 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 23/82] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:41:15 2020] GET /api/webhooks => generated 2 bytes in 11 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:15 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 23/83] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:41:15 2020] GET /api/users/current => generated 271 bytes in 26 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:15 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 24/84] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:41:15 2020] GET /api/configuration => generated 2300 bytes in 10 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:15 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 24/85] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:41:15 2020] GET /api/webhooks => generated 2 bytes in 10 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:15 +0100] "GET /scripts/bundled/assets/e417938def579af5c4d237a1cc340445.png HTTP/1.1" 404 227 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 25/86] 10.114.180.83 () {50 vars in 1393 bytes} [Wed May 6 23:41:15 2020] GET /scripts/bundled/assets/e417938def579af5c4d237a1cc340445.png => generated 227 bytes in 1 msecs (HTTP/1.1 404) 2 headers in 87 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:16 +0100] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 25/87] 10.114.180.83 () {54 vars in 1395 bytes} [Wed May 6 23:41:16 2020] GET /api/datatypes?extension_only=False => generated 53304 bytes in 12 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:16 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 26/88] 10.114.180.83 () {54 vars in 1350 bytes} [Wed May 6 23:41:16 2020] GET /api/genomes => generated 55436 bytes in 13 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:16 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 26/89] 10.114.180.83 () {52 vars in 1374 bytes} [Wed May 6 23:41:16 2020] GET /history/current_history_json => generated 562 bytes in 31 msecs (HTTP/1.1 200) 5 headers in 171 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:16 +0100] "GET /welcome HTTP/1.1" 302 267 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 27/90] 10.114.180.83 () {52 vars in 1411 bytes} [Wed May 6 23:41:16 2020] GET /welcome => generated 267 bytes in 9 msecs (HTTP/1.1 302) 4 headers in 166 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:16 +0100] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 27/91] 10.114.180.83 () {52 vars in 1370 bytes} [Wed May 6 23:41:16 2020] GET /api/users/f2db41e1fa331b3e => generated 271 bytes in 24 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:16 +0100] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 28/92] 10.114.180.83 () {52 vars in 1575 bytes} [Wed May 6 23:41:16 2020] GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True => generated 2 bytes in 28 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:16 +0100] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 28/93] 10.114.180.83 () {52 vars in 1495 bytes} [Wed May 6 23:41:16 2020] GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 112 bytes in 39 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:40 +0100] "GET / HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 29/94] 10.114.180.83 () {56 vars in 1483 bytes} [Wed May 6 23:41:40 2020] GET / => generated 127830 bytes in 40 msecs (HTTP/1.1 200) 7 headers in 200 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:41 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 29/95] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:41:41 2020] GET /api/webhooks => generated 2 bytes in 11 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:41 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 30/96] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:41:41 2020] GET /api/users/current => generated 271 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:41 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 30/97] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:41:41 2020] GET /api/configuration => generated 2300 bytes in 10 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:41 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 31/98] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:41:41 2020] GET /api/webhooks => generated 2 bytes in 10 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:41 +0100] "GET /scripts/bundled/assets/e417938def579af5c4d237a1cc340445.png HTTP/1.1" 404 227 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 31/99] 10.114.180.83 () {50 vars in 1393 bytes} [Wed May 6 23:41:41 2020] GET /scripts/bundled/assets/e417938def579af5c4d237a1cc340445.png => generated 227 bytes in 1 msecs (HTTP/1.1 404) 2 headers in 87 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:42 +0100] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 32/100] 10.114.180.83 () {54 vars in 1395 bytes} [Wed May 6 23:41:42 2020] GET /api/datatypes?extension_only=False => generated 53304 bytes in 11 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:42 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 32/101] 10.114.180.83 () {54 vars in 1350 bytes} [Wed May 6 23:41:42 2020] GET /api/genomes => generated 55436 bytes in 12 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:42 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 33/102] 10.114.180.83 () {52 vars in 1374 bytes} [Wed May 6 23:41:42 2020] GET /history/current_history_json => generated 562 bytes in 34 msecs (HTTP/1.1 200) 5 headers in 171 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:42 +0100] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 33/103] 10.114.180.83 () {52 vars in 1370 bytes} [Wed May 6 23:41:42 2020] GET /api/users/f2db41e1fa331b3e => generated 271 bytes in 24 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:42 +0100] "GET /welcome HTTP/1.1" 302 267 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 34/104] 10.114.180.83 () {52 vars in 1411 bytes} [Wed May 6 23:41:42 2020] GET /welcome => generated 267 bytes in 10 msecs (HTTP/1.1 302) 4 headers in 166 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:42 +0100] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 34/105] 10.114.180.83 () {52 vars in 1575 bytes} [Wed May 6 23:41:42 2020] GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True => generated 2 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:41:42 +0100] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 35/106] 10.114.180.83 () {52 vars in 1495 bytes} [Wed May 6 23:41:42 2020] GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 112 bytes in 40 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:40 +0100] "GET / HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 35/107] 10.114.180.83 () {56 vars in 1483 bytes} [Wed May 6 23:42:40 2020] GET / => generated 127830 bytes in 40 msecs (HTTP/1.1 200) 7 headers in 200 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:41 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 36/108] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:42:41 2020] GET /api/webhooks => generated 2 bytes in 10 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:41 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 36/109] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:42:41 2020] GET /api/users/current => generated 271 bytes in 25 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:41 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 37/110] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:42:41 2020] GET /api/configuration => generated 2300 bytes in 9 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:42 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 37/111] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:42:42 2020] GET /api/webhooks => generated 2 bytes in 11 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:42 +0100] "GET /scripts/bundled/assets/e417938def579af5c4d237a1cc340445.png HTTP/1.1" 404 227 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 38/112] 10.114.180.83 () {50 vars in 1393 bytes} [Wed May 6 23:42:42 2020] GET /scripts/bundled/assets/e417938def579af5c4d237a1cc340445.png => generated 227 bytes in 1 msecs (HTTP/1.1 404) 2 headers in 87 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:42 +0100] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 38/113] 10.114.180.83 () {54 vars in 1395 bytes} [Wed May 6 23:42:42 2020] GET /api/datatypes?extension_only=False => generated 53304 bytes in 11 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:42 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 39/114] 10.114.180.83 () {54 vars in 1350 bytes} [Wed May 6 23:42:42 2020] GET /api/genomes => generated 55436 bytes in 12 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:42 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 39/115] 10.114.180.83 () {52 vars in 1374 bytes} [Wed May 6 23:42:42 2020] GET /history/current_history_json => generated 562 bytes in 31 msecs (HTTP/1.1 200) 5 headers in 171 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:42 +0100] "GET /welcome HTTP/1.1" 302 267 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 40/116] 10.114.180.83 () {52 vars in 1411 bytes} [Wed May 6 23:42:42 2020] GET /welcome => generated 267 bytes in 9 msecs (HTTP/1.1 302) 4 headers in 166 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:42 +0100] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 40/117] 10.114.180.83 () {52 vars in 1370 bytes} [Wed May 6 23:42:42 2020] GET /api/users/f2db41e1fa331b3e => generated 271 bytes in 25 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:42 +0100] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 41/118] 10.114.180.83 () {52 vars in 1575 bytes} [Wed May 6 23:42:42 2020] GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True => generated 2 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:42 +0100] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 41/119] 10.114.180.83 () {52 vars in 1495 bytes} [Wed May 6 23:42:42 2020] GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 112 bytes in 40 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:45 +0100] "GET / HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 42/120] 10.114.180.83 () {56 vars in 1483 bytes} [Wed May 6 23:42:45 2020] GET / => generated 125745 bytes in 34 msecs (HTTP/1.1 200) 7 headers in 200 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:46 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 42/121] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:42:46 2020] GET /api/webhooks => generated 2 bytes in 13 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:46 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 43/122] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:42:46 2020] GET /api/configuration => generated 2300 bytes in 9 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:46 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 43/123] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:42:46 2020] GET /api/users/current => generated 271 bytes in 26 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:46 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 44/124] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:42:46 2020] GET /api/webhooks => generated 2 bytes in 11 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:46 +0100] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 44/125] 10.114.180.83 () {54 vars in 1395 bytes} [Wed May 6 23:42:46 2020] GET /api/datatypes?extension_only=False => generated 53304 bytes in 11 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:46 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 45/126] 10.114.180.83 () {54 vars in 1350 bytes} [Wed May 6 23:42:46 2020] GET /api/genomes => generated 55436 bytes in 11 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:46 +0100] "GET /welcome HTTP/1.1" 302 267 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 46/127] 10.114.180.83 () {52 vars in 1411 bytes} [Wed May 6 23:42:46 2020] GET /welcome => generated 267 bytes in 7 msecs (HTTP/1.1 302) 4 headers in 166 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:46 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 45/128] 10.114.180.83 () {52 vars in 1374 bytes} [Wed May 6 23:42:46 2020] GET /history/current_history_json => generated 562 bytes in 30 msecs (HTTP/1.1 200) 5 headers in 171 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:46 +0100] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 47/129] 10.114.180.83 () {52 vars in 1370 bytes} [Wed May 6 23:42:46 2020] GET /api/users/f2db41e1fa331b3e => generated 271 bytes in 25 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:46 +0100] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 46/130] 10.114.180.83 () {52 vars in 1575 bytes} [Wed May 6 23:42:46 2020] GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True => generated 2 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:47 +0100] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 48/131] 10.114.180.83 () {52 vars in 1495 bytes} [Wed May 6 23:42:47 2020] GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 112 bytes in 42 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:48 +0100] "GET / HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 47/132] 10.114.180.83 () {56 vars in 1483 bytes} [Wed May 6 23:42:48 2020] GET / => generated 125745 bytes in 31 msecs (HTTP/1.1 200) 7 headers in 200 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:49 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 49/133] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:42:49 2020] GET /api/webhooks => generated 2 bytes in 10 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:49 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 50/134] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:42:49 2020] GET /api/configuration => generated 2300 bytes in 9 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:49 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 48/135] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:42:49 2020] GET /api/users/current => generated 271 bytes in 25 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:50 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 51/136] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:42:50 2020] GET /api/webhooks => generated 2 bytes in 10 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:50 +0100] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 49/137] 10.114.180.83 () {54 vars in 1395 bytes} [Wed May 6 23:42:50 2020] GET /api/datatypes?extension_only=False => generated 53304 bytes in 10 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:50 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 52/138] 10.114.180.83 () {54 vars in 1350 bytes} [Wed May 6 23:42:50 2020] GET /api/genomes => generated 55436 bytes in 11 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:50 +0100] "GET /welcome HTTP/1.1" 302 267 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 50/139] 10.114.180.83 () {52 vars in 1411 bytes} [Wed May 6 23:42:50 2020] GET /welcome => generated 267 bytes in 10 msecs (HTTP/1.1 302) 4 headers in 166 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:50 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 53/140] 10.114.180.83 () {52 vars in 1374 bytes} [Wed May 6 23:42:50 2020] GET /history/current_history_json => generated 562 bytes in 33 msecs (HTTP/1.1 200) 5 headers in 171 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:50 +0100] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 51/141] 10.114.180.83 () {52 vars in 1370 bytes} [Wed May 6 23:42:50 2020] GET /api/users/f2db41e1fa331b3e => generated 271 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:50 +0100] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 54/142] 10.114.180.83 () {52 vars in 1575 bytes} [Wed May 6 23:42:50 2020] GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True => generated 2 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:50 +0100] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 52/143] 10.114.180.83 () {52 vars in 1495 bytes} [Wed May 6 23:42:50 2020] GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 112 bytes in 36 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:53 +0100] "GET / HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 55/144] 10.114.180.83 () {56 vars in 1483 bytes} [Wed May 6 23:42:53 2020] GET / => generated 127830 bytes in 33 msecs (HTTP/1.1 200) 7 headers in 200 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:54 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 53/145] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:42:54 2020] GET /api/webhooks => generated 2 bytes in 11 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:54 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 54/146] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:42:54 2020] GET /api/configuration => generated 2300 bytes in 10 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:54 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 56/147] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:42:54 2020] GET /api/users/current => generated 271 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:55 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 55/148] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:42:55 2020] GET /api/webhooks => generated 2 bytes in 10 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:55 +0100] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 57/149] 10.114.180.83 () {54 vars in 1395 bytes} [Wed May 6 23:42:55 2020] GET /api/datatypes?extension_only=False => generated 53304 bytes in 11 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:55 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 56/150] 10.114.180.83 () {54 vars in 1350 bytes} [Wed May 6 23:42:55 2020] GET /api/genomes => generated 55436 bytes in 11 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:55 +0100] "GET /welcome HTTP/1.1" 302 267 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 57/151] 10.114.180.83 () {52 vars in 1411 bytes} [Wed May 6 23:42:55 2020] GET /welcome => generated 267 bytes in 8 msecs (HTTP/1.1 302) 4 headers in 166 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:55 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 58/152] 10.114.180.83 () {52 vars in 1374 bytes} [Wed May 6 23:42:55 2020] GET /history/current_history_json => generated 562 bytes in 34 msecs (HTTP/1.1 200) 5 headers in 171 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:55 +0100] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 58/153] 10.114.180.83 () {52 vars in 1370 bytes} [Wed May 6 23:42:55 2020] GET /api/users/f2db41e1fa331b3e => generated 271 bytes in 26 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:55 +0100] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 59/154] 10.114.180.83 () {52 vars in 1575 bytes} [Wed May 6 23:42:55 2020] GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True => generated 2 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:42:55 +0100] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 59/155] 10.114.180.83 () {52 vars in 1495 bytes} [Wed May 6 23:42:55 2020] GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 112 bytes in 41 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:43:00 +0100] "GET /api/tools/toolshed.g2.bx.psu.edu/repos/immport-devteam/auto_collapse_pop/auto_collapse_populations/1.0/build?version=1.0&__identifer=s8v96tvr2t&tool_version=1.0 HTTP/1.1" 200 - "http://localhost:60089/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimmport-devteam%2Fauto_collapse_pop%2Fauto_collapse_populations%2F1.0&version=1.0&__identifer=s8v96tvr2t" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 60/156] 10.114.180.83 () {54 vars in 1793 bytes} [Wed May 6 23:43:00 2020] GET /api/tools/toolshed.g2.bx.psu.edu/repos/immport-devteam/auto_collapse_pop/auto_collapse_populations/1.0/build?version=1.0&__identifer=s8v96tvr2t&tool_version=1.0 => generated 4507 bytes in 45 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:43:00 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28741|app: 0|req: 60/157] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:43:00 2020] GET /api/webhooks => generated 2 bytes in 9 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_conda/envs/__dropletutils-scripts@0.0.4 | |
| added / updated specs: | |
| - dropletutils-scripts=0.0.4 | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| _r-mutex-1.0.1 | anacondar_1 3 KB conda-forge | |
| binutils_impl_linux-64-2.34| h53a641e_0 9.2 MB conda-forge | |
| binutils_linux-64-2.34 | hc952b39_18 21 KB conda-forge | |
| bioconductor-beachmat-2.0.0| r36he1b5a44_1 1.1 MB bioconda | |
| bioconductor-biobase-2.44.0| r36h516909a_1 2.3 MB bioconda | |
| bioconductor-biocgenerics-0.30.0| r36_1 683 KB bioconda | |
| bioconductor-biocparallel-1.18.0| r36he1b5a44_1 1.1 MB bioconda | |
| bioconductor-delayedarray-0.10.0| r36h516909a_1 2.2 MB bioconda | |
| bioconductor-dropletutils-1.4.2| r36he1b5a44_0 2.2 MB bioconda | |
| bioconductor-edger-3.26.5 | r36he1b5a44_0 2.2 MB bioconda | |
| bioconductor-genomeinfodb-1.20.0| r36_1 3.8 MB bioconda | |
| bioconductor-genomeinfodbdata-1.2.2| r36_0 6 KB bioconda | |
| bioconductor-genomicranges-1.36.0| r36h516909a_1 2.1 MB bioconda | |
| bioconductor-hdf5array-1.12.1| r36h516909a_0 9.5 MB bioconda | |
| bioconductor-iranges-2.18.2| r36h516909a_0 2.3 MB bioconda | |
| bioconductor-limma-3.40.2 | r36h516909a_0 2.6 MB bioconda | |
| bioconductor-rhdf5-2.28.0 | r36he1b5a44_1 2.4 MB bioconda | |
| bioconductor-rhdf5lib-1.6.0| r36h516909a_1 3.6 MB bioconda | |
| bioconductor-s4vectors-0.22.0| r36h516909a_1 2.0 MB bioconda | |
| bioconductor-singlecellexperiment-1.6.0| r36_1 1.3 MB bioconda | |
| bioconductor-summarizedexperiment-1.14.0| r36_1 2.5 MB bioconda | |
| bioconductor-xvector-0.24.0| r36h516909a_1 721 KB bioconda | |
| bioconductor-zlibbioc-1.30.0| r36h516909a_1 112 KB bioconda | |
| bwidget-1.9.14 | 0 119 KB conda-forge | |
| bzip2-1.0.8 | h516909a_2 396 KB conda-forge | |
| cairo-1.16.0 | hcf35c78_1003 1.5 MB conda-forge | |
| certifi-2020.4.5.1 | py38h32f6830_0 151 KB conda-forge | |
| curl-7.69.1 | h33f0ec9_0 137 KB conda-forge | |
| dropletutils-scripts-0.0.4 | 1 17 KB bioconda | |
| fontconfig-2.13.1 | h86ecdb6_1001 340 KB conda-forge | |
| freetype-2.10.1 | he06d7ca_0 877 KB conda-forge | |
| fribidi-1.0.9 | h516909a_0 113 KB conda-forge | |
| gcc_impl_linux-64-7.3.0 | hd420e75_5 70.6 MB conda-forge | |
| gcc_linux-64-7.3.0 | h553295d_18 22 KB conda-forge | |
| gettext-0.19.8.1 | hc5be6a0_1002 3.6 MB conda-forge | |
| gfortran_impl_linux-64-7.3.0| hdf63c60_5 9.4 MB conda-forge | |
| gfortran_linux-64-7.3.0 | h553295d_18 21 KB conda-forge | |
| glib-2.58.3 |py38h73cb85d_1004 3.3 MB conda-forge | |
| graphite2-1.3.13 | he1b5a44_1001 102 KB conda-forge | |
| gsl-2.6 | h294904e_0 3.1 MB conda-forge | |
| gxx_impl_linux-64-7.3.0 | hdf63c60_5 19.1 MB conda-forge | |
| gxx_linux-64-7.3.0 | h553295d_18 21 KB conda-forge | |
| harfbuzz-2.4.0 | h9f30f68_3 1.5 MB conda-forge | |
| icu-64.2 | he1b5a44_1 12.6 MB conda-forge | |
| jpeg-9c | h14c3975_1001 251 KB conda-forge | |
| krb5-1.17.1 | h2fd8d38_0 1.5 MB conda-forge | |
| libcurl-7.69.1 | hf7181ac_0 573 KB conda-forge | |
| libedit-3.1.20170329 | hf8c457e_1001 172 KB conda-forge | |
| libgomp-9.2.0 | h24d8f2e_2 816 KB conda-forge | |
| libiconv-1.15 | h516909a_1006 2.0 MB conda-forge | |
| libpng-1.6.37 | hed695b0_1 308 KB conda-forge | |
| libssh2-1.8.2 | h22169c7_2 257 KB conda-forge | |
| libtiff-4.1.0 | hc7e4089_6 668 KB conda-forge | |
| libuuid-2.32.1 | h14c3975_1000 26 KB conda-forge | |
| libwebp-base-1.1.0 | h516909a_3 845 KB conda-forge | |
| libxcb-1.13 | h14c3975_1002 396 KB conda-forge | |
| libxml2-2.9.10 | hee79883_0 1.3 MB conda-forge | |
| lz4-c-1.9.2 | he1b5a44_1 226 KB conda-forge | |
| make-4.3 | h516909a_0 505 KB conda-forge | |
| openblas-0.3.9 | he1df0ab_0 8.3 MB conda-forge | |
| pango-1.42.4 | h7062337_4 521 KB conda-forge | |
| pcre-8.44 | he1b5a44_0 261 KB conda-forge | |
| pixman-0.38.0 | h516909a_1003 594 KB conda-forge | |
| pthread-stubs-0.4 | h14c3975_1001 5 KB conda-forge | |
| python-3.8.2 |he5300dc_7_cpython 70.8 MB conda-forge | |
| python_abi-3.8 | 1_cp38 4 KB conda-forge | |
| r-base-3.6.3 | h316533a_2 23.3 MB conda-forge | |
| r-bh-1.72.0_3 | r36h6115d3f_1 10.5 MB conda-forge | |
| r-bitops-1.0_6 | r36hcdcec82_1004 39 KB conda-forge | |
| r-dqrng-0.2.1 | r36h0357c0b_2 165 KB conda-forge | |
| r-formatr-1.7 | r36h6115d3f_2 166 KB conda-forge | |
| r-futile.logger-1.4.3 | r36h6115d3f_1003 108 KB conda-forge | |
| r-futile.options-1.0.1 | r36h6115d3f_1002 27 KB conda-forge | |
| r-getopt-1.20.3 | r36_2 45 KB conda-forge | |
| r-lambda.r-1.2.4 | r36h6115d3f_1 120 KB conda-forge | |
| r-lattice-0.20_41 | r36hcdcec82_2 1.1 MB conda-forge | |
| r-locfit-1.5_9.4 | r36hcdcec82_1 563 KB conda-forge | |
| r-matrix-1.2_18 | r36h7fa42b6_3 3.8 MB conda-forge | |
| r-matrixstats-0.56.0 | r36hcdcec82_1 925 KB conda-forge | |
| r-optparse-1.6.6 | r36h6115d3f_1 79 KB conda-forge | |
| r-r.methodss3-1.8.0 | r36h6115d3f_1 94 KB conda-forge | |
| r-r.oo-1.23.0 | r36h6115d3f_1 965 KB conda-forge | |
| r-r.utils-2.9.2 | r36h6115d3f_1 1.4 MB conda-forge | |
| r-rcpp-1.0.4.6 | r36h0357c0b_1 1.9 MB conda-forge | |
| r-rcurl-1.98_1.2 | r36hcdcec82_1 921 KB conda-forge | |
| r-sitmo-2.0.1 | r36h0357c0b_2 155 KB conda-forge | |
| r-snow-0.4_3 | r36h6115d3f_1002 124 KB conda-forge | |
| r-workflowscriptscommon-0.0.7| r36_0 28 KB bioconda | |
| sed-4.7 | h1bed415_1000 245 KB conda-forge | |
| setuptools-46.1.3 | py38h32f6830_0 635 KB conda-forge | |
| tktable-2.10 | h555a92e_3 89 KB conda-forge | |
| xorg-kbproto-1.0.7 | h14c3975_1002 26 KB conda-forge | |
| xorg-libice-1.0.10 | h516909a_0 57 KB conda-forge | |
| xorg-libsm-1.2.3 | h84519dc_1000 25 KB conda-forge | |
| xorg-libx11-1.6.9 | h516909a_0 918 KB conda-forge | |
| xorg-libxau-1.0.9 | h14c3975_0 13 KB conda-forge | |
| xorg-libxdmcp-1.1.3 | h516909a_0 18 KB conda-forge | |
| xorg-libxext-1.3.4 | h516909a_0 51 KB conda-forge | |
| xorg-libxrender-0.9.10 | h516909a_1002 31 KB conda-forge | |
| xorg-renderproto-0.11.1 | h14c3975_1002 8 KB conda-forge | |
| xorg-xextproto-7.3.0 | h14c3975_1002 27 KB conda-forge | |
| xorg-xproto-7.0.31 | h14c3975_1007 72 KB conda-forge | |
| xz-5.2.5 | h516909a_0 430 KB conda-forge | |
| zstd-1.4.4 | h6597ccf_3 991 KB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 321.0 MB | |
| The following NEW packages will be INSTALLED: | |
| _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge | |
| _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_llvm | |
| _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 | |
| binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.34-h53a641e_0 | |
| binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.34-hc952b39_18 | |
| bioconductor-beac~ bioconda/linux-64::bioconductor-beachmat-2.0.0-r36he1b5a44_1 | |
| bioconductor-biob~ bioconda/linux-64::bioconductor-biobase-2.44.0-r36h516909a_1 | |
| bioconductor-bioc~ bioconda/noarch::bioconductor-biocgenerics-0.30.0-r36_1 | |
| bioconductor-bioc~ bioconda/linux-64::bioconductor-biocparallel-1.18.0-r36he1b5a44_1 | |
| bioconductor-dela~ bioconda/linux-64::bioconductor-delayedarray-0.10.0-r36h516909a_1 | |
| bioconductor-drop~ bioconda/linux-64::bioconductor-dropletutils-1.4.2-r36he1b5a44_0 | |
| bioconductor-edger bioconda/linux-64::bioconductor-edger-3.26.5-r36he1b5a44_0 | |
| bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodb-1.20.0-r36_1 | |
| bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodbdata-1.2.2-r36_0 | |
| bioconductor-geno~ bioconda/linux-64::bioconductor-genomicranges-1.36.0-r36h516909a_1 | |
| bioconductor-hdf5~ bioconda/linux-64::bioconductor-hdf5array-1.12.1-r36h516909a_0 | |
| bioconductor-iran~ bioconda/linux-64::bioconductor-iranges-2.18.2-r36h516909a_0 | |
| bioconductor-limma bioconda/linux-64::bioconductor-limma-3.40.2-r36h516909a_0 | |
| bioconductor-rhdf5 bioconda/linux-64::bioconductor-rhdf5-2.28.0-r36he1b5a44_1 | |
| bioconductor-rhdf~ bioconda/linux-64::bioconductor-rhdf5lib-1.6.0-r36h516909a_1 | |
| bioconductor-s4ve~ bioconda/linux-64::bioconductor-s4vectors-0.22.0-r36h516909a_1 | |
| bioconductor-sing~ bioconda/noarch::bioconductor-singlecellexperiment-1.6.0-r36_1 | |
| bioconductor-summ~ bioconda/noarch::bioconductor-summarizedexperiment-1.14.0-r36_1 | |
| bioconductor-xvec~ bioconda/linux-64::bioconductor-xvector-0.24.0-r36h516909a_1 | |
| bioconductor-zlib~ bioconda/linux-64::bioconductor-zlibbioc-1.30.0-r36h516909a_1 | |
| bwidget conda-forge/linux-64::bwidget-1.9.14-0 | |
| bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_2 | |
| ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0 | |
| cairo conda-forge/linux-64::cairo-1.16.0-hcf35c78_1003 | |
| certifi conda-forge/linux-64::certifi-2020.4.5.1-py38h32f6830_0 | |
| curl conda-forge/linux-64::curl-7.69.1-h33f0ec9_0 | |
| dropletutils-scri~ bioconda/noarch::dropletutils-scripts-0.0.4-1 | |
| fontconfig conda-forge/linux-64::fontconfig-2.13.1-h86ecdb6_1001 | |
| freetype conda-forge/linux-64::freetype-2.10.1-he06d7ca_0 | |
| fribidi conda-forge/linux-64::fribidi-1.0.9-h516909a_0 | |
| gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-7.3.0-hd420e75_5 | |
| gcc_linux-64 conda-forge/linux-64::gcc_linux-64-7.3.0-h553295d_18 | |
| gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002 | |
| gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_5 | |
| gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-7.3.0-h553295d_18 | |
| glib conda-forge/linux-64::glib-2.58.3-py38h73cb85d_1004 | |
| graphite2 conda-forge/linux-64::graphite2-1.3.13-he1b5a44_1001 | |
| gsl conda-forge/linux-64::gsl-2.6-h294904e_0 | |
| gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_5 | |
| gxx_linux-64 conda-forge/linux-64::gxx_linux-64-7.3.0-h553295d_18 | |
| harfbuzz conda-forge/linux-64::harfbuzz-2.4.0-h9f30f68_3 | |
| icu conda-forge/linux-64::icu-64.2-he1b5a44_1 | |
| jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001 | |
| krb5 conda-forge/linux-64::krb5-1.17.1-h2fd8d38_0 | |
| ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 | |
| libblas conda-forge/linux-64::libblas-3.8.0-16_openblas | |
| libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas | |
| libcurl conda-forge/linux-64::libcurl-7.69.1-hf7181ac_0 | |
| libedit conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001 | |
| libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 | |
| libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2 | |
| libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5 | |
| libgomp conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2 | |
| libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1006 | |
| liblapack conda-forge/linux-64::liblapack-3.8.0-16_openblas | |
| libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0 | |
| libpng conda-forge/linux-64::libpng-1.6.37-hed695b0_1 | |
| libssh2 conda-forge/linux-64::libssh2-1.8.2-h22169c7_2 | |
| libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2 | |
| libtiff conda-forge/linux-64::libtiff-4.1.0-hc7e4089_6 | |
| libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000 | |
| libwebp-base conda-forge/linux-64::libwebp-base-1.1.0-h516909a_3 | |
| libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002 | |
| libxml2 conda-forge/linux-64::libxml2-2.9.10-hee79883_0 | |
| llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0 | |
| lz4-c conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_1 | |
| make conda-forge/linux-64::make-4.3-h516909a_0 | |
| ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002 | |
| openblas conda-forge/linux-64::openblas-0.3.9-he1df0ab_0 | |
| openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_0 | |
| pango conda-forge/linux-64::pango-1.42.4-h7062337_4 | |
| pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0 | |
| pip conda-forge/noarch::pip-20.1-pyh9f0ad1d_0 | |
| pixman conda-forge/linux-64::pixman-0.38.0-h516909a_1003 | |
| pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001 | |
| python conda-forge/linux-64::python-3.8.2-he5300dc_7_cpython | |
| python_abi conda-forge/linux-64::python_abi-3.8-1_cp38 | |
| r-base conda-forge/linux-64::r-base-3.6.3-h316533a_2 | |
| r-bh conda-forge/noarch::r-bh-1.72.0_3-r36h6115d3f_1 | |
| r-bitops conda-forge/linux-64::r-bitops-1.0_6-r36hcdcec82_1004 | |
| r-dqrng conda-forge/linux-64::r-dqrng-0.2.1-r36h0357c0b_2 | |
| r-formatr conda-forge/noarch::r-formatr-1.7-r36h6115d3f_2 | |
| r-futile.logger conda-forge/noarch::r-futile.logger-1.4.3-r36h6115d3f_1003 | |
| r-futile.options conda-forge/noarch::r-futile.options-1.0.1-r36h6115d3f_1002 | |
| r-getopt conda-forge/noarch::r-getopt-1.20.3-r36_2 | |
| r-lambda.r conda-forge/noarch::r-lambda.r-1.2.4-r36h6115d3f_1 | |
| r-lattice conda-forge/linux-64::r-lattice-0.20_41-r36hcdcec82_2 | |
| r-locfit conda-forge/linux-64::r-locfit-1.5_9.4-r36hcdcec82_1 | |
| r-matrix conda-forge/linux-64::r-matrix-1.2_18-r36h7fa42b6_3 | |
| r-matrixstats conda-forge/linux-64::r-matrixstats-0.56.0-r36hcdcec82_1 | |
| r-optparse conda-forge/noarch::r-optparse-1.6.6-r36h6115d3f_1 | |
| r-r.methodss3 conda-forge/noarch::r-r.methodss3-1.8.0-r36h6115d3f_1 | |
| r-r.oo conda-forge/noarch::r-r.oo-1.23.0-r36h6115d3f_1 | |
| r-r.utils conda-forge/noarch::r-r.utils-2.9.2-r36h6115d3f_1 | |
| r-rcpp conda-forge/linux-64::r-rcpp-1.0.4.6-r36h0357c0b_1 | |
| r-rcurl conda-forge/linux-64::r-rcurl-1.98_1.2-r36hcdcec82_1 | |
| r-sitmo conda-forge/linux-64::r-sitmo-2.0.1-r36h0357c0b_2 | |
| r-snow conda-forge/noarch::r-snow-0.4_3-r36h6115d3f_1002 | |
| r-workflowscripts~ bioconda/noarch::r-workflowscriptscommon-0.0.7-r36_0 | |
| readline conda-forge/linux-64::readline-8.0-hf8c457e_0 | |
| sed conda-forge/linux-64::sed-4.7-h1bed415_1000 | |
| setuptools conda-forge/linux-64::setuptools-46.1.3-py38h32f6830_0 | |
| sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0 | |
| tk conda-forge/linux-64::tk-8.6.10-hed695b0_0 | |
| tktable conda-forge/linux-64::tktable-2.10-h555a92e_3 | |
| wheel conda-forge/noarch::wheel-0.34.2-py_1 | |
| xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002 | |
| xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0 | |
| xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000 | |
| xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0 | |
| xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0 | |
| xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0 | |
| xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0 | |
| xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002 | |
| xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002 | |
| xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002 | |
| xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007 | |
| xz conda-forge/linux-64::xz-5.2.5-h516909a_0 | |
| zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1006 | |
| zstd conda-forge/linux-64::zstd-1.4.4-h6597ccf_3 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| done | |
| Executing transaction: ...working... 10.25.100.188 - - [06/May/2020:23:44:02 +0100] "GET /api/tool_shed_repositories?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28739|app: 0|req: 61/158] 10.25.100.188 () {38 vars in 604 bytes} [Wed May 6 23:44:02 2020] GET /api/tool_shed_repositories?key=ff1fadcdba102650fb96c7f486b45d6b => generated 1987 bytes in 16 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:44:03,678 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:05,187 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Appending to tool panel section: Scanpy | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-06 23:44:05,189 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Adding new row for repository 'scanpy_inspect' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:44:05,195 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:05,195 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Appending to tool panel section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:05,208 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Appending to tool panel section: Scanpy | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-06 23:44:05,213 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect' at 6:5e9171dc8244 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:23,981 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.4.4.post1+galaxy2, version: 1.4.4.post1+galaxy2 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-06 23:44:23,981 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-06 23:44:23,997 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-06 23:44:24,679 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-06 23:44:24,680 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-06 23:44:34,836 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-06 23:44:34,841 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-06 23:44:35,585 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:44:35,586 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-06 23:44:35,636 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:44:35,637 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,638 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:44:35,652 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:44:35,654 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:44:35,656 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-06 23:44:35,656 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:44:35,657 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,658 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-06 23:44:35,659 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:44:35,659 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,660 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools WARNING 2020-05-06 23:44:35,932 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:44:35,932 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,933 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,933 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (299.282 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,933 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,936 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,936 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,939 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,939 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,939 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,942 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,944 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,944 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,945 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,946 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,948 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,948 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,949 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,949 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,950 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,950 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,950 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,950 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,951 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.4.4.post1+galaxy2, version: 1.4.4.post1+galaxy2 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,951 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,951 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,951 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,951 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,951 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,951 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,951 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,952 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,952 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,952 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,952 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,953 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,953 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,953 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,953 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:44:35,953 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (20.113 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:44:35,959 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:44:35,961 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:44:35,963 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:44:35,965 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-06 23:44:35,965 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:44:35,973 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (387.764 ms) | |
| galaxy.queue_worker INFO 2020-05-06 23:44:35,981 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-06 23:44:35,981 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-06 23:44:36,029 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (48.367 ms) | |
| done | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:44:54,117 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Using dependency dropletutils-scripts version 0.0.4 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:44:54,118 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Using dependency dropletutils-scripts version 0.0.4 of type conda | |
| 10.25.100.188 - - [06/May/2020:23:39:01 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| Wed May 6 23:44:54 2020 - SIGPIPE: writing to a closed pipe/socket/fd (probably the client disconnected) on request /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b (ip 10.25.100.188) !!! | |
| Wed May 6 23:44:54 2020 - uwsgi_response_writev_headers_and_body_do(): Broken pipe [core/writer.c line 306] during POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b (10.25.100.188) | |
| OSError: write error | |
| [pid: 28737|app: 0|req: 22/159] 10.25.100.188 () {42 vars in 751 bytes} [Wed May 6 23:39:01 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 0 bytes in 352580 msecs (HTTP/1.1 200) 3 headers in 0 bytes (0 switches on core 0) | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_conda/envs/__bioconductor-flowcore@1.38.2 | |
| added / updated specs: | |
| - bioconductor-flowcore=1.38.2 | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| bioconductor-biobase-2.34.0| r3.3.2_0 2.0 MB bioconda | |
| bioconductor-biocgenerics-0.22.0| r3.3.2_0 555 KB bioconda | |
| bioconductor-flowcore-1.38.2| r3.3.2_1 8.8 MB bioconda | |
| bioconductor-graph-1.50.0 | r3.3.2_1 736 KB bioconda | |
| cairo-1.14.6 | 4 1.2 MB conda-forge | |
| curl-7.52.1 | 0 559 KB conda-forge | |
| fontconfig-2.12.1 | 6 939 KB conda-forge | |
| freetype-2.7 | 1 2.8 MB conda-forge | |
| glib-2.51.4 | 0 6.0 MB conda-forge | |
| harfbuzz-1.4.3 | 0 4.0 MB conda-forge | |
| icu-58.2 | hf484d3e_1000 22.6 MB conda-forge | |
| libgcc-7.2.0 | h69d50b8_2 304 KB conda-forge | |
| libpng-1.6.28 | 1 301 KB conda-forge | |
| libtiff-4.0.7 | 0 488 KB conda-forge | |
| libxml2-2.9.5 | 0 5.0 MB conda-forge | |
| ncurses-5.9 | 10 1.1 MB conda-forge | |
| openssl-1.0.2u | h516909a_0 3.2 MB conda-forge | |
| pango-1.40.4 | 0 999 KB conda-forge | |
| pixman-0.34.0 | h14c3975_1003 595 KB conda-forge | |
| r-base-3.3.2 | 5 21.2 MB conda-forge | |
| r-bh-1.66.0_1 | r3.3.2_0 10.0 MB conda-forge | |
| r-cluster-2.0.6 | r3.3.2_0 481 KB conda-forge | |
| r-corpcor-1.6.9 | r3.3.2_0 101 KB conda-forge | |
| r-deoptimr-1.0_8 | r3.3.2_0 41 KB conda-forge | |
| r-lattice-0.20_34 | r3.3.2_0 704 KB conda-forge | |
| r-matrixstats-0.52.2 | r3.3.2_0 580 KB conda-forge | |
| r-mvtnorm-1.0_6 | r3.3.2_0 190 KB conda-forge | |
| r-pcapp-1.9_61 | r3.3.2_0 304 KB conda-forge | |
| r-rcpp-0.12.16 | r3.3.2_0 3.3 MB conda-forge | |
| r-robustbase-0.92_7 | r3.3.2_0 3.0 MB conda-forge | |
| r-rrcov-1.4_3 | r3.3.2_0 1.3 MB conda-forge | |
| readline-6.2 | 0 713 KB conda-forge | |
| tk-8.5.19 | 2 1.9 MB conda-forge | |
| zlib-1.2.8 | 3 87 KB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 105.7 MB | |
| The following NEW packages will be INSTALLED: | |
| _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge | |
| _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_llvm | |
| _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 | |
| bioconductor-biob~ bioconda/linux-64::bioconductor-biobase-2.34.0-r3.3.2_0 | |
| bioconductor-bioc~ bioconda/linux-64::bioconductor-biocgenerics-0.22.0-r3.3.2_0 | |
| bioconductor-flow~ bioconda/linux-64::bioconductor-flowcore-1.38.2-r3.3.2_1 | |
| bioconductor-graph bioconda/linux-64::bioconductor-graph-1.50.0-r3.3.2_1 | |
| bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_2 | |
| ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0 | |
| cairo conda-forge/linux-64::cairo-1.14.6-4 | |
| curl conda-forge/linux-64::curl-7.52.1-0 | |
| fontconfig conda-forge/linux-64::fontconfig-2.12.1-6 | |
| freetype conda-forge/linux-64::freetype-2.7-1 | |
| gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002 | |
| glib conda-forge/linux-64::glib-2.51.4-0 | |
| graphite2 conda-forge/linux-64::graphite2-1.3.13-he1b5a44_1001 | |
| gsl conda-forge/linux-64::gsl-2.6-h294904e_0 | |
| harfbuzz conda-forge/linux-64::harfbuzz-1.4.3-0 | |
| icu conda-forge/linux-64::icu-58.2-hf484d3e_1000 | |
| jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001 | |
| libblas conda-forge/linux-64::libblas-3.8.0-16_openblas | |
| libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas | |
| libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 | |
| libgcc conda-forge/linux-64::libgcc-7.2.0-h69d50b8_2 | |
| libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2 | |
| libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5 | |
| libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1006 | |
| libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0 | |
| libpng conda-forge/linux-64::libpng-1.6.28-1 | |
| libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2 | |
| libtiff conda-forge/linux-64::libtiff-4.0.7-0 | |
| libxml2 conda-forge/linux-64::libxml2-2.9.5-0 | |
| llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0 | |
| ncurses conda-forge/linux-64::ncurses-5.9-10 | |
| openssl conda-forge/linux-64::openssl-1.0.2u-h516909a_0 | |
| pango conda-forge/linux-64::pango-1.40.4-0 | |
| pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0 | |
| pixman conda-forge/linux-64::pixman-0.34.0-h14c3975_1003 | |
| r-base conda-forge/linux-64::r-base-3.3.2-5 | |
| r-bh conda-forge/linux-64::r-bh-1.66.0_1-r3.3.2_0 | |
| r-cluster conda-forge/linux-64::r-cluster-2.0.6-r3.3.2_0 | |
| r-corpcor conda-forge/linux-64::r-corpcor-1.6.9-r3.3.2_0 | |
| r-deoptimr conda-forge/linux-64::r-deoptimr-1.0_8-r3.3.2_0 | |
| r-lattice conda-forge/linux-64::r-lattice-0.20_34-r3.3.2_0 | |
| r-matrixstats conda-forge/linux-64::r-matrixstats-0.52.2-r3.3.2_0 | |
| r-mvtnorm conda-forge/linux-64::r-mvtnorm-1.0_6-r3.3.2_0 | |
| r-pcapp conda-forge/linux-64::r-pcapp-1.9_61-r3.3.2_0 | |
| r-rcpp conda-forge/linux-64::r-rcpp-0.12.16-r3.3.2_0 | |
| r-robustbase conda-forge/linux-64::r-robustbase-0.92_7-r3.3.2_0 | |
| r-rrcov conda-forge/linux-64::r-rrcov-1.4_3-r3.3.2_0 | |
| readline conda-forge/linux-64::readline-6.2-0 | |
| tk conda-forge/linux-64::tk-8.5.19-2 | |
| xz conda-forge/linux-64::xz-5.2.5-h516909a_0 | |
| zlib conda-forge/linux-64::zlib-1.2.8-3 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... galaxy.config WARNING 2020-05-06 23:45:24,091 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Waiting for toolbox reload timed out after 60 seconds | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:45:24,105 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-141253bb58fad23ac50749589168696eca3ed3ab1e99608dbf718dbfa9556234 scanpy=1.4.4.post1 loompy=2.0.17 h5py=2.9.0 leidenalg=0.7.0 | |
| Collecting package metadata: ...working... done | |
| Executing transaction: ...working... done | |
| Solving environment: ...working... done | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:46:08,196 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency bioconductor-flowcore version 1.38.2 of type conda | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:46:08,199 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __r@_uv_ r | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| done | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_conda/envs/__r@_uv_ | |
| added / updated specs: | |
| - r | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| glib-2.64.2 | h6f030ca_0 3.4 MB conda-forge | |
| r-3.6 | r36_1003 14 KB conda-forge | |
| r-boot-1.3_25 | r36h6115d3f_1 634 KB conda-forge | |
| r-class-7.3_17 | r36hcdcec82_1 107 KB conda-forge | |
| r-cluster-2.1.0 | r36h9bbef5b_3 554 KB conda-forge | |
| r-codetools-0.2_16 | r36h6115d3f_1002 105 KB conda-forge | |
| r-foreign-0.8_76 | r36hcdcec82_1 268 KB conda-forge | |
| r-kernsmooth-2.23_17 | r36hfa343cc_1 104 KB conda-forge | |
| r-mass-7.3_51.6 | r36hcdcec82_2 1.1 MB conda-forge | |
| r-mgcv-1.8_31 | r36h7fa42b6_1 2.7 MB conda-forge | |
| r-nlme-3.1_147 | r36h9bbef5b_1 2.3 MB conda-forge | |
| r-nnet-7.3_14 | r36hcdcec82_1 132 KB conda-forge | |
| r-recommended-3.6 | r36_1004 4 KB conda-forge | |
| r-rpart-4.1_15 | r36hcdcec82_2 735 KB conda-forge | |
| r-spatial-7.3_12 | r36hcdcec82_1 154 KB conda-forge | |
| r-survival-3.1_12 | r36hcdcec82_1 7.4 MB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 19.7 MB | |
| The following NEW packages will be INSTALLED: | |
| _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge | |
| _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_llvm | |
| _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 | |
| binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.34-h53a641e_0 | |
| binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.34-hc952b39_18 | |
| bwidget conda-forge/linux-64::bwidget-1.9.14-0 | |
| bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_2 | |
| ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0 | |
| cairo conda-forge/linux-64::cairo-1.16.0-hcf35c78_1003 | |
| certifi conda-forge/linux-64::certifi-2020.4.5.1-py38h32f6830_0 | |
| curl conda-forge/linux-64::curl-7.69.1-h33f0ec9_0 | |
| fontconfig conda-forge/linux-64::fontconfig-2.13.1-h86ecdb6_1001 | |
| freetype conda-forge/linux-64::freetype-2.10.1-he06d7ca_0 | |
| fribidi conda-forge/linux-64::fribidi-1.0.9-h516909a_0 | |
| gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-7.3.0-hd420e75_5 | |
| gcc_linux-64 conda-forge/linux-64::gcc_linux-64-7.3.0-h553295d_18 | |
| gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002 | |
| gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_5 | |
| gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-7.3.0-h553295d_18 | |
| glib conda-forge/linux-64::glib-2.64.2-h6f030ca_0 | |
| graphite2 conda-forge/linux-64::graphite2-1.3.13-he1b5a44_1001 | |
| gsl conda-forge/linux-64::gsl-2.6-h294904e_0 | |
| gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_5 | |
| gxx_linux-64 conda-forge/linux-64::gxx_linux-64-7.3.0-h553295d_18 | |
| harfbuzz conda-forge/linux-64::harfbuzz-2.4.0-h9f30f68_3 | |
| icu conda-forge/linux-64::icu-64.2-he1b5a44_1 | |
| jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001 | |
| krb5 conda-forge/linux-64::krb5-1.17.1-h2fd8d38_0 | |
| ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 | |
| libblas conda-forge/linux-64::libblas-3.8.0-16_openblas | |
| libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas | |
| libcurl conda-forge/linux-64::libcurl-7.69.1-hf7181ac_0 | |
| libedit conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001 | |
| libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 | |
| libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2 | |
| libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5 | |
| libgomp conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2 | |
| libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1006 | |
| liblapack conda-forge/linux-64::liblapack-3.8.0-16_openblas | |
| libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0 | |
| libpng conda-forge/linux-64::libpng-1.6.37-hed695b0_1 | |
| libssh2 conda-forge/linux-64::libssh2-1.8.2-h22169c7_2 | |
| libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2 | |
| libtiff conda-forge/linux-64::libtiff-4.1.0-hc7e4089_6 | |
| libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000 | |
| libwebp-base conda-forge/linux-64::libwebp-base-1.1.0-h516909a_3 | |
| libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002 | |
| libxml2 conda-forge/linux-64::libxml2-2.9.10-hee79883_0 | |
| llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0 | |
| lz4-c conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_1 | |
| make conda-forge/linux-64::make-4.3-h516909a_0 | |
| ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002 | |
| openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_0 | |
| pango conda-forge/linux-64::pango-1.42.4-h7062337_4 | |
| pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0 | |
| pip conda-forge/noarch::pip-20.1-pyh9f0ad1d_0 | |
| pixman conda-forge/linux-64::pixman-0.38.0-h516909a_1003 | |
| pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001 | |
| python conda-forge/linux-64::python-3.8.2-he5300dc_7_cpython | |
| python_abi conda-forge/linux-64::python_abi-3.8-1_cp38 | |
| r conda-forge/noarch::r-3.6-r36_1003 | |
| r-base conda-forge/linux-64::r-base-3.6.3-h316533a_2 | |
| r-boot conda-forge/noarch::r-boot-1.3_25-r36h6115d3f_1 | |
| r-class conda-forge/linux-64::r-class-7.3_17-r36hcdcec82_1 | |
| r-cluster conda-forge/linux-64::r-cluster-2.1.0-r36h9bbef5b_3 | |
| r-codetools conda-forge/noarch::r-codetools-0.2_16-r36h6115d3f_1002 | |
| r-foreign conda-forge/linux-64::r-foreign-0.8_76-r36hcdcec82_1 | |
| r-kernsmooth conda-forge/linux-64::r-kernsmooth-2.23_17-r36hfa343cc_1 | |
| r-lattice conda-forge/linux-64::r-lattice-0.20_41-r36hcdcec82_2 | |
| r-mass conda-forge/linux-64::r-mass-7.3_51.6-r36hcdcec82_2 | |
| r-matrix conda-forge/linux-64::r-matrix-1.2_18-r36h7fa42b6_3 | |
| r-mgcv conda-forge/linux-64::r-mgcv-1.8_31-r36h7fa42b6_1 | |
| r-nlme conda-forge/linux-64::r-nlme-3.1_147-r36h9bbef5b_1 | |
| r-nnet conda-forge/linux-64::r-nnet-7.3_14-r36hcdcec82_1 | |
| r-recommended conda-forge/noarch::r-recommended-3.6-r36_1004 | |
| r-rpart conda-forge/linux-64::r-rpart-4.1_15-r36hcdcec82_2 | |
| r-spatial conda-forge/linux-64::r-spatial-7.3_12-r36hcdcec82_1 | |
| r-survival conda-forge/linux-64::r-survival-3.1_12-r36hcdcec82_1 | |
| readline conda-forge/linux-64::readline-8.0-hf8c457e_0 | |
| sed conda-forge/linux-64::sed-4.7-h1bed415_1000 | |
| setuptools conda-forge/linux-64::setuptools-46.1.3-py38h32f6830_0 | |
| sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0 | |
| tk conda-forge/linux-64::tk-8.6.10-hed695b0_0 | |
| tktable conda-forge/linux-64::tktable-2.10-h555a92e_3 | |
| wheel conda-forge/noarch::wheel-0.34.2-py_1 | |
| xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002 | |
| xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0 | |
| xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000 | |
| xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0 | |
| xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0 | |
| xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0 | |
| xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0 | |
| xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002 | |
| xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002 | |
| xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002 | |
| xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007 | |
| xz conda-forge/linux-64::xz-5.2.5-h516909a_0 | |
| zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1006 | |
| zstd conda-forge/linux-64::zstd-1.4.4-h6597ccf_3 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:47:37,056 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency r version None of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:47:37,059 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency bioconductor-flowcore version 1.38.2 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:47:37,059 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency r version None of type conda | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:47:37,063 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Executing command: *******/galaxy/shared/_conda/bin/conda list --name __bioconductor-flowcore@1.38.2 --export > '*******/galaxy/shared/galaxy_wd/tmp/jobdepswfyh22zx530f5a141ecfc104767094a48c54b757c52df383fa4f5155e0b86538fba00e7c/__bioconductor-flowcore@1.38.2' | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:47:38,273 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix *******/galaxy/shared/_cache/0fff183d --file *******/galaxy/shared/galaxy_wd/tmp/jobdepswfyh22zx530f5a141ecfc104767094a48c54b757c52df383fa4f5155e0b86538fba00e7c/__bioconductor-flowcore@1.38.2 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_cache/0fff183d | |
| added / updated specs: | |
| - _libgcc_mutex==0.1=conda_forge | |
| - _openmp_mutex==4.5=1_llvm | |
| - _r-mutex==1.0.1=anacondar_1 | |
| - bioconductor-biobase==2.34.0=r3.3.2_0 | |
| - bioconductor-biocgenerics==0.22.0=r3.3.2_0 | |
| - bioconductor-flowcore==1.38.2=r3.3.2_1 | |
| - bioconductor-graph==1.50.0=r3.3.2_1 | |
| - bzip2==1.0.8=h516909a_2 | |
| - ca-certificates==2020.4.5.1=hecc5488_0 | |
| - cairo==1.14.6=4 | |
| - curl==7.52.1=0 | |
| - fontconfig==2.12.1=6 | |
| - freetype==2.7=1 | |
| - gettext==0.19.8.1=hc5be6a0_1002 | |
| - glib==2.51.4=0 | |
| - graphite2==1.3.13=he1b5a44_1001 | |
| - gsl==2.6=h294904e_0 | |
| - harfbuzz==1.4.3=0 | |
| - icu==58.2=hf484d3e_1000 | |
| - jpeg==9c=h14c3975_1001 | |
| - libblas==3.8.0=16_openblas | |
| - libcblas==3.8.0=16_openblas | |
| - libffi==3.2.1=he1b5a44_1007 | |
| - libgcc-ng==9.2.0=h24d8f2e_2 | |
| - libgcc==7.2.0=h69d50b8_2 | |
| - libgfortran-ng==7.3.0=hdf63c60_5 | |
| - libiconv==1.15=h516909a_1006 | |
| - libopenblas==0.3.9=h5ec1e0e_0 | |
| - libpng==1.6.28=1 | |
| - libstdcxx-ng==9.2.0=hdf63c60_2 | |
| - libtiff==4.0.7=0 | |
| - libxml2==2.9.5=0 | |
| - llvm-openmp==10.0.0=hc9558a2_0 | |
| - ncurses==5.9=10 | |
| - openssl==1.0.2u=h516909a_0 | |
| - pango==1.40.4=0 | |
| - pcre==8.44=he1b5a44_0 | |
| - pixman==0.34.0=h14c3975_1003 | |
| - r-base==3.3.2=5 | |
| - r-bh==1.66.0_1=r3.3.2_0 | |
| - r-cluster==2.0.6=r3.3.2_0 | |
| - r-corpcor==1.6.9=r3.3.2_0 | |
| - r-deoptimr==1.0_8=r3.3.2_0 | |
| - r-lattice==0.20_34=r3.3.2_0 | |
| - r-matrixstats==0.52.2=r3.3.2_0 | |
| - r-mvtnorm==1.0_6=r3.3.2_0 | |
| - r-pcapp==1.9_61=r3.3.2_0 | |
| - r-rcpp==0.12.16=r3.3.2_0 | |
| - r-robustbase==0.92_7=r3.3.2_0 | |
| - r-rrcov==1.4_3=r3.3.2_0 | |
| - readline==6.2=0 | |
| - tk==8.5.19=2 | |
| - xz==5.2.5=h516909a_0 | |
| - zlib==1.2.8=3 | |
| The following NEW packages will be INSTALLED: | |
| _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge | |
| _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_llvm | |
| _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 | |
| bioconductor-biob~ bioconda/linux-64::bioconductor-biobase-2.34.0-r3.3.2_0 | |
| bioconductor-bioc~ bioconda/linux-64::bioconductor-biocgenerics-0.22.0-r3.3.2_0 | |
| bioconductor-flow~ bioconda/linux-64::bioconductor-flowcore-1.38.2-r3.3.2_1 | |
| bioconductor-graph bioconda/linux-64::bioconductor-graph-1.50.0-r3.3.2_1 | |
| bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_2 | |
| ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0 | |
| cairo conda-forge/linux-64::cairo-1.14.6-4 | |
| curl conda-forge/linux-64::curl-7.52.1-0 | |
| fontconfig conda-forge/linux-64::fontconfig-2.12.1-6 | |
| freetype conda-forge/linux-64::freetype-2.7-1 | |
| gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002 | |
| glib conda-forge/linux-64::glib-2.51.4-0 | |
| graphite2 conda-forge/linux-64::graphite2-1.3.13-he1b5a44_1001 | |
| gsl conda-forge/linux-64::gsl-2.6-h294904e_0 | |
| harfbuzz conda-forge/linux-64::harfbuzz-1.4.3-0 | |
| icu conda-forge/linux-64::icu-58.2-hf484d3e_1000 | |
| jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001 | |
| libblas conda-forge/linux-64::libblas-3.8.0-16_openblas | |
| libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas | |
| libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 | |
| libgcc conda-forge/linux-64::libgcc-7.2.0-h69d50b8_2 | |
| libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2 | |
| libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5 | |
| libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1006 | |
| libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0 | |
| libpng conda-forge/linux-64::libpng-1.6.28-1 | |
| libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2 | |
| libtiff conda-forge/linux-64::libtiff-4.0.7-0 | |
| libxml2 conda-forge/linux-64::libxml2-2.9.5-0 | |
| llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0 | |
| ncurses conda-forge/linux-64::ncurses-5.9-10 | |
| openssl conda-forge/linux-64::openssl-1.0.2u-h516909a_0 | |
| pango conda-forge/linux-64::pango-1.40.4-0 | |
| pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0 | |
| pixman conda-forge/linux-64::pixman-0.34.0-h14c3975_1003 | |
| r-base conda-forge/linux-64::r-base-3.3.2-5 | |
| r-bh conda-forge/linux-64::r-bh-1.66.0_1-r3.3.2_0 | |
| r-cluster conda-forge/linux-64::r-cluster-2.0.6-r3.3.2_0 | |
| r-corpcor conda-forge/linux-64::r-corpcor-1.6.9-r3.3.2_0 | |
| r-deoptimr conda-forge/linux-64::r-deoptimr-1.0_8-r3.3.2_0 | |
| r-lattice conda-forge/linux-64::r-lattice-0.20_34-r3.3.2_0 | |
| r-matrixstats conda-forge/linux-64::r-matrixstats-0.52.2-r3.3.2_0 | |
| r-mvtnorm conda-forge/linux-64::r-mvtnorm-1.0_6-r3.3.2_0 | |
| r-pcapp conda-forge/linux-64::r-pcapp-1.9_61-r3.3.2_0 | |
| r-rcpp conda-forge/linux-64::r-rcpp-0.12.16-r3.3.2_0 | |
| r-robustbase conda-forge/linux-64::r-robustbase-0.92_7-r3.3.2_0 | |
| r-rrcov conda-forge/linux-64::r-rrcov-1.4_3-r3.3.2_0 | |
| readline conda-forge/linux-64::readline-6.2-0 | |
| tk conda-forge/linux-64::tk-8.5.19-2 | |
| xz conda-forge/linux-64::xz-5.2.5-h516909a_0 | |
| zlib conda-forge/linux-64::zlib-1.2.8-3 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:48:27,157 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Executing command: *******/galaxy/shared/_conda/bin/conda clean --tarballs -y | |
| Cache location: *******/galaxy/shared/_conda/pkgs | |
| Will remove the following tarballs: | |
| *******/galaxy/shared/_conda/pkgs | |
| ---------------------------------------- | |
| python-3.7.3-h0371630_0.tar.bz2 36.7 MB | |
| ca-certificates-2019.1.23-0.tar.bz2 126 KB | |
| libgcc-ng-8.2.0-hdf63c60_1.tar.bz2 7.6 MB | |
| libstdcxx-ng-8.2.0-hdf63c60_1.tar.bz2 2.9 MB | |
| libffi-3.2.1-hd88cf55_4.tar.bz2 43 KB | |
| ncurses-6.1-he6710b0_1.tar.bz2 958 KB | |
| openssl-1.1.1b-h7b6447c_1.tar.bz2 4.0 MB | |
| xz-5.2.4-h14c3975_4.tar.bz2 366 KB | |
| yaml-0.1.7-had09818_2.tar.bz2 85 KB | |
| zlib-1.2.11-h7b6447c_3.tar.bz2 120 KB | |
| libedit-3.1.20181209-hc058e9b_0.tar.bz2 188 KB | |
| readline-7.0-h7b6447c_5.tar.bz2 392 KB | |
| tk-8.6.8-hbc83047_0.tar.bz2 3.1 MB | |
| sqlite-3.27.2-h7b6447c_0.tar.bz2 1.9 MB | |
| asn1crypto-0.24.0-py37_0.tar.bz2 154 KB | |
| certifi-2019.3.9-py37_0.tar.bz2 155 KB | |
| chardet-3.0.4-py37_1.tar.bz2 164 KB | |
| idna-2.8-py37_0.tar.bz2 101 KB | |
| pycosat-0.6.3-py37h14c3975_0.tar.bz2 105 KB | |
| pycparser-2.19-py37_0.tar.bz2 172 KB | |
| pysocks-1.6.8-py37_0.tar.bz2 22 KB | |
| ruamel_yaml-0.15.46-py37h14c3975_0.tar.bz2 245 KB | |
| six-1.12.0-py37_0.tar.bz2 22 KB | |
| cffi-1.12.2-py37h2e261b9_1.tar.bz2 222 KB | |
| setuptools-41.0.0-py37_0.tar.bz2 641 KB | |
| cryptography-2.6.1-py37h1ba5d50_0.tar.bz2 616 KB | |
| wheel-0.33.1-py37_0.tar.bz2 39 KB | |
| pip-19.0.3-py37_0.tar.bz2 1.8 MB | |
| pyopenssl-19.0.0-py37_0.tar.bz2 82 KB | |
| urllib3-1.24.1-py37_0.tar.bz2 149 KB | |
| requests-2.21.0-py37_0.tar.bz2 85 KB | |
| conda-4.6.14-py37_0.tar.bz2 2.1 MB | |
| _libgcc_mutex-0.1-main.tar.bz2 2 KB | |
| python_abi-3.7-1_cp37m.tar.bz2 4 KB | |
| ca-certificates-2020.4.5.1-hecc5488_0.tar.bz2 146 KB | |
| openssl-1.1.1g-h516909a_0.tar.bz2 2.1 MB | |
| certifi-2020.4.5.1-py37hc8dfbb8_0.tar.bz2 151 KB | |
| llvm-openmp-10.0.0-hc9558a2_0.tar.bz2 2.8 MB | |
| libcblas-3.8.0-16_openblas.tar.bz2 10 KB | |
| certifi-2019.11.28-py27_0.tar.bz2 149 KB | |
| wheel-0.34.2-py_1.tar.bz2 24 KB | |
| six-1.14.0-py_1.tar.bz2 13 KB | |
| pandas-0.17.1-np19py27_0.tar.bz2 12.2 MB | |
| libffi-3.2.1-he1b5a44_1007.tar.bz2 47 KB | |
| python-2.7.15-h5a48372_1011_cpython.tar.bz2 12.2 MB | |
| liblapack-3.8.0-16_openblas.tar.bz2 10 KB | |
| readline-8.0-hf8c457e_0.tar.bz2 441 KB | |
| pip-20.1-pyh9f0ad1d_0.tar.bz2 1.1 MB | |
| libstdcxx-ng-9.2.0-hdf63c60_2.tar.bz2 4.5 MB | |
| numpy-1.9.3-py27he5ce36f_1209.tar.bz2 3.3 MB | |
| libgcc-ng-9.2.0-h24d8f2e_2.tar.bz2 8.2 MB | |
| _openmp_mutex-4.5-1_llvm.tar.bz2 5 KB | |
| _libgcc_mutex-0.1-conda_forge.tar.bz2 3 KB | |
| tk-8.6.10-hed695b0_0.tar.bz2 3.2 MB | |
| pytz-2020.1-pyh9f0ad1d_0.tar.bz2 227 KB | |
| libblas-3.8.0-16_openblas.tar.bz2 10 KB | |
| python-dateutil-2.8.1-py_0.tar.bz2 220 KB | |
| setuptools-44.0.0-py27_0.tar.bz2 663 KB | |
| libopenblas-0.3.9-h5ec1e0e_0.tar.bz2 7.8 MB | |
| ncurses-6.1-hf484d3e_1002.tar.bz2 1.3 MB | |
| sqlite-3.30.1-hcee41ef_0.tar.bz2 2.0 MB | |
| libgfortran-ng-7.3.0-hdf63c60_5.tar.bz2 1.7 MB | |
| zlib-1.2.11-h516909a_1006.tar.bz2 105 KB | |
| ld_impl_linux-64-2.34-h53a641e_0.tar.bz2 616 KB | |
| r-r.utils-2.9.2-r36h6115d3f_1.tar.bz2 1.4 MB | |
| python_abi-3.8-1_cp38.tar.bz2 4 KB | |
| gfortran_linux-64-7.3.0-h553295d_18.tar.bz2 21 KB | |
| bioconductor-iranges-2.18.2-r36h516909a_0.tar.bz2 2.3 MB | |
| r-getopt-1.20.3-r36_2.tar.bz2 45 KB | |
| r-bitops-1.0_6-r36hcdcec82_1004.tar.bz2 39 KB | |
| xorg-xextproto-7.3.0-h14c3975_1002.tar.bz2 27 KB | |
| r-snow-0.4_3-r36h6115d3f_1002.tar.bz2 124 KB | |
| setuptools-46.1.3-py38h32f6830_0.tar.bz2 635 KB | |
| bioconductor-rhdf5lib-1.6.0-r36h516909a_1.tar.bz2 3.6 MB | |
| xorg-libxau-1.0.9-h14c3975_0.tar.bz2 13 KB | |
| lz4-c-1.9.2-he1b5a44_1.tar.bz2 226 KB | |
| icu-64.2-he1b5a44_1.tar.bz2 12.6 MB | |
| r-optparse-1.6.6-r36h6115d3f_1.tar.bz2 79 KB | |
| zstd-1.4.4-h6597ccf_3.tar.bz2 991 KB | |
| xorg-xproto-7.0.31-h14c3975_1007.tar.bz2 72 KB | |
| gettext-0.19.8.1-hc5be6a0_1002.tar.bz2 3.6 MB | |
| pixman-0.38.0-h516909a_1003.tar.bz2 594 KB | |
| bioconductor-genomicranges-1.36.0-r36h516909a_1.tar.bz2 2.1 MB | |
| r-lattice-0.20_41-r36hcdcec82_2.tar.bz2 1.1 MB | |
| r-formatr-1.7-r36h6115d3f_2.tar.bz2 166 KB | |
| libtiff-4.1.0-hc7e4089_6.tar.bz2 668 KB | |
| r-dqrng-0.2.1-r36h0357c0b_2.tar.bz2 165 KB | |
| harfbuzz-2.4.0-h9f30f68_3.tar.bz2 1.5 MB | |
| xorg-libice-1.0.10-h516909a_0.tar.bz2 57 KB | |
| freetype-2.10.1-he06d7ca_0.tar.bz2 877 KB | |
| gcc_impl_linux-64-7.3.0-hd420e75_5.tar.bz2 70.6 MB | |
| pcre-8.44-he1b5a44_0.tar.bz2 261 KB | |
| bioconductor-zlibbioc-1.30.0-r36h516909a_1.tar.bz2 112 KB | |
| bioconductor-xvector-0.24.0-r36h516909a_1.tar.bz2 721 KB | |
| r-bh-1.72.0_3-r36h6115d3f_1.tar.bz2 10.5 MB | |
| xorg-libxdmcp-1.1.3-h516909a_0.tar.bz2 18 KB | |
| gxx_linux-64-7.3.0-h553295d_18.tar.bz2 21 KB | |
| python-3.8.2-he5300dc_7_cpython.tar.bz2 70.8 MB | |
| r-futile.logger-1.4.3-r36h6115d3f_1003.tar.bz2 108 KB | |
| gfortran_impl_linux-64-7.3.0-hdf63c60_5.tar.bz2 9.4 MB | |
| _r-mutex-1.0.1-anacondar_1.tar.bz2 3 KB | |
| bioconductor-biocgenerics-0.30.0-r36_1.tar.bz2 683 KB | |
| bioconductor-genomeinfodbdata-1.2.2-r36_0.tar.bz2 6 KB | |
| bioconductor-hdf5array-1.12.1-r36h516909a_0.tar.bz2 9.5 MB | |
| bioconductor-limma-3.40.2-r36h516909a_0.tar.bz2 2.6 MB | |
| bioconductor-summarizedexperiment-1.14.0-r36_1.tar.bz2 2.5 MB | |
| libcurl-7.69.1-hf7181ac_0.tar.bz2 573 KB | |
| xorg-renderproto-0.11.1-h14c3975_1002.tar.bz2 8 KB | |
| libuuid-2.32.1-h14c3975_1000.tar.bz2 26 KB | |
| glib-2.58.3-py38h73cb85d_1004.tar.bz2 3.3 MB | |
| gxx_impl_linux-64-7.3.0-hdf63c60_5.tar.bz2 19.1 MB | |
| sed-4.7-h1bed415_1000.tar.bz2 245 KB | |
| r-base-3.6.3-h316533a_2.tar.bz2 23.3 MB | |
| bwidget-1.9.14-0.tar.bz2 119 KB | |
| libiconv-1.15-h516909a_1006.tar.bz2 2.0 MB | |
| binutils_impl_linux-64-2.34-h53a641e_0.tar.bz2 9.2 MB | |
| xorg-libsm-1.2.3-h84519dc_1000.tar.bz2 25 KB | |
| bioconductor-biocparallel-1.18.0-r36he1b5a44_1.tar.bz2 1.1 MB | |
| libpng-1.6.37-hed695b0_1.tar.bz2 308 KB | |
| bioconductor-biobase-2.44.0-r36h516909a_1.tar.bz2 2.3 MB | |
| tktable-2.10-h555a92e_3.tar.bz2 89 KB | |
| krb5-1.17.1-h2fd8d38_0.tar.bz2 1.5 MB | |
| r-r.oo-1.23.0-r36h6115d3f_1.tar.bz2 965 KB | |
| bioconductor-rhdf5-2.28.0-r36he1b5a44_1.tar.bz2 2.4 MB | |
| dropletutils-scripts-0.0.4-1.tar.bz2 17 KB | |
| curl-7.69.1-h33f0ec9_0.tar.bz2 137 KB | |
| cairo-1.16.0-hcf35c78_1003.tar.bz2 1.5 MB | |
| r-matrix-1.2_18-r36h7fa42b6_3.tar.bz2 3.8 MB | |
| r-matrixstats-0.56.0-r36hcdcec82_1.tar.bz2 925 KB | |
| graphite2-1.3.13-he1b5a44_1001.tar.bz2 102 KB | |
| libgomp-9.2.0-h24d8f2e_2.tar.bz2 816 KB | |
| binutils_linux-64-2.34-hc952b39_18.tar.bz2 21 KB | |
| gcc_linux-64-7.3.0-h553295d_18.tar.bz2 22 KB | |
| bioconductor-genomeinfodb-1.20.0-r36_1.tar.bz2 3.8 MB | |
| xorg-libxrender-0.9.10-h516909a_1002.tar.bz2 31 KB | |
| fontconfig-2.13.1-h86ecdb6_1001.tar.bz2 340 KB | |
| r-sitmo-2.0.1-r36h0357c0b_2.tar.bz2 155 KB | |
| bioconductor-edger-3.26.5-r36he1b5a44_0.tar.bz2 2.2 MB | |
| r-workflowscriptscommon-0.0.7-r36_0.tar.bz2 28 KB | |
| bioconductor-delayedarray-0.10.0-r36h516909a_1.tar.bz2 2.2 MB | |
| r-rcpp-1.0.4.6-r36h0357c0b_1.tar.bz2 1.9 MB | |
| bioconductor-beachmat-2.0.0-r36he1b5a44_1.tar.bz2 1.1 MB | |
| r-rcurl-1.98_1.2-r36hcdcec82_1.tar.bz2 921 KB | |
| jpeg-9c-h14c3975_1001.tar.bz2 251 KB | |
| bioconductor-dropletutils-1.4.2-r36he1b5a44_0.tar.bz2 2.2 MB | |
| bioconductor-s4vectors-0.22.0-r36h516909a_1.tar.bz2 2.0 MB | |
| libxml2-2.9.10-hee79883_0.tar.bz2 1.3 MB | |
| bioconductor-singlecellexperiment-1.6.0-r36_1.tar.bz2 1.3 MB | |
| make-4.3-h516909a_0.tar.bz2 505 KB | |
| libssh2-1.8.2-h22169c7_2.tar.bz2 257 KB | |
| bzip2-1.0.8-h516909a_2.tar.bz2 396 KB | |
| xorg-libxext-1.3.4-h516909a_0.tar.bz2 51 KB | |
| pango-1.42.4-h7062337_4.tar.bz2 521 KB | |
| xorg-libx11-1.6.9-h516909a_0.tar.bz2 918 KB | |
| libwebp-base-1.1.0-h516909a_3.tar.bz2 845 KB | |
| r-locfit-1.5_9.4-r36hcdcec82_1.tar.bz2 563 KB | |
| openblas-0.3.9-he1df0ab_0.tar.bz2 8.3 MB | |
| fribidi-1.0.9-h516909a_0.tar.bz2 113 KB | |
| pthread-stubs-0.4-h14c3975_1001.tar.bz2 5 KB | |
| libxcb-1.13-h14c3975_1002.tar.bz2 396 KB | |
| r-r.methodss3-1.8.0-r36h6115d3f_1.tar.bz2 94 KB | |
| libedit-3.1.20170329-hf8c457e_1001.tar.bz2 172 KB | |
| r-lambda.r-1.2.4-r36h6115d3f_1.tar.bz2 120 KB | |
| r-futile.options-1.0.1-r36h6115d3f_1002.tar.bz2 27 KB | |
| xorg-kbproto-1.0.7-h14c3975_1002.tar.bz2 26 KB | |
| xz-5.2.5-h516909a_0.tar.bz2 430 KB | |
| gsl-2.6-h294904e_0.tar.bz2 3.1 MB | |
| certifi-2020.4.5.1-py38h32f6830_0.tar.bz2 151 KB | |
| pixman-0.34.0-h14c3975_1003.tar.bz2 595 KB | |
| bioconductor-flowcore-1.38.2-r3.3.2_1.tar.bz2 8.8 MB | |
| r-rrcov-1.4_3-r3.3.2_0.tar.bz2 1.3 MB | |
| r-corpcor-1.6.9-r3.3.2_0.tar.bz2 101 KB | |
| bioconductor-graph-1.50.0-r3.3.2_1.tar.bz2 736 KB | |
| r-matrixstats-0.52.2-r3.3.2_0.tar.bz2 580 KB | |
| r-base-3.3.2-5.tar.bz2 21.2 MB | |
| ncurses-5.9-10.tar.bz2 1.1 MB | |
| libxml2-2.9.5-0.tar.bz2 5.0 MB | |
| bioconductor-biobase-2.34.0-r3.3.2_0.tar.bz2 2.0 MB | |
| pango-1.40.4-0.tar.bz2 999 KB | |
| r-pcapp-1.9_61-r3.3.2_0.tar.bz2 304 KB | |
| r-deoptimr-1.0_8-r3.3.2_0.tar.bz2 41 KB | |
| r-cluster-2.0.6-r3.3.2_0.tar.bz2 481 KB | |
| r-bh-1.66.0_1-r3.3.2_0.tar.bz2 10.0 MB | |
| zlib-1.2.8-3.tar.bz2 87 KB | |
| cairo-1.14.6-4.tar.bz2 1.2 MB | |
| r-rcpp-0.12.16-r3.3.2_0.tar.bz2 3.3 MB | |
| tk-8.5.19-2.tar.bz2 1.9 MB | |
| curl-7.52.1-0.tar.bz2 559 KB | |
| icu-58.2-hf484d3e_1000.tar.bz2 22.6 MB | |
| r-lattice-0.20_34-r3.3.2_0.tar.bz2 704 KB | |
| libpng-1.6.28-1.tar.bz2 301 KB | |
| libgcc-7.2.0-h69d50b8_2.tar.bz2 304 KB | |
| r-robustbase-0.92_7-r3.3.2_0.tar.bz2 3.0 MB | |
| fontconfig-2.12.1-6.tar.bz2 939 KB | |
| openssl-1.0.2u-h516909a_0.tar.bz2 3.2 MB | |
| r-mvtnorm-1.0_6-r3.3.2_0.tar.bz2 190 KB | |
| freetype-2.7-1.tar.bz2 2.8 MB | |
| harfbuzz-1.4.3-0.tar.bz2 4.0 MB | |
| libtiff-4.0.7-0.tar.bz2 488 KB | |
| readline-6.2-0.tar.bz2 713 KB | |
| bioconductor-biocgenerics-0.22.0-r3.3.2_0.tar.bz2 555 KB | |
| glib-2.51.4-0.tar.bz2 6.0 MB | |
| gstreamer-1.14.5-h36ae1b5_2.tar.bz2 4.5 MB | |
| pytables-3.5.2-py37ha1aa75f_0.tar.bz2 1.5 MB | |
| h5py-2.9.0-nompi_hf008753_1101.tar.bz2 1.2 MB | |
| pyqt-5.9.2-py37hcca6a23_4.tar.bz2 5.7 MB | |
| qt-5.9.7-h52cfd70_2.tar.bz2 85.9 MB | |
| r-foreign-0.8_76-r36hcdcec82_1.tar.bz2 268 KB | |
| r-boot-1.3_25-r36h6115d3f_1.tar.bz2 634 KB | |
| r-recommended-3.6-r36_1004.tar.bz2 4 KB | |
| r-class-7.3_17-r36hcdcec82_1.tar.bz2 107 KB | |
| r-codetools-0.2_16-r36h6115d3f_1002.tar.bz2 105 KB | |
| r-nnet-7.3_14-r36hcdcec82_1.tar.bz2 132 KB | |
| r-rpart-4.1_15-r36hcdcec82_2.tar.bz2 735 KB | |
| r-mass-7.3_51.6-r36hcdcec82_2.tar.bz2 1.1 MB | |
| r-3.6-r36_1003.tar.bz2 14 KB | |
| r-mgcv-1.8_31-r36h7fa42b6_1.tar.bz2 2.7 MB | |
| r-nlme-3.1_147-r36h9bbef5b_1.tar.bz2 2.3 MB | |
| glib-2.64.2-h6f030ca_0.tar.bz2 3.4 MB | |
| r-cluster-2.1.0-r36h9bbef5b_3.tar.bz2 554 KB | |
| r-spatial-7.3_12-r36hcdcec82_1.tar.bz2 154 KB | |
| r-survival-3.1_12-r36hcdcec82_1.tar.bz2 7.4 MB | |
| r-kernsmooth-2.23_17-r36hfa343cc_1.tar.bz2 104 KB | |
| scikit-learn-0.22.2.post1-py37hcdab131_0.tar.bz2 7.1 MB | |
| lzo-2.10-h14c3975_1000.tar.bz2 319 KB | |
| typing-3.6.4-py37_0.tar.bz2 44 KB | |
| gmp-6.2.0-he1b5a44_2.tar.bz2 811 KB | |
| decorator-4.4.2-py_0.tar.bz2 11 KB | |
| zipp-3.1.0-py_0.tar.bz2 10 KB | |
| importlib_metadata-1.6.0-0.tar.bz2 3 KB | |
| blosc-1.18.1-he1b5a44_0.tar.bz2 893 KB | |
| numba-0.48.0-py37hb3f55d8_0.tar.bz2 3.4 MB | |
| scipy-1.4.1-py37ha3d9a3c_3.tar.bz2 18.8 MB | |
| pyparsing-2.4.7-pyh9f0ad1d_0.tar.bz2 60 KB | |
| python-3.7.6-h8356626_5_cpython.tar.bz2 52.9 MB | |
| mock-4.0.2-py37hc8dfbb8_0.tar.bz2 51 KB | |
| llvmlite-0.31.0-py37h5202443_1.tar.bz2 338 KB | |
| libxml2-2.9.9-h13577e0_2.tar.bz2 1.3 MB | |
| hdf5-1.10.4-nompi_h3c11f04_1106.tar.bz2 5.3 MB | |
| pandas-1.0.3-py37h0da4684_1.tar.bz2 11.1 MB | |
| --------------------------------------------------- | |
| Total: 777.7 MB | |
| Removed python-3.7.3-h0371630_0.tar.bz2 | |
| Removed ca-certificates-2019.1.23-0.tar.bz2 | |
| Removed libgcc-ng-8.2.0-hdf63c60_1.tar.bz2 | |
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| Removed ncurses-6.1-he6710b0_1.tar.bz2 | |
| Removed openssl-1.1.1b-h7b6447c_1.tar.bz2 | |
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| Removed yaml-0.1.7-had09818_2.tar.bz2 | |
| Removed zlib-1.2.11-h7b6447c_3.tar.bz2 | |
| Removed libedit-3.1.20181209-hc058e9b_0.tar.bz2 | |
| Removed readline-7.0-h7b6447c_5.tar.bz2 | |
| Removed tk-8.6.8-hbc83047_0.tar.bz2 | |
| Removed sqlite-3.27.2-h7b6447c_0.tar.bz2 | |
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| Removed pycparser-2.19-py37_0.tar.bz2 | |
| Removed pysocks-1.6.8-py37_0.tar.bz2 | |
| Removed ruamel_yaml-0.15.46-py37h14c3975_0.tar.bz2 | |
| Removed six-1.12.0-py37_0.tar.bz2 | |
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| Removed setuptools-41.0.0-py37_0.tar.bz2 | |
| Removed cryptography-2.6.1-py37h1ba5d50_0.tar.bz2 | |
| Removed wheel-0.33.1-py37_0.tar.bz2 | |
| Removed pip-19.0.3-py37_0.tar.bz2 | |
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| Removed urllib3-1.24.1-py37_0.tar.bz2 | |
| Removed requests-2.21.0-py37_0.tar.bz2 | |
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| Removed certifi-2019.11.28-py27_0.tar.bz2 | |
| Removed wheel-0.34.2-py_1.tar.bz2 | |
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| Removed pip-20.1-pyh9f0ad1d_0.tar.bz2 | |
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| Removed bioconductor-hdf5array-1.12.1-r36h516909a_0.tar.bz2 | |
| Removed bioconductor-limma-3.40.2-r36h516909a_0.tar.bz2 | |
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| Removed r-r.oo-1.23.0-r36h6115d3f_1.tar.bz2 | |
| Removed bioconductor-rhdf5-2.28.0-r36he1b5a44_1.tar.bz2 | |
| Removed dropletutils-scripts-0.0.4-1.tar.bz2 | |
| Removed curl-7.69.1-h33f0ec9_0.tar.bz2 | |
| Removed cairo-1.16.0-hcf35c78_1003.tar.bz2 | |
| Removed r-matrix-1.2_18-r36h7fa42b6_3.tar.bz2 | |
| Removed r-matrixstats-0.56.0-r36hcdcec82_1.tar.bz2 | |
| Removed graphite2-1.3.13-he1b5a44_1001.tar.bz2 | |
| Removed libgomp-9.2.0-h24d8f2e_2.tar.bz2 | |
| Removed binutils_linux-64-2.34-hc952b39_18.tar.bz2 | |
| Removed gcc_linux-64-7.3.0-h553295d_18.tar.bz2 | |
| Removed bioconductor-genomeinfodb-1.20.0-r36_1.tar.bz2 | |
| Removed xorg-libxrender-0.9.10-h516909a_1002.tar.bz2 | |
| Removed fontconfig-2.13.1-h86ecdb6_1001.tar.bz2 | |
| Removed r-sitmo-2.0.1-r36h0357c0b_2.tar.bz2 | |
| Removed bioconductor-edger-3.26.5-r36he1b5a44_0.tar.bz2 | |
| Removed r-workflowscriptscommon-0.0.7-r36_0.tar.bz2 | |
| Removed bioconductor-delayedarray-0.10.0-r36h516909a_1.tar.bz2 | |
| Removed r-rcpp-1.0.4.6-r36h0357c0b_1.tar.bz2 | |
| Removed bioconductor-beachmat-2.0.0-r36he1b5a44_1.tar.bz2 | |
| Removed r-rcurl-1.98_1.2-r36hcdcec82_1.tar.bz2 | |
| Removed jpeg-9c-h14c3975_1001.tar.bz2 | |
| Removed bioconductor-dropletutils-1.4.2-r36he1b5a44_0.tar.bz2 | |
| Removed bioconductor-s4vectors-0.22.0-r36h516909a_1.tar.bz2 | |
| Removed libxml2-2.9.10-hee79883_0.tar.bz2 | |
| Removed bioconductor-singlecellexperiment-1.6.0-r36_1.tar.bz2 | |
| Removed make-4.3-h516909a_0.tar.bz2 | |
| Removed libssh2-1.8.2-h22169c7_2.tar.bz2 | |
| Removed bzip2-1.0.8-h516909a_2.tar.bz2 | |
| Removed xorg-libxext-1.3.4-h516909a_0.tar.bz2 | |
| Removed pango-1.42.4-h7062337_4.tar.bz2 | |
| Removed xorg-libx11-1.6.9-h516909a_0.tar.bz2 | |
| Removed libwebp-base-1.1.0-h516909a_3.tar.bz2 | |
| Removed r-locfit-1.5_9.4-r36hcdcec82_1.tar.bz2 | |
| Removed openblas-0.3.9-he1df0ab_0.tar.bz2 | |
| Removed fribidi-1.0.9-h516909a_0.tar.bz2 | |
| Removed pthread-stubs-0.4-h14c3975_1001.tar.bz2 | |
| Removed libxcb-1.13-h14c3975_1002.tar.bz2 | |
| Removed r-r.methodss3-1.8.0-r36h6115d3f_1.tar.bz2 | |
| Removed libedit-3.1.20170329-hf8c457e_1001.tar.bz2 | |
| Removed r-lambda.r-1.2.4-r36h6115d3f_1.tar.bz2 | |
| Removed r-futile.options-1.0.1-r36h6115d3f_1002.tar.bz2 | |
| Removed xorg-kbproto-1.0.7-h14c3975_1002.tar.bz2 | |
| Removed xz-5.2.5-h516909a_0.tar.bz2 | |
| Removed gsl-2.6-h294904e_0.tar.bz2 | |
| Removed certifi-2020.4.5.1-py38h32f6830_0.tar.bz2 | |
| Removed pixman-0.34.0-h14c3975_1003.tar.bz2 | |
| Removed bioconductor-flowcore-1.38.2-r3.3.2_1.tar.bz2 | |
| Removed r-rrcov-1.4_3-r3.3.2_0.tar.bz2 | |
| Removed r-corpcor-1.6.9-r3.3.2_0.tar.bz2 | |
| Removed bioconductor-graph-1.50.0-r3.3.2_1.tar.bz2 | |
| Removed r-matrixstats-0.52.2-r3.3.2_0.tar.bz2 | |
| Removed r-base-3.3.2-5.tar.bz2 | |
| Removed ncurses-5.9-10.tar.bz2 | |
| Removed libxml2-2.9.5-0.tar.bz2 | |
| Removed bioconductor-biobase-2.34.0-r3.3.2_0.tar.bz2 | |
| Removed pango-1.40.4-0.tar.bz2 | |
| Removed r-pcapp-1.9_61-r3.3.2_0.tar.bz2 | |
| Removed r-deoptimr-1.0_8-r3.3.2_0.tar.bz2 | |
| Removed r-cluster-2.0.6-r3.3.2_0.tar.bz2 | |
| Removed r-bh-1.66.0_1-r3.3.2_0.tar.bz2 | |
| Removed zlib-1.2.8-3.tar.bz2 | |
| Removed cairo-1.14.6-4.tar.bz2 | |
| Removed r-rcpp-0.12.16-r3.3.2_0.tar.bz2 | |
| Removed tk-8.5.19-2.tar.bz2 | |
| Removed curl-7.52.1-0.tar.bz2 | |
| Removed icu-58.2-hf484d3e_1000.tar.bz2 | |
| Removed r-lattice-0.20_34-r3.3.2_0.tar.bz2 | |
| Removed libpng-1.6.28-1.tar.bz2 | |
| Removed libgcc-7.2.0-h69d50b8_2.tar.bz2 | |
| Removed r-robustbase-0.92_7-r3.3.2_0.tar.bz2 | |
| Removed fontconfig-2.12.1-6.tar.bz2 | |
| Removed openssl-1.0.2u-h516909a_0.tar.bz2 | |
| Removed r-mvtnorm-1.0_6-r3.3.2_0.tar.bz2 | |
| Removed freetype-2.7-1.tar.bz2 | |
| Removed harfbuzz-1.4.3-0.tar.bz2 | |
| Removed libtiff-4.0.7-0.tar.bz2 | |
| Removed readline-6.2-0.tar.bz2 | |
| Removed bioconductor-biocgenerics-0.22.0-r3.3.2_0.tar.bz2 | |
| Removed glib-2.51.4-0.tar.bz2 | |
| Removed gstreamer-1.14.5-h36ae1b5_2.tar.bz2 | |
| Removed pytables-3.5.2-py37ha1aa75f_0.tar.bz2 | |
| Removed h5py-2.9.0-nompi_hf008753_1101.tar.bz2 | |
| Removed pyqt-5.9.2-py37hcca6a23_4.tar.bz2 | |
| Removed qt-5.9.7-h52cfd70_2.tar.bz2 | |
| Removed r-foreign-0.8_76-r36hcdcec82_1.tar.bz2 | |
| Removed r-boot-1.3_25-r36h6115d3f_1.tar.bz2 | |
| Removed r-recommended-3.6-r36_1004.tar.bz2 | |
| Removed r-class-7.3_17-r36hcdcec82_1.tar.bz2 | |
| Removed r-codetools-0.2_16-r36h6115d3f_1002.tar.bz2 | |
| Removed r-nnet-7.3_14-r36hcdcec82_1.tar.bz2 | |
| Removed r-rpart-4.1_15-r36hcdcec82_2.tar.bz2 | |
| Removed r-mass-7.3_51.6-r36hcdcec82_2.tar.bz2 | |
| Removed r-3.6-r36_1003.tar.bz2 | |
| Removed r-mgcv-1.8_31-r36h7fa42b6_1.tar.bz2 | |
| Removed r-nlme-3.1_147-r36h9bbef5b_1.tar.bz2 | |
| Removed glib-2.64.2-h6f030ca_0.tar.bz2 | |
| Removed r-cluster-2.1.0-r36h9bbef5b_3.tar.bz2 | |
| Removed r-spatial-7.3_12-r36hcdcec82_1.tar.bz2 | |
| Removed r-survival-3.1_12-r36hcdcec82_1.tar.bz2 | |
| Removed r-kernsmooth-2.23_17-r36hfa343cc_1.tar.bz2 | |
| Removed scikit-learn-0.22.2.post1-py37hcdab131_0.tar.bz2 | |
| Removed lzo-2.10-h14c3975_1000.tar.bz2 | |
| Removed typing-3.6.4-py37_0.tar.bz2 | |
| Removed gmp-6.2.0-he1b5a44_2.tar.bz2 | |
| Removed decorator-4.4.2-py_0.tar.bz2 | |
| Removed zipp-3.1.0-py_0.tar.bz2 | |
| Removed importlib_metadata-1.6.0-0.tar.bz2 | |
| Removed blosc-1.18.1-he1b5a44_0.tar.bz2 | |
| Removed numba-0.48.0-py37hb3f55d8_0.tar.bz2 | |
| Removed scipy-1.4.1-py37ha3d9a3c_3.tar.bz2 | |
| Removed pyparsing-2.4.7-pyh9f0ad1d_0.tar.bz2 | |
| Removed python-3.7.6-h8356626_5_cpython.tar.bz2 | |
| Removed mock-4.0.2-py37hc8dfbb8_0.tar.bz2 | |
| Removed llvmlite-0.31.0-py37h5202443_1.tar.bz2 | |
| Removed libxml2-2.9.9-h13577e0_2.tar.bz2 | |
| Removed hdf5-1.10.4-nompi_h3c11f04_1106.tar.bz2 | |
| Removed pandas-1.0.3-py37h0da4684_1.tar.bz2 | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:48:28,548 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Executing command: *******/galaxy/shared/_conda/bin/conda list --name __r@_uv_ --export > '*******/galaxy/shared/galaxy_wd/tmp/jobdepsox5fww7wd72ce9470954fded9b6320d7553894dbc2685dfc709bc40fe22113cf16375d6a/__r@_uv_' | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:48:29,756 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Executing command: *******/galaxy/shared/_conda/bin/conda install -y --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix *******/galaxy/shared/_cache/0fff183d --file *******/galaxy/shared/galaxy_wd/tmp/jobdepsox5fww7wd72ce9470954fded9b6320d7553894dbc2685dfc709bc40fe22113cf16375d6a/__r@_uv_ | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_cache/0fff183d | |
| added / updated specs: | |
| - _libgcc_mutex==0.1=conda_forge | |
| - _openmp_mutex==4.5=1_llvm | |
| - _r-mutex==1.0.1=anacondar_1 | |
| - binutils_impl_linux-64==2.34=h53a641e_0 | |
| - binutils_linux-64==2.34=hc952b39_18 | |
| - bwidget==1.9.14=0 | |
| - bzip2==1.0.8=h516909a_2 | |
| - ca-certificates==2020.4.5.1=hecc5488_0 | |
| - cairo==1.16.0=hcf35c78_1003 | |
| - certifi==2020.4.5.1=py38h32f6830_0 | |
| - curl==7.69.1=h33f0ec9_0 | |
| - fontconfig==2.13.1=h86ecdb6_1001 | |
| - freetype==2.10.1=he06d7ca_0 | |
| - fribidi==1.0.9=h516909a_0 | |
| - gcc_impl_linux-64==7.3.0=hd420e75_5 | |
| - gcc_linux-64==7.3.0=h553295d_18 | |
| - gettext==0.19.8.1=hc5be6a0_1002 | |
| - gfortran_impl_linux-64==7.3.0=hdf63c60_5 | |
| - gfortran_linux-64==7.3.0=h553295d_18 | |
| - glib==2.64.2=h6f030ca_0 | |
| - graphite2==1.3.13=he1b5a44_1001 | |
| - gsl==2.6=h294904e_0 | |
| - gxx_impl_linux-64==7.3.0=hdf63c60_5 | |
| - gxx_linux-64==7.3.0=h553295d_18 | |
| - harfbuzz==2.4.0=h9f30f68_3 | |
| - icu==64.2=he1b5a44_1 | |
| - jpeg==9c=h14c3975_1001 | |
| - krb5==1.17.1=h2fd8d38_0 | |
| - ld_impl_linux-64==2.34=h53a641e_0 | |
| - libblas==3.8.0=16_openblas | |
| - libcblas==3.8.0=16_openblas | |
| - libcurl==7.69.1=hf7181ac_0 | |
| - libedit==3.1.20170329=hf8c457e_1001 | |
| - libffi==3.2.1=he1b5a44_1007 | |
| - libgcc-ng==9.2.0=h24d8f2e_2 | |
| - libgfortran-ng==7.3.0=hdf63c60_5 | |
| - libgomp==9.2.0=h24d8f2e_2 | |
| - libiconv==1.15=h516909a_1006 | |
| - liblapack==3.8.0=16_openblas | |
| - libopenblas==0.3.9=h5ec1e0e_0 | |
| - libpng==1.6.37=hed695b0_1 | |
| - libssh2==1.8.2=h22169c7_2 | |
| - libstdcxx-ng==9.2.0=hdf63c60_2 | |
| - libtiff==4.1.0=hc7e4089_6 | |
| - libuuid==2.32.1=h14c3975_1000 | |
| - libwebp-base==1.1.0=h516909a_3 | |
| - libxcb==1.13=h14c3975_1002 | |
| - libxml2==2.9.10=hee79883_0 | |
| - llvm-openmp==10.0.0=hc9558a2_0 | |
| - lz4-c==1.9.2=he1b5a44_1 | |
| - make==4.3=h516909a_0 | |
| - ncurses==6.1=hf484d3e_1002 | |
| - openssl==1.1.1g=h516909a_0 | |
| - pango==1.42.4=h7062337_4 | |
| - pcre==8.44=he1b5a44_0 | |
| - pip==20.1=pyh9f0ad1d_0 | |
| - pixman==0.38.0=h516909a_1003 | |
| - pthread-stubs==0.4=h14c3975_1001 | |
| - python==3.8.2=he5300dc_7_cpython | |
| - python_abi==3.8=1_cp38 | |
| - r-base==3.6.3=h316533a_2 | |
| - r-boot==1.3_25=r36h6115d3f_1 | |
| - r-class==7.3_17=r36hcdcec82_1 | |
| - r-cluster==2.1.0=r36h9bbef5b_3 | |
| - r-codetools==0.2_16=r36h6115d3f_1002 | |
| - r-foreign==0.8_76=r36hcdcec82_1 | |
| - r-kernsmooth==2.23_17=r36hfa343cc_1 | |
| - r-lattice==0.20_41=r36hcdcec82_2 | |
| - r-mass==7.3_51.6=r36hcdcec82_2 | |
| - r-matrix==1.2_18=r36h7fa42b6_3 | |
| - r-mgcv==1.8_31=r36h7fa42b6_1 | |
| - r-nlme==3.1_147=r36h9bbef5b_1 | |
| - r-nnet==7.3_14=r36hcdcec82_1 | |
| - r-recommended==3.6=r36_1004 | |
| - r-rpart==4.1_15=r36hcdcec82_2 | |
| - r-spatial==7.3_12=r36hcdcec82_1 | |
| - r-survival==3.1_12=r36hcdcec82_1 | |
| - r==3.6=r36_1003 | |
| - readline==8.0=hf8c457e_0 | |
| - sed==4.7=h1bed415_1000 | |
| - setuptools==46.1.3=py38h32f6830_0 | |
| - sqlite==3.30.1=hcee41ef_0 | |
| - tk==8.6.10=hed695b0_0 | |
| - tktable==2.10=h555a92e_3 | |
| - wheel==0.34.2=py_1 | |
| - xorg-kbproto==1.0.7=h14c3975_1002 | |
| - xorg-libice==1.0.10=h516909a_0 | |
| - xorg-libsm==1.2.3=h84519dc_1000 | |
| - xorg-libx11==1.6.9=h516909a_0 | |
| - xorg-libxau==1.0.9=h14c3975_0 | |
| - xorg-libxdmcp==1.1.3=h516909a_0 | |
| - xorg-libxext==1.3.4=h516909a_0 | |
| - xorg-libxrender==0.9.10=h516909a_1002 | |
| - xorg-renderproto==0.11.1=h14c3975_1002 | |
| - xorg-xextproto==7.3.0=h14c3975_1002 | |
| - xorg-xproto==7.0.31=h14c3975_1007 | |
| - xz==5.2.5=h516909a_0 | |
| - zlib==1.2.11=h516909a_1006 | |
| - zstd==1.4.4=h6597ccf_3 | |
| The following NEW packages will be INSTALLED: | |
| binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.34-h53a641e_0 | |
| binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.34-hc952b39_18 | |
| bwidget conda-forge/linux-64::bwidget-1.9.14-0 | |
| certifi conda-forge/linux-64::certifi-2020.4.5.1-py38h32f6830_0 | |
| fribidi conda-forge/linux-64::fribidi-1.0.9-h516909a_0 | |
| gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-7.3.0-hd420e75_5 | |
| gcc_linux-64 conda-forge/linux-64::gcc_linux-64-7.3.0-h553295d_18 | |
| gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_5 | |
| gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-7.3.0-h553295d_18 | |
| gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_5 | |
| gxx_linux-64 conda-forge/linux-64::gxx_linux-64-7.3.0-h553295d_18 | |
| krb5 conda-forge/linux-64::krb5-1.17.1-h2fd8d38_0 | |
| ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 | |
| libcurl conda-forge/linux-64::libcurl-7.69.1-hf7181ac_0 | |
| libedit conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001 | |
| libgomp conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2 | |
| liblapack conda-forge/linux-64::liblapack-3.8.0-16_openblas | |
| libssh2 conda-forge/linux-64::libssh2-1.8.2-h22169c7_2 | |
| libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000 | |
| libwebp-base conda-forge/linux-64::libwebp-base-1.1.0-h516909a_3 | |
| libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002 | |
| lz4-c conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_1 | |
| make conda-forge/linux-64::make-4.3-h516909a_0 | |
| pip conda-forge/noarch::pip-20.1-pyh9f0ad1d_0 | |
| pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001 | |
| python conda-forge/linux-64::python-3.8.2-he5300dc_7_cpython | |
| python_abi conda-forge/linux-64::python_abi-3.8-1_cp38 | |
| r conda-forge/noarch::r-3.6-r36_1003 | |
| r-boot conda-forge/noarch::r-boot-1.3_25-r36h6115d3f_1 | |
| r-class conda-forge/linux-64::r-class-7.3_17-r36hcdcec82_1 | |
| r-codetools conda-forge/noarch::r-codetools-0.2_16-r36h6115d3f_1002 | |
| r-foreign conda-forge/linux-64::r-foreign-0.8_76-r36hcdcec82_1 | |
| r-kernsmooth conda-forge/linux-64::r-kernsmooth-2.23_17-r36hfa343cc_1 | |
| r-mass conda-forge/linux-64::r-mass-7.3_51.6-r36hcdcec82_2 | |
| r-matrix conda-forge/linux-64::r-matrix-1.2_18-r36h7fa42b6_3 | |
| r-mgcv conda-forge/linux-64::r-mgcv-1.8_31-r36h7fa42b6_1 | |
| r-nlme conda-forge/linux-64::r-nlme-3.1_147-r36h9bbef5b_1 | |
| r-nnet conda-forge/linux-64::r-nnet-7.3_14-r36hcdcec82_1 | |
| r-recommended conda-forge/noarch::r-recommended-3.6-r36_1004 | |
| r-rpart conda-forge/linux-64::r-rpart-4.1_15-r36hcdcec82_2 | |
| r-spatial conda-forge/linux-64::r-spatial-7.3_12-r36hcdcec82_1 | |
| r-survival conda-forge/linux-64::r-survival-3.1_12-r36hcdcec82_1 | |
| sed conda-forge/linux-64::sed-4.7-h1bed415_1000 | |
| setuptools conda-forge/linux-64::setuptools-46.1.3-py38h32f6830_0 | |
| sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0 | |
| tktable conda-forge/linux-64::tktable-2.10-h555a92e_3 | |
| wheel conda-forge/noarch::wheel-0.34.2-py_1 | |
| xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002 | |
| xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0 | |
| xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000 | |
| xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0 | |
| xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0 | |
| xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0 | |
| xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0 | |
| xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002 | |
| xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002 | |
| xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002 | |
| xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007 | |
| zstd conda-forge/linux-64::zstd-1.4.4-h6597ccf_3 | |
| The following packages will be REMOVED: | |
| bioconductor-biobase-2.34.0-r3.3.2_0 | |
| bioconductor-biocgenerics-0.22.0-r3.3.2_0 | |
| bioconductor-flowcore-1.38.2-r3.3.2_1 | |
| bioconductor-graph-1.50.0-r3.3.2_1 | |
| r-bh-1.66.0_1-r3.3.2_0 | |
| r-corpcor-1.6.9-r3.3.2_0 | |
| r-deoptimr-1.0_8-r3.3.2_0 | |
| r-matrixstats-0.52.2-r3.3.2_0 | |
| r-mvtnorm-1.0_6-r3.3.2_0 | |
| r-pcapp-1.9_61-r3.3.2_0 | |
| r-rcpp-0.12.16-r3.3.2_0 | |
| r-robustbase-0.92_7-r3.3.2_0 | |
| r-rrcov-1.4_3-r3.3.2_0 | |
| The following packages will be UPDATED: | |
| cairo 1.14.6-4 --> 1.16.0-hcf35c78_1003 | |
| curl 7.52.1-0 --> 7.69.1-h33f0ec9_0 | |
| fontconfig 2.12.1-6 --> 2.13.1-h86ecdb6_1001 | |
| freetype 2.7-1 --> 2.10.1-he06d7ca_0 | |
| glib 2.51.4-0 --> 2.64.2-h6f030ca_0 | |
| harfbuzz 1.4.3-0 --> 2.4.0-h9f30f68_3 | |
| icu 58.2-hf484d3e_1000 --> 64.2-he1b5a44_1 | |
| libpng 1.6.28-1 --> 1.6.37-hed695b0_1 | |
| libtiff 4.0.7-0 --> 4.1.0-hc7e4089_6 | |
| libxml2 2.9.5-0 --> 2.9.10-hee79883_0 | |
| ncurses 5.9-10 --> 6.1-hf484d3e_1002 | |
| openssl 1.0.2u-h516909a_0 --> 1.1.1g-h516909a_0 | |
| pango 1.40.4-0 --> 1.42.4-h7062337_4 | |
| pixman 0.34.0-h14c3975_1003 --> 0.38.0-h516909a_1003 | |
| r-base 3.3.2-5 --> 3.6.3-h316533a_2 | |
| r-cluster 2.0.6-r3.3.2_0 --> 2.1.0-r36h9bbef5b_3 | |
| r-lattice 0.20_34-r3.3.2_0 --> 0.20_41-r36hcdcec82_2 | |
| readline 6.2-0 --> 8.0-hf8c457e_0 | |
| tk 8.5.19-2 --> 8.6.10-hed695b0_0 | |
| zlib 1.2.8-3 --> 1.2.11-h516909a_1006 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_conda/envs/mulled-v1-141253bb58fad23ac50749589168696eca3ed3ab1e99608dbf718dbfa9556234 | |
| added / updated specs: | |
| - h5py=2.9.0 | |
| - leidenalg=0.7.0 | |
| - loompy=2.0.17 | |
| - scanpy=1.4.4.post1 | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| anndata-0.7.1 | py37_0 155 KB conda-forge | |
| blosc-1.18.1 | he1b5a44_0 893 KB conda-forge | |
| cairo-1.16.0 | h18b612c_1001 1.5 MB conda-forge | |
| cycler-0.10.0 | py_2 9 KB conda-forge | |
| dbus-1.13.6 | he372182_0 602 KB conda-forge | |
| decorator-4.4.2 | py_0 11 KB conda-forge | |
| expat-2.2.9 | he1b5a44_2 191 KB conda-forge | |
| fontconfig-2.13.1 | he4413a7_1000 327 KB conda-forge | |
| glib-2.64.2 | h6f030ca_0 3.4 MB conda-forge | |
| gmp-6.2.0 | he1b5a44_2 811 KB conda-forge | |
| gst-plugins-base-1.14.5 | h0935bb2_2 6.8 MB conda-forge | |
| gstreamer-1.14.5 | h36ae1b5_2 4.5 MB conda-forge | |
| h5py-2.9.0 |nompi_hf008753_1101 1.2 MB conda-forge | |
| hdf5-1.10.4 |nompi_h3c11f04_1106 5.3 MB conda-forge | |
| igraph-0.7.1 | h2166141_1005 3.4 MB conda-forge | |
| importlib-metadata-1.6.0 | py37hc8dfbb8_0 43 KB conda-forge | |
| importlib_metadata-1.6.0 | 0 3 KB conda-forge | |
| joblib-0.14.1 | py_0 198 KB conda-forge | |
| kiwisolver-1.2.0 | py37h99015e2_0 87 KB conda-forge | |
| leidenalg-0.7.0 | py37h3340039_2 114 KB conda-forge | |
| libllvm8-8.0.1 | hc9558a2_0 23.2 MB conda-forge | |
| libxml2-2.9.9 | h13577e0_2 1.3 MB conda-forge | |
| llvmlite-0.31.0 | py37h5202443_1 338 KB conda-forge | |
| loompy-2.0.17 | py_0 32 KB conda-forge | |
| louvain-0.6.1 | py37he1b5a44_2 97 KB conda-forge | |
| lzo-2.10 | h14c3975_1000 319 KB conda-forge | |
| matplotlib-3.0.3 | py37_1 6 KB conda-forge | |
| matplotlib-base-3.0.3 | py37h5f35d83_1 6.7 MB conda-forge | |
| mock-4.0.2 | py37hc8dfbb8_0 51 KB conda-forge | |
| natsort-7.0.1 | py_0 32 KB conda-forge | |
| networkx-2.4 | py_1 1.2 MB conda-forge | |
| numba-0.48.0 | py37hb3f55d8_0 3.4 MB conda-forge | |
| numexpr-2.7.1 | py37h0da4684_1 197 KB conda-forge | |
| numpy-1.18.4 | py37h8960a57_0 5.2 MB conda-forge | |
| packaging-20.1 | py_0 31 KB conda-forge | |
| pandas-1.0.3 | py37h0da4684_1 11.1 MB conda-forge | |
| patsy-0.5.1 | py_0 187 KB conda-forge | |
| pycairo-1.19.1 | py37h01af8b0_3 77 KB conda-forge | |
| pyparsing-2.4.7 | pyh9f0ad1d_0 60 KB conda-forge | |
| pyqt-5.9.2 | py37hcca6a23_4 5.7 MB conda-forge | |
| pytables-3.5.2 | py37ha1aa75f_0 1.5 MB conda-forge | |
| python-3.7.6 |h8356626_5_cpython 52.9 MB conda-forge | |
| python-igraph-0.7.1.post7 | py37h516909a_0 567 KB conda-forge | |
| qt-5.9.7 | h52cfd70_2 85.9 MB conda-forge | |
| scanpy-1.4.4.post1 | py_3 209 KB bioconda | |
| scikit-learn-0.22.2.post1 | py37hcdab131_0 7.1 MB conda-forge | |
| scipy-1.4.1 | py37ha3d9a3c_3 18.8 MB conda-forge | |
| seaborn-0.10.1 | py_0 158 KB conda-forge | |
| setuptools-46.1.3 | py37hc8dfbb8_0 634 KB conda-forge | |
| sip-4.19.8 |py37hf484d3e_1000 290 KB conda-forge | |
| statsmodels-0.11.1 | py37h8f50634_1 10.1 MB conda-forge | |
| tbb-2020.1 | hc9558a2_0 1.4 MB conda-forge | |
| tornado-6.0.4 | py37h8f50634_1 639 KB conda-forge | |
| tqdm-4.46.0 | pyh9f0ad1d_0 50 KB conda-forge | |
| typing-3.6.4 | py37_0 44 KB | |
| umap-learn-0.4.2 | py37hc8dfbb8_0 108 KB conda-forge | |
| zipp-3.1.0 | py_0 10 KB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 268.9 MB | |
| The following NEW packages will be INSTALLED: | |
| _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge | |
| _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_llvm | |
| anndata conda-forge/linux-64::anndata-0.7.1-py37_0 | |
| blosc conda-forge/linux-64::blosc-1.18.1-he1b5a44_0 | |
| bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_2 | |
| ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0 | |
| cairo conda-forge/linux-64::cairo-1.16.0-h18b612c_1001 | |
| certifi conda-forge/linux-64::certifi-2020.4.5.1-py37hc8dfbb8_0 | |
| cycler conda-forge/noarch::cycler-0.10.0-py_2 | |
| dbus conda-forge/linux-64::dbus-1.13.6-he372182_0 | |
| decorator conda-forge/noarch::decorator-4.4.2-py_0 | |
| expat conda-forge/linux-64::expat-2.2.9-he1b5a44_2 | |
| fontconfig conda-forge/linux-64::fontconfig-2.13.1-he4413a7_1000 | |
| freetype conda-forge/linux-64::freetype-2.10.1-he06d7ca_0 | |
| gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002 | |
| glib conda-forge/linux-64::glib-2.64.2-h6f030ca_0 | |
| gmp conda-forge/linux-64::gmp-6.2.0-he1b5a44_2 | |
| gst-plugins-base conda-forge/linux-64::gst-plugins-base-1.14.5-h0935bb2_2 | |
| gstreamer conda-forge/linux-64::gstreamer-1.14.5-h36ae1b5_2 | |
| h5py conda-forge/linux-64::h5py-2.9.0-nompi_hf008753_1101 | |
| hdf5 conda-forge/linux-64::hdf5-1.10.4-nompi_h3c11f04_1106 | |
| icu conda-forge/linux-64::icu-58.2-hf484d3e_1000 | |
| igraph conda-forge/linux-64::igraph-0.7.1-h2166141_1005 | |
| importlib-metadata conda-forge/linux-64::importlib-metadata-1.6.0-py37hc8dfbb8_0 | |
| importlib_metadata conda-forge/noarch::importlib_metadata-1.6.0-0 | |
| joblib conda-forge/noarch::joblib-0.14.1-py_0 | |
| jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001 | |
| kiwisolver conda-forge/linux-64::kiwisolver-1.2.0-py37h99015e2_0 | |
| ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 | |
| leidenalg conda-forge/linux-64::leidenalg-0.7.0-py37h3340039_2 | |
| libblas conda-forge/linux-64::libblas-3.8.0-16_openblas | |
| libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas | |
| libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 | |
| libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2 | |
| libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5 | |
| libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1006 | |
| liblapack conda-forge/linux-64::liblapack-3.8.0-16_openblas | |
| libllvm8 conda-forge/linux-64::libllvm8-8.0.1-hc9558a2_0 | |
| libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0 | |
| libpng conda-forge/linux-64::libpng-1.6.37-hed695b0_1 | |
| libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2 | |
| libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000 | |
| libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002 | |
| libxml2 conda-forge/linux-64::libxml2-2.9.9-h13577e0_2 | |
| llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0 | |
| llvmlite conda-forge/linux-64::llvmlite-0.31.0-py37h5202443_1 | |
| loompy conda-forge/noarch::loompy-2.0.17-py_0 | |
| louvain conda-forge/linux-64::louvain-0.6.1-py37he1b5a44_2 | |
| lzo conda-forge/linux-64::lzo-2.10-h14c3975_1000 | |
| matplotlib conda-forge/linux-64::matplotlib-3.0.3-py37_1 | |
| matplotlib-base conda-forge/linux-64::matplotlib-base-3.0.3-py37h5f35d83_1 | |
| mock conda-forge/linux-64::mock-4.0.2-py37hc8dfbb8_0 | |
| natsort conda-forge/noarch::natsort-7.0.1-py_0 | |
| ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002 | |
| networkx conda-forge/noarch::networkx-2.4-py_1 | |
| numba conda-forge/linux-64::numba-0.48.0-py37hb3f55d8_0 | |
| numexpr conda-forge/linux-64::numexpr-2.7.1-py37h0da4684_1 | |
| numpy conda-forge/linux-64::numpy-1.18.4-py37h8960a57_0 | |
| openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_0 | |
| packaging conda-forge/noarch::packaging-20.1-py_0 | |
| pandas conda-forge/linux-64::pandas-1.0.3-py37h0da4684_1 | |
| patsy conda-forge/noarch::patsy-0.5.1-py_0 | |
| pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0 | |
| pip conda-forge/noarch::pip-20.1-pyh9f0ad1d_0 | |
| pixman conda-forge/linux-64::pixman-0.38.0-h516909a_1003 | |
| pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001 | |
| pycairo conda-forge/linux-64::pycairo-1.19.1-py37h01af8b0_3 | |
| pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0 | |
| pyqt conda-forge/linux-64::pyqt-5.9.2-py37hcca6a23_4 | |
| pytables conda-forge/linux-64::pytables-3.5.2-py37ha1aa75f_0 | |
| python conda-forge/linux-64::python-3.7.6-h8356626_5_cpython | |
| python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0 | |
| python-igraph conda-forge/linux-64::python-igraph-0.7.1.post7-py37h516909a_0 | |
| python_abi conda-forge/linux-64::python_abi-3.7-1_cp37m | |
| pytz conda-forge/noarch::pytz-2020.1-pyh9f0ad1d_0 | |
| qt conda-forge/linux-64::qt-5.9.7-h52cfd70_2 | |
| readline conda-forge/linux-64::readline-8.0-hf8c457e_0 | |
| scanpy bioconda/noarch::scanpy-1.4.4.post1-py_3 | |
| scikit-learn conda-forge/linux-64::scikit-learn-0.22.2.post1-py37hcdab131_0 | |
| scipy conda-forge/linux-64::scipy-1.4.1-py37ha3d9a3c_3 | |
| seaborn conda-forge/noarch::seaborn-0.10.1-py_0 | |
| setuptools conda-forge/linux-64::setuptools-46.1.3-py37hc8dfbb8_0 | |
| sip conda-forge/linux-64::sip-4.19.8-py37hf484d3e_1000 | |
| six conda-forge/noarch::six-1.14.0-py_1 | |
| sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0 | |
| statsmodels conda-forge/linux-64::statsmodels-0.11.1-py37h8f50634_1 | |
| tbb conda-forge/linux-64::tbb-2020.1-hc9558a2_0 | |
| tk conda-forge/linux-64::tk-8.6.10-hed695b0_0 | |
| tornado conda-forge/linux-64::tornado-6.0.4-py37h8f50634_1 | |
| tqdm conda-forge/noarch::tqdm-4.46.0-pyh9f0ad1d_0 | |
| typing pkgs/main/linux-64::typing-3.6.4-py37_0 | |
| umap-learn conda-forge/linux-64::umap-learn-0.4.2-py37hc8dfbb8_0 | |
| wheel conda-forge/noarch::wheel-0.34.2-py_1 | |
| xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002 | |
| xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0 | |
| xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000 | |
| xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0 | |
| xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0 | |
| xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0 | |
| xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0 | |
| xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002 | |
| xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002 | |
| xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002 | |
| xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007 | |
| xz conda-forge/linux-64::xz-5.2.5-h516909a_0 | |
| zipp conda-forge/noarch::zipp-3.1.0-py_0 | |
| zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1006 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... 10.114.180.83 - - [06/May/2020:23:49:36 +0100] "GET / HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 62/160] 10.114.180.83 () {56 vars in 1483 bytes} [Wed May 6 23:49:36 2020] GET / => generated 127830 bytes in 73 msecs (HTTP/1.1 200) 7 headers in 200 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:37 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 23/161] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:49:37 2020] GET /api/webhooks => generated 2 bytes in 22 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:38 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 63/162] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:49:38 2020] GET /api/users/current => generated 271 bytes in 54 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:38 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 24/163] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:49:38 2020] GET /api/configuration => generated 2300 bytes in 15 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:38 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 64/164] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:49:38 2020] GET /api/webhooks => generated 2 bytes in 18 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:38 +0100] "GET /scripts/bundled/assets/e417938def579af5c4d237a1cc340445.png HTTP/1.1" 404 227 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 25/165] 10.114.180.83 () {50 vars in 1393 bytes} [Wed May 6 23:49:38 2020] GET /scripts/bundled/assets/e417938def579af5c4d237a1cc340445.png => generated 227 bytes in 2 msecs (HTTP/1.1 404) 2 headers in 87 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:38 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 26/166] 10.114.180.83 () {54 vars in 1350 bytes} [Wed May 6 23:49:38 2020] GET /api/genomes => generated 55436 bytes in 21 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:38 +0100] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 65/167] 10.114.180.83 () {54 vars in 1395 bytes} [Wed May 6 23:49:38 2020] GET /api/datatypes?extension_only=False => generated 53304 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:38 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 27/168] 10.114.180.83 () {52 vars in 1374 bytes} [Wed May 6 23:49:38 2020] GET /history/current_history_json => generated 562 bytes in 50 msecs (HTTP/1.1 200) 5 headers in 171 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:38 +0100] "GET /welcome HTTP/1.1" 302 267 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 66/169] 10.114.180.83 () {52 vars in 1411 bytes} [Wed May 6 23:49:38 2020] GET /welcome => generated 267 bytes in 16 msecs (HTTP/1.1 302) 4 headers in 166 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:39 +0100] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 28/170] 10.114.180.83 () {52 vars in 1370 bytes} [Wed May 6 23:49:39 2020] GET /api/users/f2db41e1fa331b3e => generated 271 bytes in 35 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:39 +0100] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 67/171] 10.114.180.83 () {52 vars in 1575 bytes} [Wed May 6 23:49:39 2020] GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True => generated 2 bytes in 38 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:39 +0100] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 29/172] 10.114.180.83 () {52 vars in 1495 bytes} [Wed May 6 23:49:39 2020] GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 112 bytes in 54 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:51 +0100] "GET / HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 68/173] 10.114.180.83 () {56 vars in 1483 bytes} [Wed May 6 23:49:51 2020] GET / => generated 127830 bytes in 43 msecs (HTTP/1.1 200) 7 headers in 200 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:52 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 30/174] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:49:52 2020] GET /api/webhooks => generated 2 bytes in 13 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| done | |
| Executing transaction: ...working... 10.114.180.83 - - [06/May/2020:23:49:52 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 31/175] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:49:52 2020] GET /api/configuration => generated 2300 bytes in 11 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:52 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 69/176] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:49:52 2020] GET /api/users/current => generated 271 bytes in 31 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:52 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 32/177] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:49:52 2020] GET /api/webhooks => generated 2 bytes in 15 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:52 +0100] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 70/178] 10.114.180.83 () {54 vars in 1395 bytes} [Wed May 6 23:49:52 2020] GET /api/datatypes?extension_only=False => generated 53304 bytes in 17 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:52 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 33/179] 10.114.180.83 () {54 vars in 1350 bytes} [Wed May 6 23:49:52 2020] GET /api/genomes => generated 55436 bytes in 20 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:52 +0100] "GET /welcome HTTP/1.1" 302 267 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 71/180] 10.114.180.83 () {52 vars in 1411 bytes} [Wed May 6 23:49:52 2020] GET /welcome => generated 267 bytes in 10 msecs (HTTP/1.1 302) 4 headers in 166 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:52 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 34/181] 10.114.180.83 () {52 vars in 1374 bytes} [Wed May 6 23:49:52 2020] GET /history/current_history_json => generated 562 bytes in 38 msecs (HTTP/1.1 200) 5 headers in 171 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:53 +0100] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 72/182] 10.114.180.83 () {52 vars in 1370 bytes} [Wed May 6 23:49:53 2020] GET /api/users/f2db41e1fa331b3e => generated 271 bytes in 40 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:53 +0100] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 35/183] 10.114.180.83 () {52 vars in 1575 bytes} [Wed May 6 23:49:53 2020] GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True => generated 2 bytes in 41 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:49:53 +0100] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 73/184] 10.114.180.83 () {52 vars in 1495 bytes} [Wed May 6 23:49:53 2020] GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 112 bytes in 66 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| done | |
| ==> WARNING: A newer version of conda exists. <== | |
| current version: 4.6.14 | |
| latest version: 4.8.3 | |
| Please update conda by running | |
| $ conda update -n base conda | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:50:47,595 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Executing command: *******/galaxy/shared/_conda/bin/conda clean --tarballs -y | |
| Cache location: *******/galaxy/shared/_conda/pkgs | |
| Will remove the following tarballs: | |
| *******/galaxy/shared/_conda/pkgs | |
| ---------------------------------------- | |
| joblib-0.14.1-py_0.tar.bz2 198 KB | |
| matplotlib-base-3.0.3-py37h5f35d83_1.tar.bz2 6.7 MB | |
| tornado-6.0.4-py37h8f50634_1.tar.bz2 639 KB | |
| anndata-0.7.1-py37_0.tar.bz2 155 KB | |
| sip-4.19.8-py37hf484d3e_1000.tar.bz2 290 KB | |
| tqdm-4.46.0-pyh9f0ad1d_0.tar.bz2 50 KB | |
| dbus-1.13.6-he372182_0.tar.bz2 602 KB | |
| statsmodels-0.11.1-py37h8f50634_1.tar.bz2 10.1 MB | |
| packaging-20.1-py_0.tar.bz2 31 KB | |
| gst-plugins-base-1.14.5-h0935bb2_2.tar.bz2 6.8 MB | |
| tbb-2020.1-hc9558a2_0.tar.bz2 1.4 MB | |
| cairo-1.16.0-h18b612c_1001.tar.bz2 1.5 MB | |
| networkx-2.4-py_1.tar.bz2 1.2 MB | |
| loompy-2.0.17-py_0.tar.bz2 32 KB | |
| expat-2.2.9-he1b5a44_2.tar.bz2 191 KB | |
| leidenalg-0.7.0-py37h3340039_2.tar.bz2 114 KB | |
| louvain-0.6.1-py37he1b5a44_2.tar.bz2 97 KB | |
| umap-learn-0.4.2-py37hc8dfbb8_0.tar.bz2 108 KB | |
| setuptools-46.1.3-py37hc8dfbb8_0.tar.bz2 634 KB | |
| numpy-1.18.4-py37h8960a57_0.tar.bz2 5.2 MB | |
| patsy-0.5.1-py_0.tar.bz2 187 KB | |
| cycler-0.10.0-py_2.tar.bz2 9 KB | |
| python-igraph-0.7.1.post7-py37h516909a_0.tar.bz2 567 KB | |
| natsort-7.0.1-py_0.tar.bz2 32 KB | |
| fontconfig-2.13.1-he4413a7_1000.tar.bz2 327 KB | |
| importlib-metadata-1.6.0-py37hc8dfbb8_0.tar.bz2 43 KB | |
| glib-2.64.2-h6f030ca_0.tar.bz2 3.4 MB | |
| matplotlib-3.0.3-py37_1.tar.bz2 6 KB | |
| seaborn-0.10.1-py_0.tar.bz2 158 KB | |
| kiwisolver-1.2.0-py37h99015e2_0.tar.bz2 87 KB | |
| igraph-0.7.1-h2166141_1005.tar.bz2 3.4 MB | |
| libllvm8-8.0.1-hc9558a2_0.tar.bz2 23.2 MB | |
| scanpy-1.4.4.post1-py_3.tar.bz2 209 KB | |
| numexpr-2.7.1-py37h0da4684_1.tar.bz2 197 KB | |
| pycairo-1.19.1-py37h01af8b0_3.tar.bz2 77 KB | |
| --------------------------------------------------- | |
| Total: 67.9 MB | |
| Removed joblib-0.14.1-py_0.tar.bz2 | |
| Removed matplotlib-base-3.0.3-py37h5f35d83_1.tar.bz2 | |
| Removed tornado-6.0.4-py37h8f50634_1.tar.bz2 | |
| Removed anndata-0.7.1-py37_0.tar.bz2 | |
| Removed sip-4.19.8-py37hf484d3e_1000.tar.bz2 | |
| Removed tqdm-4.46.0-pyh9f0ad1d_0.tar.bz2 | |
| Removed dbus-1.13.6-he372182_0.tar.bz2 | |
| Removed statsmodels-0.11.1-py37h8f50634_1.tar.bz2 | |
| Removed packaging-20.1-py_0.tar.bz2 | |
| Removed gst-plugins-base-1.14.5-h0935bb2_2.tar.bz2 | |
| Removed tbb-2020.1-hc9558a2_0.tar.bz2 | |
| Removed cairo-1.16.0-h18b612c_1001.tar.bz2 | |
| Removed networkx-2.4-py_1.tar.bz2 | |
| Removed loompy-2.0.17-py_0.tar.bz2 | |
| Removed expat-2.2.9-he1b5a44_2.tar.bz2 | |
| Removed leidenalg-0.7.0-py37h3340039_2.tar.bz2 | |
| Removed louvain-0.6.1-py37he1b5a44_2.tar.bz2 | |
| Removed umap-learn-0.4.2-py37hc8dfbb8_0.tar.bz2 | |
| Removed setuptools-46.1.3-py37hc8dfbb8_0.tar.bz2 | |
| Removed numpy-1.18.4-py37h8960a57_0.tar.bz2 | |
| Removed patsy-0.5.1-py_0.tar.bz2 | |
| Removed cycler-0.10.0-py_2.tar.bz2 | |
| Removed python-igraph-0.7.1.post7-py37h516909a_0.tar.bz2 | |
| Removed natsort-7.0.1-py_0.tar.bz2 | |
| Removed fontconfig-2.13.1-he4413a7_1000.tar.bz2 | |
| Removed importlib-metadata-1.6.0-py37hc8dfbb8_0.tar.bz2 | |
| Removed glib-2.64.2-h6f030ca_0.tar.bz2 | |
| Removed matplotlib-3.0.3-py37_1.tar.bz2 | |
| Removed seaborn-0.10.1-py_0.tar.bz2 | |
| Removed kiwisolver-1.2.0-py37h99015e2_0.tar.bz2 | |
| Removed igraph-0.7.1-h2166141_1005.tar.bz2 | |
| Removed libllvm8-8.0.1-hc9558a2_0.tar.bz2 | |
| Removed scanpy-1.4.4.post1-py_3.tar.bz2 | |
| Removed numexpr-2.7.1-py37h0da4684_1.tar.bz2 | |
| Removed pycairo-1.19.1-py37h01af8b0_3.tar.bz2 | |
| 10.25.100.188 - - [06/May/2020:23:33:59 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| Wed May 6 23:50:48 2020 - SIGPIPE: writing to a closed pipe/socket/fd (probably the client disconnected) on request /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b (ip 10.25.100.188) !!! | |
| Wed May 6 23:50:48 2020 - uwsgi_response_writev_headers_and_body_do(): Broken pipe [core/writer.c line 306] during POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b (10.25.100.188) | |
| OSError: write error | |
| [pid: 28743|app: 0|req: 17/185] 10.25.100.188 () {42 vars in 751 bytes} [Wed May 6 23:33:59 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 0 bytes in 1008963 msecs (HTTP/1.1 200) 3 headers in 0 bytes (0 switches on core 0) | |
| 10.25.100.188 - - [06/May/2020:23:50:55 +0100] "GET /api/tool_shed_repositories?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28737|app: 0|req: 36/186] 10.25.100.188 () {38 vars in 604 bytes} [Wed May 6 23:50:55 2020] GET /api/tool_shed_repositories?key=ff1fadcdba102650fb96c7f486b45d6b => generated 2598 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:50:57,546 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:50:59,504 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Flow Text File Tools | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-06 23:50:59,511 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Adding new row for repository 'check_headers' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:50:59,517 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:50:59,518 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:50:59,546 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Flow Text File Tools | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-06 23:50:59,555 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/immport-devteam/check_headers' at 0:e88c99a4fb36 | |
| done | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:51:13,386 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency scanpy version 1.4.4.post1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:51:13,386 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency loompy version 2.0.17 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:51:13,386 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency h5py version 2.9.0 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:51:13,387 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency leidenalg version 0.7.0 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:51:13,389 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency scanpy version 1.4.4.post1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:51:13,389 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency loompy version 2.0.17 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:51:13,389 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency h5py version 2.9.0 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:51:13,389 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency leidenalg version 0.7.0 of type conda | |
| 10.25.100.188 - - [06/May/2020:23:44:02 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| Wed May 6 23:51:13 2020 - SIGPIPE: writing to a closed pipe/socket/fd (probably the client disconnected) on request /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b (ip 10.25.100.188) !!! | |
| Wed May 6 23:51:13 2020 - uwsgi_response_writev_headers_and_body_do(): Broken pipe [core/writer.c line 306] during POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b (10.25.100.188) | |
| OSError: write error | |
| [pid: 28741|app: 0|req: 61/187] 10.25.100.188 () {42 vars in 751 bytes} [Wed May 6 23:44:02 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 0 bytes in 430538 msecs (HTTP/1.1 200) 3 headers in 0 bytes (0 switches on core 0) | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:51:22,110 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowtext', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:51:23,282 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowtext', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:51:23,291 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowtext', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:23,293 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/check_headers/get_headers/1.1, version: 1.1 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-06 23:51:23,293 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-06 23:51:23,311 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-06 23:51:23,970 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-06 23:51:23,971 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-06 23:51:34,110 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-06 23:51:34,115 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-06 23:51:34,817 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:51:34,817 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-06 23:51:34,860 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:51:34,860 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,862 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:51:34,876 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:51:34,878 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:51:34,881 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-06 23:51:34,881 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:51:34,881 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,883 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-06 23:51:34,884 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:51:34,884 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,885 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:51:34,889 [p:28737,w:1,m:0] [Thread-1] Datatype class not found for extension 'flowtext', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools WARNING 2020-05-06 23:51:34,890 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:51:34,890 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,891 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,892 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (32.192 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,892 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,896 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,896 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,899 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,900 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,900 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,903 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,905 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,906 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,907 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,908 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,911 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,911 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,912 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,912 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,913 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,914 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,914 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,914 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,914 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,915 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,915 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,915 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,915 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,915 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,915 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,916 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,916 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,916 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,916 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,917 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,917 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/check_headers/get_headers/1.1, version: 1.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,918 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,918 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,918 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:51:34,918 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (26.234 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:51:34,925 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:51:34,928 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:51:34,930 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:51:34,932 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-06 23:51:34,932 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:51:34,942 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (124.867 ms) | |
| galaxy.queue_worker INFO 2020-05-06 23:51:34,951 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-06 23:51:34,951 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-06 23:51:34,973 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (22.049 ms) | |
| galaxy.config WARNING 2020-05-06 23:52:23,329 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Waiting for toolbox reload timed out after 60 seconds | |
| 10.25.100.188 - - [06/May/2020:23:50:56 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28739|app: 0|req: 74/188] 10.25.100.188 () {42 vars in 751 bytes} [Wed May 6 23:50:56 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 637 bytes in 86509 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:52:24,704 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:52:26,748 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: Flow Text File Tools | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-06 23:52:26,754 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Adding new row for repository 'collapse_pop' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:52:26,759 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:52:26,759 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:52:26,785 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: Flow Text File Tools | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-06 23:52:26,793 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/immport-devteam/collapse_pop' at 0:59f859ea3122 | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:52:52,641 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:52:54,101 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:52:54,112 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:52:54,115 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/collapse_pop/collapse_populations/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-06 23:52:54,115 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-06 23:52:54,131 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-06 23:52:54,844 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-06 23:52:54,844 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-06 23:53:04,983 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-06 23:53:04,988 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-06 23:53:05,568 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:53:05,568 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-06 23:53:05,612 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:53:05,612 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,614 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:53:05,629 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:53:05,631 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:53:05,634 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-06 23:53:05,635 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:53:05,635 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,636 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-06 23:53:05,637 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:53:05,637 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,639 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:53:05,643 [p:28737,w:1,m:0] [Thread-1] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools WARNING 2020-05-06 23:53:05,645 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:53:05,645 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,646 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,647 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (35.785 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,647 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,651 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,651 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,654 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,655 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,655 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,659 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,661 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,661 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,662 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,663 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,666 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,667 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,667 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,668 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,669 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,669 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,669 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,669 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,670 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,670 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,670 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,670 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,670 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,671 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,671 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,671 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,671 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,672 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,672 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,672 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,673 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/collapse_pop/collapse_populations/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,673 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,674 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,674 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:05,674 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (27.015 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:53:05,680 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:53:05,683 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:53:05,685 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:53:05,688 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-06 23:53:05,688 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:53:05,698 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (130.328 ms) | |
| galaxy.queue_worker INFO 2020-05-06 23:53:05,708 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-06 23:53:05,708 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-06 23:53:05,736 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (27.082 ms) | |
| galaxy.config WARNING 2020-05-06 23:53:54,147 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Waiting for toolbox reload timed out after 60 seconds | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:53:54,156 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency pandas version 0.17.1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:53:54,156 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency pandas version 0.17.1 of type conda | |
| 10.25.100.188 - - [06/May/2020:23:52:24 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28743|app: 0|req: 18/189] 10.25.100.188 () {42 vars in 751 bytes} [Wed May 6 23:52:24 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 621 bytes in 90144 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:53:55,639 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:57,294 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Appending to tool panel section: FCS File Tools | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-06 23:53:57,300 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Adding new row for repository 'convert_fcs_to_text' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:53:57,306 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:57,307 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Appending to tool panel section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:53:57,332 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Appending to tool panel section: FCS File Tools | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-06 23:53:57,341 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/immport-devteam/convert_fcs_to_text' at 0:8e10184368a0 | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:54:28,166 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:54:29,352 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:54:29,361 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:29,363 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/convert_fcs_to_text/convert_fcs_to_text/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-06 23:54:29,364 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-06 23:54:29,380 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-06 23:54:29,702 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-06 23:54:29,703 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-06 23:54:39,842 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-06 23:54:39,847 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-06 23:54:40,461 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:54:40,461 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-06 23:54:40,509 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:54:40,509 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,511 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:54:40,525 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:54:40,527 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:54:40,530 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-06 23:54:40,530 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:54:40,530 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,532 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-06 23:54:40,532 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:54:40,533 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,534 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools WARNING 2020-05-06 23:54:40,535 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:54:40,535 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,536 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,536 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (28.187 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,537 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,540 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,541 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,544 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,544 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,545 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,548 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,550 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,551 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,552 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,553 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,556 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,556 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,557 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,557 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,558 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,558 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,559 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,559 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,559 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,559 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,560 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,560 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,560 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,560 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,560 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,561 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,561 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,561 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,561 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,562 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/convert_fcs_to_text/convert_fcs_to_text/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,562 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,563 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,563 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,563 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:54:40,563 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (26.919 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:54:40,570 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:54:40,574 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:54:40,576 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:54:40,578 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-06 23:54:40,578 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:54:40,587 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (126.518 ms) | |
| galaxy.queue_worker INFO 2020-05-06 23:54:40,597 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-06 23:54:40,597 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.config DEBUG 2020-05-06 23:54:40,608 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Finished waiting for toolbox reload (11228.050 ms) | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:54:40,624 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-1c69867621cc696bf9c174e09a7fa90a91900c4fe7fa6f1c45f9f13758c5da7c r=3.3.0 bioconductor-flowcore=1.38.2 | |
| galaxy.tools.search DEBUG 2020-05-06 23:54:40,770 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (173.317 ms) | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... failed | |
| PackagesNotFoundError: The following packages are not available from current channels: | |
| - r=3.3.0 | |
| Current channels: | |
| - https://conda.anaconda.org/iuc/linux-64 | |
| - https://conda.anaconda.org/iuc/noarch | |
| - https://conda.anaconda.org/conda-forge/linux-64 | |
| - https://conda.anaconda.org/conda-forge/noarch | |
| - https://conda.anaconda.org/bioconda/linux-64 | |
| - https://conda.anaconda.org/bioconda/noarch | |
| - https://repo.anaconda.com/pkgs/main/linux-64 | |
| - https://repo.anaconda.com/pkgs/main/noarch | |
| - https://repo.anaconda.com/pkgs/free/linux-64 | |
| - https://repo.anaconda.com/pkgs/free/noarch | |
| - https://repo.anaconda.com/pkgs/r/linux-64 | |
| - https://repo.anaconda.com/pkgs/r/noarch | |
| To search for alternate channels that may provide the conda package you're | |
| looking for, navigate to | |
| https://anaconda.org | |
| and use the search bar at the top of the page. | |
| galaxy.tool_util.deps.resolvers.conda DEBUG 2020-05-06 23:55:10,157 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Removing failed conda install of [CondaTarget[r,version=3.3.0], CondaTarget[bioconductor-flowcore,version=1.38.2]] | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:55:10,161 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __r@3.3.0 r=3.3.0 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... failed | |
| PackagesNotFoundError: The following packages are not available from current channels: | |
| - r=3.3.0 | |
| Current channels: | |
| - https://conda.anaconda.org/iuc/linux-64 | |
| - https://conda.anaconda.org/iuc/noarch | |
| - https://conda.anaconda.org/conda-forge/linux-64 | |
| - https://conda.anaconda.org/conda-forge/noarch | |
| - https://conda.anaconda.org/bioconda/linux-64 | |
| - https://conda.anaconda.org/bioconda/noarch | |
| - https://repo.anaconda.com/pkgs/main/linux-64 | |
| - https://repo.anaconda.com/pkgs/main/noarch | |
| - https://repo.anaconda.com/pkgs/free/linux-64 | |
| - https://repo.anaconda.com/pkgs/free/noarch | |
| - https://repo.anaconda.com/pkgs/r/linux-64 | |
| - https://repo.anaconda.com/pkgs/r/noarch | |
| To search for alternate channels that may provide the conda package you're | |
| looking for, navigate to | |
| https://anaconda.org | |
| and use the search bar at the top of the page. | |
| galaxy.tool_util.deps.resolvers.conda DEBUG 2020-05-06 23:55:18,026 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Removing failed conda install of r, version '3.3.0' | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:55:18,028 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Using dependency bioconductor-flowcore version 1.38.2 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:55:18,029 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Using dependency r version None of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:55:18,031 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Using dependency bioconductor-flowcore version 1.38.2 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:55:18,031 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Using dependency r version None of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:55:18,033 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Cached dependencies directory '*******/galaxy/shared/_cache/0fff183d' already exists, skipping build | |
| 10.25.100.188 - - [06/May/2020:23:53:54 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28737|app: 0|req: 37/190] 10.25.100.188 () {42 vars in 751 bytes} [Wed May 6 23:53:54 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 645 bytes in 83310 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:55:19,399 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:55:21,583 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Appending to tool panel section: Flow Analysis Tools | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-06 23:55:21,589 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Adding new row for repository 'cross_sample' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:55:21,598 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:55:21,598 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Appending to tool panel section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:55:21,624 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Appending to tool panel section: Flow Analysis Tools | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-06 23:55:21,632 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/immport-devteam/cross_sample' at 3:5f670146a9af | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:55:54,145 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Datatype class not found for extension 'flowtext', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:55:54,146 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Datatype class not found for extension 'flowmfi', which is used in the 'format' attribute of parameter 'centroid' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:55:55,088 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Datatype class not found for extension 'flowtext', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:55:55,088 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Datatype class not found for extension 'flowmfi', which is used in the 'format' attribute of parameter 'centroid' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:55:55,099 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Datatype class not found for extension 'flowtext', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:55:55,099 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Datatype class not found for extension 'flowmfi', which is used in the 'format' attribute of parameter 'centroid' | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:55:55,102 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/cross_sample/run_cross_sample/1.1, version: 1.1 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-06 23:55:55,103 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-06 23:55:55,121 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-06 23:55:55,439 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-06 23:55:55,439 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-06 23:56:05,590 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-06 23:56:05,595 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-06 23:56:05,884 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:56:05,885 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-06 23:56:05,929 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:56:05,930 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,931 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:56:05,947 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:56:05,949 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:56:05,952 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-06 23:56:05,952 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:56:05,953 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,954 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-06 23:56:05,955 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:56:05,955 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,956 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:56:05,960 [p:28737,w:1,m:0] [Thread-1] Datatype class not found for extension 'flowtext', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:56:05,961 [p:28737,w:1,m:0] [Thread-1] Datatype class not found for extension 'flowmfi', which is used in the 'format' attribute of parameter 'centroid' | |
| galaxy.tools WARNING 2020-05-06 23:56:05,964 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:56:05,964 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,965 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,965 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (36.293 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,965 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,969 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,969 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,972 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,973 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,973 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,976 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,978 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,979 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,980 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,981 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,983 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,984 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,984 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,985 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,986 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,986 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,986 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,986 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,987 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,987 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,987 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,987 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,987 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,987 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,988 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,988 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,988 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,989 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,989 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,989 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,990 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,991 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/cross_sample/run_cross_sample/1.1, version: 1.1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,991 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,991 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:56:05,991 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (26.109 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:56:05,998 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:56:06,001 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:56:06,004 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:56:06,006 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-06 23:56:06,007 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:56:06,017 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (132.538 ms) | |
| galaxy.queue_worker INFO 2020-05-06 23:56:06,027 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-06 23:56:06,027 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-06 23:56:06,073 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (45.841 ms) | |
| galaxy.config WARNING 2020-05-06 23:56:55,137 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Waiting for toolbox reload timed out after 60 seconds | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:56:55,161 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-b03de498b053ca38a641c0727a0e34942e4bf39eca42e838c2143fdf3c612828 scipy=0.16.0 pandas=0.17.1 flock=1.0 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_conda/envs/mulled-v1-b03de498b053ca38a641c0727a0e34942e4bf39eca42e838c2143fdf3c612828 | |
| added / updated specs: | |
| - flock=1.0 | |
| - pandas=0.17.1 | |
| - scipy=0.16.0 | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| _openmp_mutex-4.5 | 0_gnu 435 KB conda-forge | |
| blas-2.11 | openblas 10 KB conda-forge | |
| flock-1.0 | h470a237_2 34 KB bioconda | |
| libblas-3.8.0 | 11_openblas 10 KB conda-forge | |
| libcblas-3.8.0 | 11_openblas 10 KB conda-forge | |
| libgfortran-3.0.0 | 1 281 KB conda-forge | |
| liblapack-3.8.0 | 11_openblas 10 KB conda-forge | |
| liblapacke-3.8.0 | 11_openblas 10 KB conda-forge | |
| libopenblas-0.3.6 | h5a2b251_2 7.7 MB | |
| openblas-0.2.14 | 4 3.6 MB | |
| scipy-0.16.0 | np19py27_1 28.2 MB | |
| ------------------------------------------------------------ | |
| Total: 40.3 MB | |
| The following NEW packages will be INSTALLED: | |
| _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge | |
| _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-0_gnu | |
| blas conda-forge/linux-64::blas-2.11-openblas | |
| ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0 | |
| certifi conda-forge/linux-64::certifi-2019.11.28-py27_0 | |
| flock bioconda/linux-64::flock-1.0-h470a237_2 | |
| ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 | |
| libblas conda-forge/linux-64::libblas-3.8.0-11_openblas | |
| libcblas conda-forge/linux-64::libcblas-3.8.0-11_openblas | |
| libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 | |
| libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2 | |
| libgfortran conda-forge/linux-64::libgfortran-3.0.0-1 | |
| libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5 | |
| libgomp conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2 | |
| liblapack conda-forge/linux-64::liblapack-3.8.0-11_openblas | |
| liblapacke conda-forge/linux-64::liblapacke-3.8.0-11_openblas | |
| libopenblas pkgs/main/linux-64::libopenblas-0.3.6-h5a2b251_2 | |
| libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2 | |
| ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002 | |
| numpy conda-forge/linux-64::numpy-1.9.3-py27he5ce36f_1209 | |
| openblas pkgs/free/linux-64::openblas-0.2.14-4 | |
| openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_0 | |
| pandas pkgs/free/linux-64::pandas-0.17.1-np19py27_0 | |
| pip conda-forge/noarch::pip-20.1-pyh9f0ad1d_0 | |
| python conda-forge/linux-64::python-2.7.15-h5a48372_1011_cpython | |
| python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0 | |
| pytz conda-forge/noarch::pytz-2020.1-pyh9f0ad1d_0 | |
| readline conda-forge/linux-64::readline-8.0-hf8c457e_0 | |
| scipy pkgs/free/linux-64::scipy-0.16.0-np19py27_1 | |
| setuptools conda-forge/linux-64::setuptools-44.0.0-py27_0 | |
| six conda-forge/noarch::six-1.14.0-py_1 | |
| sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0 | |
| tk conda-forge/linux-64::tk-8.6.10-hed695b0_0 | |
| wheel conda-forge/noarch::wheel-0.34.2-py_1 | |
| zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1006 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... 10.114.180.83 - - [06/May/2020:23:57:52 +0100] "GET / HTTP/1.1" 200 - "http://localhost:60089/user?__identifer=9roprnldcwn" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 75/191] 10.114.180.83 () {56 vars in 1483 bytes} [Wed May 6 23:57:52 2020] GET / => generated 129608 bytes in 65 msecs (HTTP/1.1 200) 7 headers in 200 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:57:53 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 19/192] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:57:53 2020] GET /api/webhooks => generated 2 bytes in 115 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:57:53 +0100] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 76/193] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:57:53 2020] GET /api/configuration => generated 2300 bytes in 20 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:57:53 +0100] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 38/194] 10.114.180.83 () {50 vars in 1300 bytes} [Wed May 6 23:57:53 2020] GET /api/users/current => generated 271 bytes in 52 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:57:54 +0100] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 20/195] 10.114.180.83 () {52 vars in 1342 bytes} [Wed May 6 23:57:54 2020] GET /api/webhooks => generated 2 bytes in 14 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:57:54 +0100] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 39/196] 10.114.180.83 () {54 vars in 1395 bytes} [Wed May 6 23:57:54 2020] GET /api/datatypes?extension_only=False => generated 53304 bytes in 14 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:57:54 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 77/197] 10.114.180.83 () {54 vars in 1350 bytes} [Wed May 6 23:57:54 2020] GET /api/genomes => generated 55436 bytes in 18 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:57:54 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 21/198] 10.114.180.83 () {52 vars in 1374 bytes} [Wed May 6 23:57:54 2020] GET /history/current_history_json => generated 562 bytes in 61 msecs (HTTP/1.1 200) 5 headers in 171 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:57:54 +0100] "GET /welcome HTTP/1.1" 302 267 "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 40/199] 10.114.180.83 () {52 vars in 1411 bytes} [Wed May 6 23:57:54 2020] GET /welcome => generated 267 bytes in 15 msecs (HTTP/1.1 302) 4 headers in 166 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:57:54 +0100] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28739|app: 0|req: 78/200] 10.114.180.83 () {52 vars in 1370 bytes} [Wed May 6 23:57:54 2020] GET /api/users/f2db41e1fa331b3e => generated 271 bytes in 44 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:57:54 +0100] "GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28743|app: 0|req: 22/201] 10.114.180.83 () {52 vars in 1575 bytes} [Wed May 6 23:57:54 2020] GET /api/histories/f597429621d6eb2b/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True => generated 2 bytes in 48 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.114.180.83 - - [06/May/2020:23:57:54 +0100] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:60089/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36" | |
| [pid: 28737|app: 0|req: 41/202] 10.114.180.83 () {52 vars in 1495 bytes} [Wed May 6 23:57:54 2020] GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 112 bytes in 78 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| done | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:58:08,354 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency scipy version 0.16.0 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:58:08,355 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency pandas version 0.17.1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:58:08,355 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency flock version 1.0 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:58:08,356 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency scipy version 0.16.0 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:58:08,356 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency pandas version 0.17.1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-06 23:58:08,356 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency flock version 1.0 of type conda | |
| 10.25.100.188 - - [06/May/2020:23:55:18 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28741|app: 0|req: 62/203] 10.25.100.188 () {42 vars in 751 bytes} [Wed May 6 23:55:18 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 654 bytes in 169723 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:58:09,976 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:11,803 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Flow Visualization Tools | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-06 23:58:11,809 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Adding new row for repository 'cs_overview' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-06 23:58:11,815 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:11,815 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:11,842 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Flow Visualization Tools | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-06 23:58:11,853 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/immport-devteam/cs_overview' at 0:8c17aa8032c2 | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:22,705 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowstat1', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:22,706 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowstat2', which is used in the 'format' attribute of parameter 'inputmfi' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:22,706 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowmfi', which is used in the 'format' attribute of parameter 'mfi' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:22,707 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'cs_outputs' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:23,654 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowstat1', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:23,654 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowstat2', which is used in the 'format' attribute of parameter 'inputmfi' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:23,655 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowmfi', which is used in the 'format' attribute of parameter 'mfi' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:23,655 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'cs_outputs' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:23,664 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowstat1', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:23,664 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowstat2', which is used in the 'format' attribute of parameter 'inputmfi' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:23,664 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowmfi', which is used in the 'format' attribute of parameter 'mfi' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:23,664 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'cs_outputs' | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:23,666 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/cs_overview/cross_sample_overview/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-06 23:58:23,667 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-06 23:58:23,684 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-06 23:58:24,684 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-06 23:58:24,685 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-06 23:58:34,817 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-06 23:58:34,821 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-06 23:58:34,948 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:58:34,949 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-06 23:58:34,994 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:58:34,994 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:34,996 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:58:35,010 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:58:35,012 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-06 23:58:35,015 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-06 23:58:35,015 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:58:35,016 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,017 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-06 23:58:35,018 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:58:35,018 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,019 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:35,023 [p:28737,w:1,m:0] [Thread-1] Datatype class not found for extension 'flowstat1', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:35,024 [p:28737,w:1,m:0] [Thread-1] Datatype class not found for extension 'flowstat2', which is used in the 'format' attribute of parameter 'inputmfi' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:35,024 [p:28737,w:1,m:0] [Thread-1] Datatype class not found for extension 'flowmfi', which is used in the 'format' attribute of parameter 'mfi' | |
| galaxy.tools.parameters.basic WARNING 2020-05-06 23:58:35,024 [p:28737,w:1,m:0] [Thread-1] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'cs_outputs' | |
| galaxy.tools WARNING 2020-05-06 23:58:35,026 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-06 23:58:35,026 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,027 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,027 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (33.562 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,027 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,031 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,031 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,034 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,035 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,035 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,039 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,041 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,041 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,042 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,043 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,046 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,047 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,047 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,048 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,049 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,049 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,049 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,049 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,050 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,050 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,050 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,050 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,050 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,050 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,050 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,051 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,051 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,051 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,051 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,052 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,053 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,054 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,054 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/cs_overview/cross_sample_overview/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,054 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-06 23:58:35,055 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (27.588 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-06 23:58:35,061 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:58:35,063 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:58:35,067 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-06 23:58:35,069 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-06 23:58:35,069 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-06 23:58:35,077 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (128.688 ms) | |
| galaxy.queue_worker INFO 2020-05-06 23:58:35,086 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-06 23:58:35,086 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-06 23:58:35,140 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (53.604 ms) | |
| galaxy.config WARNING 2020-05-06 23:59:23,700 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Waiting for toolbox reload timed out after 60 seconds | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-06 23:59:23,712 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __jinja2@2.8 jinja2=2.8 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_conda/envs/__jinja2@2.8 | |
| added / updated specs: | |
| - jinja2=2.8 | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| certifi-2020.4.5.1 | py36h9f0ad1d_0 151 KB conda-forge | |
| jinja2-2.8 | py36_1 262 KB conda-forge | |
| markupsafe-1.1.1 | py36h8c4c3a4_1 26 KB conda-forge | |
| python-3.6.10 |h8356626_1011_cpython 34.1 MB conda-forge | |
| python_abi-3.6 | 1_cp36m 4 KB conda-forge | |
| setuptools-46.1.3 | py36h9f0ad1d_0 653 KB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 35.1 MB | |
| The following NEW packages will be INSTALLED: | |
| _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge | |
| _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-0_gnu | |
| ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0 | |
| certifi conda-forge/linux-64::certifi-2020.4.5.1-py36h9f0ad1d_0 | |
| jinja2 conda-forge/linux-64::jinja2-2.8-py36_1 | |
| ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 | |
| libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 | |
| libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2 | |
| libgomp conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2 | |
| libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2 | |
| markupsafe conda-forge/linux-64::markupsafe-1.1.1-py36h8c4c3a4_1 | |
| ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002 | |
| openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_0 | |
| pip conda-forge/noarch::pip-20.1-pyh9f0ad1d_0 | |
| python conda-forge/linux-64::python-3.6.10-h8356626_1011_cpython | |
| python_abi conda-forge/linux-64::python_abi-3.6-1_cp36m | |
| readline conda-forge/linux-64::readline-8.0-hf8c457e_0 | |
| setuptools conda-forge/linux-64::setuptools-46.1.3-py36h9f0ad1d_0 | |
| sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0 | |
| tk conda-forge/linux-64::tk-8.6.10-hed695b0_0 | |
| wheel conda-forge/noarch::wheel-0.34.2-py_1 | |
| xz conda-forge/linux-64::xz-5.2.5-h516909a_0 | |
| zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1006 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:00:15,892 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Using dependency jinja2 version 2.8 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:00:15,893 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Using dependency jinja2 version 2.8 of type conda | |
| 10.25.100.188 - - [06/May/2020:23:58:09 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28739|app: 0|req: 79/204] 10.25.100.188 () {42 vars in 751 bytes} [Wed May 6 23:58:09 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 633 bytes in 126867 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:00:18,673 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:21,044 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: FCS File Tools | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-07 00:00:21,050 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Adding new row for repository 'extract_fcs_keywords' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:00:21,057 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:21,057 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:21,089 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: FCS File Tools | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-07 00:00:21,098 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/immport-devteam/extract_fcs_keywords' at 0:dc00746654dc | |
| galaxy.tools.parameters.basic WARNING 2020-05-07 00:00:38,094 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-07 00:00:39,098 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-07 00:00:39,107 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:39,110 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/extract_fcs_keywords/extract_fcs_keywords/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-07 00:00:39,110 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-07 00:00:39,129 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-07 00:00:39,862 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-07 00:00:39,862 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-07 00:00:50,001 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-07 00:00:50,007 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-07 00:00:50,768 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:00:50,769 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-07 00:00:50,882 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:00:50,882 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,884 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:00:50,899 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:00:50,901 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:00:50,904 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-07 00:00:50,905 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:00:50,905 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,906 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-07 00:00:50,907 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:00:50,907 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,909 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.parameters.basic WARNING 2020-05-07 00:00:50,913 [p:28737,w:1,m:0] [Thread-1] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools WARNING 2020-05-07 00:00:50,915 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:00:50,915 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,916 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,916 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (37.359 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,916 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,920 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,921 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,924 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,925 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,925 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,928 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,930 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,931 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,932 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,933 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,936 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,937 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,937 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,938 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,939 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,939 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,939 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,939 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,940 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,940 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,940 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,940 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,940 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,941 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,941 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,941 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,941 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,942 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,942 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,943 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/extract_fcs_keywords/extract_fcs_keywords/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,943 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,944 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,945 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,945 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:00:50,945 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (29.047 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-07 00:00:50,952 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:00:50,955 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:00:50,958 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:00:50,961 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-07 00:00:50,961 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:00:50,970 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (201.553 ms) | |
| galaxy.queue_worker INFO 2020-05-07 00:00:50,981 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-07 00:00:50,981 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-07 00:00:51,007 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (25.584 ms) | |
| galaxy.config WARNING 2020-05-07 00:01:39,144 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Waiting for toolbox reload timed out after 60 seconds | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:01:39,155 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-1c69867621cc696bf9c174e09a7fa90a91900c4fe7fa6f1c45f9f13758c5da7c r=3.3.0 bioconductor-flowcore=1.38.2 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... failed | |
| PackagesNotFoundError: The following packages are not available from current channels: | |
| - r=3.3.0 | |
| Current channels: | |
| - https://conda.anaconda.org/iuc/linux-64 | |
| - https://conda.anaconda.org/iuc/noarch | |
| - https://conda.anaconda.org/conda-forge/linux-64 | |
| - https://conda.anaconda.org/conda-forge/noarch | |
| - https://conda.anaconda.org/bioconda/linux-64 | |
| - https://conda.anaconda.org/bioconda/noarch | |
| - https://repo.anaconda.com/pkgs/main/linux-64 | |
| - https://repo.anaconda.com/pkgs/main/noarch | |
| - https://repo.anaconda.com/pkgs/free/linux-64 | |
| - https://repo.anaconda.com/pkgs/free/noarch | |
| - https://repo.anaconda.com/pkgs/r/linux-64 | |
| - https://repo.anaconda.com/pkgs/r/noarch | |
| To search for alternate channels that may provide the conda package you're | |
| looking for, navigate to | |
| https://anaconda.org | |
| and use the search bar at the top of the page. | |
| galaxy.tool_util.deps.resolvers.conda DEBUG 2020-05-07 00:01:47,493 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Removing failed conda install of [CondaTarget[r,version=3.3.0], CondaTarget[bioconductor-flowcore,version=1.38.2]] | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:01:47,495 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __r@3.3.0 r=3.3.0 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... failed | |
| PackagesNotFoundError: The following packages are not available from current channels: | |
| - r=3.3.0 | |
| Current channels: | |
| - https://conda.anaconda.org/iuc/linux-64 | |
| - https://conda.anaconda.org/iuc/noarch | |
| - https://conda.anaconda.org/conda-forge/linux-64 | |
| - https://conda.anaconda.org/conda-forge/noarch | |
| - https://conda.anaconda.org/bioconda/linux-64 | |
| - https://conda.anaconda.org/bioconda/noarch | |
| - https://repo.anaconda.com/pkgs/main/linux-64 | |
| - https://repo.anaconda.com/pkgs/main/noarch | |
| - https://repo.anaconda.com/pkgs/free/linux-64 | |
| - https://repo.anaconda.com/pkgs/free/noarch | |
| - https://repo.anaconda.com/pkgs/r/linux-64 | |
| - https://repo.anaconda.com/pkgs/r/noarch | |
| To search for alternate channels that may provide the conda package you're | |
| looking for, navigate to | |
| https://anaconda.org | |
| and use the search bar at the top of the page. | |
| galaxy.tool_util.deps.resolvers.conda DEBUG 2020-05-07 00:01:54,767 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Removing failed conda install of r, version '3.3.0' | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:01:54,769 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency bioconductor-flowcore version 1.38.2 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:01:54,770 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency r version None of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:01:54,772 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency bioconductor-flowcore version 1.38.2 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:01:54,772 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency r version None of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:01:54,774 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Cached dependencies directory '*******/galaxy/shared/_cache/0fff183d' already exists, skipping build | |
| 10.25.100.188 - - [07/May/2020:00:00:16 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28743|app: 0|req: 23/205] 10.25.100.188 () {42 vars in 751 bytes} [Thu May 7 00:00:16 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 629 bytes in 98138 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:01:56,062 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:01:57,795 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Appending to tool panel section: Flow Text File Tools | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-07 00:01:57,804 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Adding new row for repository 'extract_pop' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:01:57,811 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:01:57,811 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Appending to tool panel section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:01:57,840 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Appending to tool panel section: Flow Text File Tools | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-07 00:01:57,849 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/immport-devteam/extract_pop' at 0:21b2dc3934ed | |
| galaxy.tools.parameters.basic WARNING 2020-05-07 00:02:10,697 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-07 00:02:11,615 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.parameters.basic WARNING 2020-05-07 00:02:11,623 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Datatype class not found for extension 'flowclr', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:11,626 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/extract_pop/extract_pop/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-07 00:02:11,626 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-07 00:02:11,645 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-07 00:02:11,662 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-07 00:02:11,663 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-07 00:02:21,797 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-07 00:02:21,803 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-07 00:02:22,544 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:02:22,544 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-07 00:02:22,589 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:02:22,589 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,591 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:02:22,604 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:02:22,606 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:02:22,609 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-07 00:02:22,609 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:02:22,609 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,611 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-07 00:02:22,612 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:02:22,612 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,613 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools WARNING 2020-05-07 00:02:22,615 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:02:22,615 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,616 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,616 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (28.247 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,617 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,620 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,621 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,624 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,624 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,624 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,628 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,629 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,630 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,631 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,632 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,634 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,635 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,636 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,636 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,637 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,637 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,637 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,637 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,638 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,638 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,638 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,638 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,638 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,638 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,639 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,639 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,639 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,639 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,639 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,640 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,641 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/extract_pop/extract_pop/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,642 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,642 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,643 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:22,643 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (26.362 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-07 00:02:22,650 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:02:22,652 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:02:22,654 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:02:22,657 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-07 00:02:22,657 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:02:22,667 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (123.471 ms) | |
| galaxy.config DEBUG 2020-05-07 00:02:22,676 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Finished waiting for toolbox reload (11030.902 ms) | |
| galaxy.queue_worker INFO 2020-05-07 00:02:22,679 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-07 00:02:22,680 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:02:22,682 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Using dependency pandas version 0.17.1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:02:22,683 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Using dependency pandas version 0.17.1 of type conda | |
| 10.25.100.188 - - [07/May/2020:00:01:55 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28737|app: 0|req: 42/206] 10.25.100.188 () {42 vars in 751 bytes} [Thu May 7 00:01:55 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 656 bytes in 27340 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tools.search DEBUG 2020-05-07 00:02:22,713 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (33.705 ms) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:02:24,557 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:26,115 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Appending to tool panel section: FCS File Tools | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-07 00:02:26,121 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Adding new row for repository 'fcs_gate_trans' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:02:26,127 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:26,128 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Appending to tool panel section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:26,155 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Appending to tool panel section: FCS File Tools | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-07 00:02:26,164 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/immport-devteam/fcs_gate_trans' at 0:78b8ab344edd | |
| galaxy.tools.parameters.basic WARNING 2020-05-07 00:02:33,576 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools WARNING 2020-05-07 00:02:33,577 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Tool fcs_gate_trans_convert: a when tag has not been defined for 'transform (trans_method) --> None', assuming empty inputs. | |
| galaxy.tools WARNING 2020-05-07 00:02:33,578 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Tool fcs_gate_trans_convert: a when tag has not been defined for 'transform (trans_method) --> logicle', assuming empty inputs. | |
| galaxy.tools.parameters.basic WARNING 2020-05-07 00:02:35,040 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools WARNING 2020-05-07 00:02:35,041 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Tool toolshed.g2.bx.psu.edu/repos/immport-devteam/fcs_gate_trans/fcs_gate_trans_convert/1.0: a when tag has not been defined for 'transform (trans_method) --> None', assuming empty inputs. | |
| galaxy.tools WARNING 2020-05-07 00:02:35,041 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Tool toolshed.g2.bx.psu.edu/repos/immport-devteam/fcs_gate_trans/fcs_gate_trans_convert/1.0: a when tag has not been defined for 'transform (trans_method) --> logicle', assuming empty inputs. | |
| galaxy.tools.parameters.basic WARNING 2020-05-07 00:02:35,052 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools WARNING 2020-05-07 00:02:35,053 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Tool toolshed.g2.bx.psu.edu/repos/immport-devteam/fcs_gate_trans/fcs_gate_trans_convert/1.0: a when tag has not been defined for 'transform (trans_method) --> None', assuming empty inputs. | |
| galaxy.tools WARNING 2020-05-07 00:02:35,053 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Tool toolshed.g2.bx.psu.edu/repos/immport-devteam/fcs_gate_trans/fcs_gate_trans_convert/1.0: a when tag has not been defined for 'transform (trans_method) --> logicle', assuming empty inputs. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:35,059 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/fcs_gate_trans/fcs_gate_trans_convert/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-07 00:02:35,059 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-07 00:02:35,077 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-07 00:02:35,944 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-07 00:02:35,945 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-07 00:02:46,079 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-07 00:02:46,081 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-07 00:02:46,385 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:02:46,385 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-07 00:02:46,423 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:02:46,423 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,425 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:02:46,438 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:02:46,440 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:02:46,442 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-07 00:02:46,442 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:02:46,442 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,443 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-07 00:02:46,444 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:02:46,444 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,446 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.parameters.basic WARNING 2020-05-07 00:02:46,451 [p:28737,w:1,m:0] [Thread-1] Datatype class not found for extension 'fcs', which is used in the 'format' attribute of parameter 'input' | |
| galaxy.tools WARNING 2020-05-07 00:02:46,451 [p:28737,w:1,m:0] [Thread-1] Tool toolshed.g2.bx.psu.edu/repos/immport-devteam/fcs_gate_trans/fcs_gate_trans_convert/1.0: a when tag has not been defined for 'transform (trans_method) --> None', assuming empty inputs. | |
| galaxy.tools WARNING 2020-05-07 00:02:46,451 [p:28737,w:1,m:0] [Thread-1] Tool toolshed.g2.bx.psu.edu/repos/immport-devteam/fcs_gate_trans/fcs_gate_trans_convert/1.0: a when tag has not been defined for 'transform (trans_method) --> logicle', assuming empty inputs. | |
| galaxy.tools WARNING 2020-05-07 00:02:46,453 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:02:46,453 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,454 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,454 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (31.773 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,455 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,459 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,459 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,462 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,462 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,463 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,466 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,468 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,469 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,470 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,470 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,473 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,474 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,474 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,475 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,476 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,476 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,476 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,476 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,477 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,477 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,477 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,477 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,477 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,477 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,477 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,478 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,478 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,478 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,478 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,480 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/immport-devteam/fcs_gate_trans/fcs_gate_trans_convert/1.0, version: 1.0 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,480 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,481 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,482 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,482 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:02:46,482 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (27.799 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-07 00:02:46,488 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:02:46,490 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:02:46,492 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:02:46,494 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-07 00:02:46,494 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:02:46,503 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (117.927 ms) | |
| galaxy.queue_worker INFO 2020-05-07 00:02:46,512 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-07 00:02:46,512 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-07 00:02:46,801 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (288.505 ms) | |
| galaxy.config WARNING 2020-05-07 00:03:35,093 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Waiting for toolbox reload timed out after 60 seconds | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:03:35,110 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-3a5ddaa6b78fe2caa835bb27413e7ba7c56e564f1c0ce259285a14adca2432ac r=3.3.0 bioconductor-flowcore=1.38.2 bioconductor-flowdensity=1.6.0 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... failed | |
| PackagesNotFoundError: The following packages are not available from current channels: | |
| - r=3.3.0 | |
| Current channels: | |
| - https://conda.anaconda.org/iuc/linux-64 | |
| - https://conda.anaconda.org/iuc/noarch | |
| - https://conda.anaconda.org/conda-forge/linux-64 | |
| - https://conda.anaconda.org/conda-forge/noarch | |
| - https://conda.anaconda.org/bioconda/linux-64 | |
| - https://conda.anaconda.org/bioconda/noarch | |
| - https://repo.anaconda.com/pkgs/main/linux-64 | |
| - https://repo.anaconda.com/pkgs/main/noarch | |
| - https://repo.anaconda.com/pkgs/free/linux-64 | |
| - https://repo.anaconda.com/pkgs/free/noarch | |
| - https://repo.anaconda.com/pkgs/r/linux-64 | |
| - https://repo.anaconda.com/pkgs/r/noarch | |
| To search for alternate channels that may provide the conda package you're | |
| looking for, navigate to | |
| https://anaconda.org | |
| and use the search bar at the top of the page. | |
| galaxy.tool_util.deps.resolvers.conda DEBUG 2020-05-07 00:03:45,292 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Removing failed conda install of [CondaTarget[r,version=3.3.0], CondaTarget[bioconductor-flowcore,version=1.38.2], CondaTarget[bioconductor-flowdensity,version=1.6.0]] | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:03:45,294 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __r@3.3.0 r=3.3.0 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... failed | |
| PackagesNotFoundError: The following packages are not available from current channels: | |
| - r=3.3.0 | |
| Current channels: | |
| - https://conda.anaconda.org/iuc/linux-64 | |
| - https://conda.anaconda.org/iuc/noarch | |
| - https://conda.anaconda.org/conda-forge/linux-64 | |
| - https://conda.anaconda.org/conda-forge/noarch | |
| - https://conda.anaconda.org/bioconda/linux-64 | |
| - https://conda.anaconda.org/bioconda/noarch | |
| - https://repo.anaconda.com/pkgs/main/linux-64 | |
| - https://repo.anaconda.com/pkgs/main/noarch | |
| - https://repo.anaconda.com/pkgs/free/linux-64 | |
| - https://repo.anaconda.com/pkgs/free/noarch | |
| - https://repo.anaconda.com/pkgs/r/linux-64 | |
| - https://repo.anaconda.com/pkgs/r/noarch | |
| To search for alternate channels that may provide the conda package you're | |
| looking for, navigate to | |
| https://anaconda.org | |
| and use the search bar at the top of the page. | |
| galaxy.tool_util.deps.resolvers.conda DEBUG 2020-05-07 00:03:52,859 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Removing failed conda install of r, version '3.3.0' | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:03:52,861 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency bioconductor-flowcore version 1.38.2 of type conda | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:03:52,862 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __bioconductor-flowdensity@1.6.0 bioconductor-flowdensity=1.6.0 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_conda/envs/__bioconductor-flowdensity@1.6.0 | |
| added / updated specs: | |
| - bioconductor-flowdensity=1.6.0 | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| bioconductor-biobase-2.46.0| r36h516909a_0 2.3 MB bioconda | |
| bioconductor-biocgenerics-0.32.0| r36_0 691 KB bioconda | |
| bioconductor-cytolib-1.8.0 | r36_0 321 KB bioconda | |
| bioconductor-flowcore-1.52.0| r36he1b5a44_0 7.6 MB bioconda | |
| bioconductor-flowdensity-1.6.0| 0 4.4 MB bioconda | |
| r-abind-1.4_5 | r36h6115d3f_1003 76 KB conda-forge | |
| r-assertthat-0.2.1 | r36h6115d3f_2 70 KB conda-forge | |
| r-backports-1.1.6 | r36hcdcec82_2 77 KB conda-forge | |
| r-car-3.0_7 | r36h6115d3f_1 1.5 MB conda-forge | |
| r-cardata-3.0_3 | r36h6115d3f_1 1.8 MB conda-forge | |
| r-catools-1.18.0 | r36h0357c0b_1 223 KB conda-forge | |
| r-cellranger-1.1.0 | r36h6115d3f_1003 108 KB conda-forge | |
| r-cli-2.0.2 | r36h6115d3f_1 395 KB conda-forge | |
| r-clipr-0.7.0 | r36h6115d3f_1 64 KB conda-forge | |
| r-crayon-1.3.4 | r36h6115d3f_1003 747 KB conda-forge | |
| r-curl-4.3 | r36hcdcec82_1 702 KB conda-forge | |
| r-data.table-1.12.8 | r36hcdcec82_1 1.8 MB conda-forge | |
| r-digest-0.6.25 | r36h0357c0b_2 199 KB conda-forge | |
| r-dotcall64-1.0_0 | r36h9bbef5b_1005 49 KB conda-forge | |
| r-ellipsis-0.3.0 | r36hcdcec82_1 47 KB conda-forge | |
| r-fansi-0.4.1 | r36hcdcec82_1 196 KB conda-forge | |
| r-fields-10.3 | r36h9bbef5b_1 3.8 MB conda-forge | |
| r-forcats-0.5.0 | r36h6115d3f_1 376 KB conda-forge | |
| r-gdata-2.18.0 | r36h6115d3f_1003 1.1 MB conda-forge | |
| r-geomap-2.4_4 | r36hcdcec82_1002 3.2 MB conda-forge | |
| r-glue-1.4.0 | r36hcdcec82_1 144 KB conda-forge | |
| r-gplots-3.0.3 | r36h6115d3f_1 595 KB conda-forge | |
| r-gtools-3.8.2 | r36hcdcec82_1 333 KB conda-forge | |
| r-haven-2.2.0 | r36hde08347_1 352 KB conda-forge | |
| r-hms-0.5.3 | r36h6115d3f_1 122 KB conda-forge | |
| r-lifecycle-0.2.0 | r36h6115d3f_1 112 KB conda-forge | |
| r-lme4-1.1_23 | r36h0357c0b_1 4.9 MB conda-forge | |
| r-magrittr-1.5 | r36h6115d3f_1003 167 KB conda-forge | |
| r-maps-3.3.0 | r36hcdcec82_1004 3.4 MB conda-forge | |
| r-maptools-0.9_9 | r36hcdcec82_1 2.1 MB conda-forge | |
| r-matrixmodels-0.4_1 | r36h6115d3f_1003 354 KB conda-forge | |
| r-mba-0.0_9 | r36h0357c0b_1004 198 KB conda-forge | |
| r-minqa-1.2.4 | r36h6786f55_1005 141 KB conda-forge | |
| r-nloptr-1.2.2.1 | r36h0357c0b_1 505 KB conda-forge | |
| r-openxlsx-4.1.5 | r36h0357c0b_0 1.9 MB conda-forge | |
| r-pbkrtest-0.4_7 | r36h6115d3f_1003 281 KB conda-forge | |
| r-pillar-1.4.4 | r36h6115d3f_0 197 KB conda-forge | |
| r-pkgconfig-2.0.3 | r36h6115d3f_1 24 KB conda-forge | |
| r-prettyunits-1.1.1 | r36h6115d3f_1 41 KB conda-forge | |
| r-progress-1.2.2 | r36h6115d3f_2 90 KB conda-forge | |
| r-purrr-0.3.4 | r36hcdcec82_1 411 KB conda-forge | |
| r-quantreg-5.55 | r36h9bbef5b_1 1.5 MB conda-forge | |
| r-r6-2.4.1 | r36h6115d3f_1 63 KB conda-forge | |
| r-rcppeigen-0.3.3.7.0 | r36h0357c0b_1 1.5 MB conda-forge | |
| r-readr-1.3.1 | r36h0357c0b_1003 832 KB conda-forge | |
| r-readxl-1.3.1 | r36hde08347_4 856 KB conda-forge | |
| r-rematch-1.0.1 | r36h6115d3f_1003 19 KB conda-forge | |
| r-rfoc-3.4_6 | r36h6115d3f_2 653 KB conda-forge | |
| r-rio-0.5.16 | r36h6115d3f_1002 493 KB conda-forge | |
| r-rlang-0.4.6 | r36hcdcec82_0 1.0 MB conda-forge | |
| r-rpmg-2.2_3 | r36h6115d3f_1 212 KB conda-forge | |
| r-rseis-3.9_0 | r36hcdcec82_1 3.5 MB conda-forge | |
| r-rwave-2.4_8 | r36hcdcec82_1002 1.0 MB conda-forge | |
| r-sp-1.4_1 | r36hcdcec82_1 1.9 MB conda-forge | |
| r-spam-2.5_1 | r36hbf399a0_2 2.6 MB conda-forge | |
| r-sparsem-1.78 | r36h9bbef5b_1 1.0 MB conda-forge | |
| r-splancs-2.01_40 | r36h9bbef5b_1005 337 KB conda-forge | |
| r-statmod-1.4.34 | r36h6e990d7_1 280 KB conda-forge | |
| r-stringi-1.4.6 | r36h0e574ca_2 783 KB conda-forge | |
| r-tibble-3.0.1 | r36hcdcec82_1 382 KB conda-forge | |
| r-tidyselect-1.0.0 | r36h6115d3f_1 221 KB conda-forge | |
| r-utf8-1.1.4 | r36hcdcec82_1003 161 KB conda-forge | |
| r-vctrs-0.2.4 | r36hcdcec82_1 894 KB conda-forge | |
| r-zeallot-0.1.0 | r36h6115d3f_1002 62 KB conda-forge | |
| r-zip-2.0.4 | r36hcdcec82_1 146 KB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 68.3 MB | |
| The following NEW packages will be INSTALLED: | |
| _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge | |
| _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_llvm | |
| _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 | |
| binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.34-h53a641e_0 | |
| binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.34-hc952b39_18 | |
| bioconductor-biob~ bioconda/linux-64::bioconductor-biobase-2.46.0-r36h516909a_0 | |
| bioconductor-bioc~ bioconda/noarch::bioconductor-biocgenerics-0.32.0-r36_0 | |
| bioconductor-cyto~ bioconda/noarch::bioconductor-cytolib-1.8.0-r36_0 | |
| bioconductor-flow~ bioconda/linux-64::bioconductor-flowcore-1.52.0-r36he1b5a44_0 | |
| bioconductor-flow~ bioconda/linux-64::bioconductor-flowdensity-1.6.0-0 | |
| bwidget conda-forge/linux-64::bwidget-1.9.14-0 | |
| bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_2 | |
| ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0 | |
| cairo conda-forge/linux-64::cairo-1.16.0-hcf35c78_1003 | |
| certifi conda-forge/linux-64::certifi-2020.4.5.1-py38h32f6830_0 | |
| curl conda-forge/linux-64::curl-7.69.1-h33f0ec9_0 | |
| fontconfig conda-forge/linux-64::fontconfig-2.13.1-h86ecdb6_1001 | |
| freetype conda-forge/linux-64::freetype-2.10.1-he06d7ca_0 | |
| fribidi conda-forge/linux-64::fribidi-1.0.9-h516909a_0 | |
| gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-7.3.0-hd420e75_5 | |
| gcc_linux-64 conda-forge/linux-64::gcc_linux-64-7.3.0-h553295d_18 | |
| gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002 | |
| gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_5 | |
| gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-7.3.0-h553295d_18 | |
| glib conda-forge/linux-64::glib-2.58.3-py38h73cb85d_1004 | |
| graphite2 conda-forge/linux-64::graphite2-1.3.13-he1b5a44_1001 | |
| gsl conda-forge/linux-64::gsl-2.6-h294904e_0 | |
| gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_5 | |
| gxx_linux-64 conda-forge/linux-64::gxx_linux-64-7.3.0-h553295d_18 | |
| harfbuzz conda-forge/linux-64::harfbuzz-2.4.0-h9f30f68_3 | |
| icu conda-forge/linux-64::icu-64.2-he1b5a44_1 | |
| jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001 | |
| krb5 conda-forge/linux-64::krb5-1.17.1-h2fd8d38_0 | |
| ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 | |
| libblas conda-forge/linux-64::libblas-3.8.0-16_openblas | |
| libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas | |
| libcurl conda-forge/linux-64::libcurl-7.69.1-hf7181ac_0 | |
| libedit conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001 | |
| libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 | |
| libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2 | |
| libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5 | |
| libgomp conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2 | |
| libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1006 | |
| liblapack conda-forge/linux-64::liblapack-3.8.0-16_openblas | |
| libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0 | |
| libpng conda-forge/linux-64::libpng-1.6.37-hed695b0_1 | |
| libssh2 conda-forge/linux-64::libssh2-1.8.2-h22169c7_2 | |
| libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2 | |
| libtiff conda-forge/linux-64::libtiff-4.1.0-hc7e4089_6 | |
| libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000 | |
| libwebp-base conda-forge/linux-64::libwebp-base-1.1.0-h516909a_3 | |
| libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002 | |
| libxml2 conda-forge/linux-64::libxml2-2.9.10-hee79883_0 | |
| llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0 | |
| lz4-c conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_1 | |
| make conda-forge/linux-64::make-4.3-h516909a_0 | |
| ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002 | |
| openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_0 | |
| pango conda-forge/linux-64::pango-1.42.4-h7062337_4 | |
| pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0 | |
| pip conda-forge/noarch::pip-20.1-pyh9f0ad1d_0 | |
| pixman conda-forge/linux-64::pixman-0.38.0-h516909a_1003 | |
| pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001 | |
| python conda-forge/linux-64::python-3.8.2-he5300dc_7_cpython | |
| python_abi conda-forge/linux-64::python_abi-3.8-1_cp38 | |
| r conda-forge/noarch::r-3.6-r36_1003 | |
| r-abind conda-forge/noarch::r-abind-1.4_5-r36h6115d3f_1003 | |
| r-assertthat conda-forge/noarch::r-assertthat-0.2.1-r36h6115d3f_2 | |
| r-backports conda-forge/linux-64::r-backports-1.1.6-r36hcdcec82_2 | |
| r-base conda-forge/linux-64::r-base-3.6.3-h316533a_2 | |
| r-bh conda-forge/noarch::r-bh-1.72.0_3-r36h6115d3f_1 | |
| r-bitops conda-forge/linux-64::r-bitops-1.0_6-r36hcdcec82_1004 | |
| r-boot conda-forge/noarch::r-boot-1.3_25-r36h6115d3f_1 | |
| r-car conda-forge/noarch::r-car-3.0_7-r36h6115d3f_1 | |
| r-cardata conda-forge/noarch::r-cardata-3.0_3-r36h6115d3f_1 | |
| r-catools conda-forge/linux-64::r-catools-1.18.0-r36h0357c0b_1 | |
| r-cellranger conda-forge/noarch::r-cellranger-1.1.0-r36h6115d3f_1003 | |
| r-class conda-forge/linux-64::r-class-7.3_17-r36hcdcec82_1 | |
| r-cli conda-forge/noarch::r-cli-2.0.2-r36h6115d3f_1 | |
| r-clipr conda-forge/noarch::r-clipr-0.7.0-r36h6115d3f_1 | |
| r-cluster conda-forge/linux-64::r-cluster-2.1.0-r36h9bbef5b_3 | |
| r-codetools conda-forge/noarch::r-codetools-0.2_16-r36h6115d3f_1002 | |
| r-crayon conda-forge/noarch::r-crayon-1.3.4-r36h6115d3f_1003 | |
| r-curl conda-forge/linux-64::r-curl-4.3-r36hcdcec82_1 | |
| r-data.table conda-forge/linux-64::r-data.table-1.12.8-r36hcdcec82_1 | |
| r-digest conda-forge/linux-64::r-digest-0.6.25-r36h0357c0b_2 | |
| r-dotcall64 conda-forge/linux-64::r-dotcall64-1.0_0-r36h9bbef5b_1005 | |
| r-ellipsis conda-forge/linux-64::r-ellipsis-0.3.0-r36hcdcec82_1 | |
| r-fansi conda-forge/linux-64::r-fansi-0.4.1-r36hcdcec82_1 | |
| r-fields conda-forge/linux-64::r-fields-10.3-r36h9bbef5b_1 | |
| r-forcats conda-forge/noarch::r-forcats-0.5.0-r36h6115d3f_1 | |
| r-foreign conda-forge/linux-64::r-foreign-0.8_76-r36hcdcec82_1 | |
| r-gdata conda-forge/noarch::r-gdata-2.18.0-r36h6115d3f_1003 | |
| r-geomap conda-forge/linux-64::r-geomap-2.4_4-r36hcdcec82_1002 | |
| r-glue conda-forge/linux-64::r-glue-1.4.0-r36hcdcec82_1 | |
| r-gplots conda-forge/noarch::r-gplots-3.0.3-r36h6115d3f_1 | |
| r-gtools conda-forge/linux-64::r-gtools-3.8.2-r36hcdcec82_1 | |
| r-haven conda-forge/linux-64::r-haven-2.2.0-r36hde08347_1 | |
| r-hms conda-forge/noarch::r-hms-0.5.3-r36h6115d3f_1 | |
| r-kernsmooth conda-forge/linux-64::r-kernsmooth-2.23_17-r36hfa343cc_1 | |
| r-lattice conda-forge/linux-64::r-lattice-0.20_41-r36hcdcec82_2 | |
| r-lifecycle conda-forge/noarch::r-lifecycle-0.2.0-r36h6115d3f_1 | |
| r-lme4 conda-forge/linux-64::r-lme4-1.1_23-r36h0357c0b_1 | |
| r-magrittr conda-forge/noarch::r-magrittr-1.5-r36h6115d3f_1003 | |
| r-maps conda-forge/linux-64::r-maps-3.3.0-r36hcdcec82_1004 | |
| r-maptools conda-forge/linux-64::r-maptools-0.9_9-r36hcdcec82_1 | |
| r-mass conda-forge/linux-64::r-mass-7.3_51.6-r36hcdcec82_2 | |
| r-matrix conda-forge/linux-64::r-matrix-1.2_18-r36h7fa42b6_3 | |
| r-matrixmodels conda-forge/noarch::r-matrixmodels-0.4_1-r36h6115d3f_1003 | |
| r-matrixstats conda-forge/linux-64::r-matrixstats-0.56.0-r36hcdcec82_1 | |
| r-mba conda-forge/linux-64::r-mba-0.0_9-r36h0357c0b_1004 | |
| r-mgcv conda-forge/linux-64::r-mgcv-1.8_31-r36h7fa42b6_1 | |
| r-minqa conda-forge/linux-64::r-minqa-1.2.4-r36h6786f55_1005 | |
| r-nlme conda-forge/linux-64::r-nlme-3.1_147-r36h9bbef5b_1 | |
| r-nloptr conda-forge/linux-64::r-nloptr-1.2.2.1-r36h0357c0b_1 | |
| r-nnet conda-forge/linux-64::r-nnet-7.3_14-r36hcdcec82_1 | |
| r-openxlsx conda-forge/linux-64::r-openxlsx-4.1.5-r36h0357c0b_0 | |
| r-pbkrtest conda-forge/noarch::r-pbkrtest-0.4_7-r36h6115d3f_1003 | |
| r-pillar conda-forge/noarch::r-pillar-1.4.4-r36h6115d3f_0 | |
| r-pkgconfig conda-forge/noarch::r-pkgconfig-2.0.3-r36h6115d3f_1 | |
| r-prettyunits conda-forge/noarch::r-prettyunits-1.1.1-r36h6115d3f_1 | |
| r-progress conda-forge/noarch::r-progress-1.2.2-r36h6115d3f_2 | |
| r-purrr conda-forge/linux-64::r-purrr-0.3.4-r36hcdcec82_1 | |
| r-quantreg conda-forge/linux-64::r-quantreg-5.55-r36h9bbef5b_1 | |
| r-r6 conda-forge/noarch::r-r6-2.4.1-r36h6115d3f_1 | |
| r-rcpp conda-forge/linux-64::r-rcpp-1.0.4.6-r36h0357c0b_1 | |
| r-rcppeigen conda-forge/linux-64::r-rcppeigen-0.3.3.7.0-r36h0357c0b_1 | |
| r-readr conda-forge/linux-64::r-readr-1.3.1-r36h0357c0b_1003 | |
| r-readxl conda-forge/linux-64::r-readxl-1.3.1-r36hde08347_4 | |
| r-recommended conda-forge/noarch::r-recommended-3.6-r36_1004 | |
| r-rematch conda-forge/noarch::r-rematch-1.0.1-r36h6115d3f_1003 | |
| r-rfoc conda-forge/noarch::r-rfoc-3.4_6-r36h6115d3f_2 | |
| r-rio conda-forge/noarch::r-rio-0.5.16-r36h6115d3f_1002 | |
| r-rlang conda-forge/linux-64::r-rlang-0.4.6-r36hcdcec82_0 | |
| r-rpart conda-forge/linux-64::r-rpart-4.1_15-r36hcdcec82_2 | |
| r-rpmg conda-forge/noarch::r-rpmg-2.2_3-r36h6115d3f_1 | |
| r-rseis conda-forge/linux-64::r-rseis-3.9_0-r36hcdcec82_1 | |
| r-rwave conda-forge/linux-64::r-rwave-2.4_8-r36hcdcec82_1002 | |
| r-sp conda-forge/linux-64::r-sp-1.4_1-r36hcdcec82_1 | |
| r-spam conda-forge/linux-64::r-spam-2.5_1-r36hbf399a0_2 | |
| r-sparsem conda-forge/linux-64::r-sparsem-1.78-r36h9bbef5b_1 | |
| r-spatial conda-forge/linux-64::r-spatial-7.3_12-r36hcdcec82_1 | |
| r-splancs conda-forge/linux-64::r-splancs-2.01_40-r36h9bbef5b_1005 | |
| r-statmod conda-forge/linux-64::r-statmod-1.4.34-r36h6e990d7_1 | |
| r-stringi conda-forge/linux-64::r-stringi-1.4.6-r36h0e574ca_2 | |
| r-survival conda-forge/linux-64::r-survival-3.1_12-r36hcdcec82_1 | |
| r-tibble conda-forge/linux-64::r-tibble-3.0.1-r36hcdcec82_1 | |
| r-tidyselect conda-forge/linux-64::r-tidyselect-1.0.0-r36h6115d3f_1 | |
| r-utf8 conda-forge/linux-64::r-utf8-1.1.4-r36hcdcec82_1003 | |
| r-vctrs conda-forge/linux-64::r-vctrs-0.2.4-r36hcdcec82_1 | |
| r-zeallot conda-forge/noarch::r-zeallot-0.1.0-r36h6115d3f_1002 | |
| r-zip conda-forge/linux-64::r-zip-2.0.4-r36hcdcec82_1 | |
| readline conda-forge/linux-64::readline-8.0-hf8c457e_0 | |
| sed conda-forge/linux-64::sed-4.7-h1bed415_1000 | |
| setuptools conda-forge/linux-64::setuptools-46.1.3-py38h32f6830_0 | |
| sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0 | |
| tk conda-forge/linux-64::tk-8.6.10-hed695b0_0 | |
| tktable conda-forge/linux-64::tktable-2.10-h555a92e_3 | |
| wheel conda-forge/noarch::wheel-0.34.2-py_1 | |
| xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002 | |
| xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0 | |
| xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000 | |
| xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0 | |
| xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0 | |
| xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0 | |
| xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0 | |
| xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002 | |
| xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002 | |
| xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002 | |
| xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007 | |
| xz conda-forge/linux-64::xz-5.2.5-h516909a_0 | |
| zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1006 | |
| zstd conda-forge/linux-64::zstd-1.4.4-h6597ccf_3 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:06:58,926 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency bioconductor-flowdensity version 1.6.0 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:06:58,929 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency r version None of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:06:58,932 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency bioconductor-flowcore version 1.38.2 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:06:58,932 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency bioconductor-flowdensity version 1.6.0 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:06:58,933 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency r version None of type conda | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:06:58,943 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda list --name __bioconductor-flowcore@1.38.2 --export > '*******/galaxy/shared/galaxy_wd/tmp/jobdepsca7olea2530f5a141ecfc104767094a48c54b757c52df383fa4f5155e0b86538fba00e7c/__bioconductor-flowcore@1.38.2' | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:07:00,194 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix *******/galaxy/shared/_cache/7717432d --file *******/galaxy/shared/galaxy_wd/tmp/jobdepsca7olea2530f5a141ecfc104767094a48c54b757c52df383fa4f5155e0b86538fba00e7c/__bioconductor-flowcore@1.38.2 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_cache/7717432d | |
| added / updated specs: | |
| - _libgcc_mutex==0.1=conda_forge | |
| - _openmp_mutex==4.5=1_llvm | |
| - _r-mutex==1.0.1=anacondar_1 | |
| - bioconductor-biobase==2.34.0=r3.3.2_0 | |
| - bioconductor-biocgenerics==0.22.0=r3.3.2_0 | |
| - bioconductor-flowcore==1.38.2=r3.3.2_1 | |
| - bioconductor-graph==1.50.0=r3.3.2_1 | |
| - bzip2==1.0.8=h516909a_2 | |
| - ca-certificates==2020.4.5.1=hecc5488_0 | |
| - cairo==1.14.6=4 | |
| - curl==7.52.1=0 | |
| - fontconfig==2.12.1=6 | |
| - freetype==2.7=1 | |
| - gettext==0.19.8.1=hc5be6a0_1002 | |
| - glib==2.51.4=0 | |
| - graphite2==1.3.13=he1b5a44_1001 | |
| - gsl==2.6=h294904e_0 | |
| - harfbuzz==1.4.3=0 | |
| - icu==58.2=hf484d3e_1000 | |
| - jpeg==9c=h14c3975_1001 | |
| - libblas==3.8.0=16_openblas | |
| - libcblas==3.8.0=16_openblas | |
| - libffi==3.2.1=he1b5a44_1007 | |
| - libgcc-ng==9.2.0=h24d8f2e_2 | |
| - libgcc==7.2.0=h69d50b8_2 | |
| - libgfortran-ng==7.3.0=hdf63c60_5 | |
| - libiconv==1.15=h516909a_1006 | |
| - libopenblas==0.3.9=h5ec1e0e_0 | |
| - libpng==1.6.28=1 | |
| - libstdcxx-ng==9.2.0=hdf63c60_2 | |
| - libtiff==4.0.7=0 | |
| - libxml2==2.9.5=0 | |
| - llvm-openmp==10.0.0=hc9558a2_0 | |
| - ncurses==5.9=10 | |
| - openssl==1.0.2u=h516909a_0 | |
| - pango==1.40.4=0 | |
| - pcre==8.44=he1b5a44_0 | |
| - pixman==0.34.0=h14c3975_1003 | |
| - r-base==3.3.2=5 | |
| - r-bh==1.66.0_1=r3.3.2_0 | |
| - r-cluster==2.0.6=r3.3.2_0 | |
| - r-corpcor==1.6.9=r3.3.2_0 | |
| - r-deoptimr==1.0_8=r3.3.2_0 | |
| - r-lattice==0.20_34=r3.3.2_0 | |
| - r-matrixstats==0.52.2=r3.3.2_0 | |
| - r-mvtnorm==1.0_6=r3.3.2_0 | |
| - r-pcapp==1.9_61=r3.3.2_0 | |
| - r-rcpp==0.12.16=r3.3.2_0 | |
| - r-robustbase==0.92_7=r3.3.2_0 | |
| - r-rrcov==1.4_3=r3.3.2_0 | |
| - readline==6.2=0 | |
| - tk==8.5.19=2 | |
| - xz==5.2.5=h516909a_0 | |
| - zlib==1.2.8=3 | |
| The following NEW packages will be INSTALLED: | |
| _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge | |
| _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_llvm | |
| _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 | |
| bioconductor-biob~ bioconda/linux-64::bioconductor-biobase-2.34.0-r3.3.2_0 | |
| bioconductor-bioc~ bioconda/linux-64::bioconductor-biocgenerics-0.22.0-r3.3.2_0 | |
| bioconductor-flow~ bioconda/linux-64::bioconductor-flowcore-1.38.2-r3.3.2_1 | |
| bioconductor-graph bioconda/linux-64::bioconductor-graph-1.50.0-r3.3.2_1 | |
| bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_2 | |
| ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0 | |
| cairo conda-forge/linux-64::cairo-1.14.6-4 | |
| curl conda-forge/linux-64::curl-7.52.1-0 | |
| fontconfig conda-forge/linux-64::fontconfig-2.12.1-6 | |
| freetype conda-forge/linux-64::freetype-2.7-1 | |
| gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002 | |
| glib conda-forge/linux-64::glib-2.51.4-0 | |
| graphite2 conda-forge/linux-64::graphite2-1.3.13-he1b5a44_1001 | |
| gsl conda-forge/linux-64::gsl-2.6-h294904e_0 | |
| harfbuzz conda-forge/linux-64::harfbuzz-1.4.3-0 | |
| icu conda-forge/linux-64::icu-58.2-hf484d3e_1000 | |
| jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001 | |
| libblas conda-forge/linux-64::libblas-3.8.0-16_openblas | |
| libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas | |
| libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 | |
| libgcc conda-forge/linux-64::libgcc-7.2.0-h69d50b8_2 | |
| libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2 | |
| libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5 | |
| libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1006 | |
| libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0 | |
| libpng conda-forge/linux-64::libpng-1.6.28-1 | |
| libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2 | |
| libtiff conda-forge/linux-64::libtiff-4.0.7-0 | |
| libxml2 conda-forge/linux-64::libxml2-2.9.5-0 | |
| llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0 | |
| ncurses conda-forge/linux-64::ncurses-5.9-10 | |
| openssl conda-forge/linux-64::openssl-1.0.2u-h516909a_0 | |
| pango conda-forge/linux-64::pango-1.40.4-0 | |
| pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0 | |
| pixman conda-forge/linux-64::pixman-0.34.0-h14c3975_1003 | |
| r-base conda-forge/linux-64::r-base-3.3.2-5 | |
| r-bh conda-forge/linux-64::r-bh-1.66.0_1-r3.3.2_0 | |
| r-cluster conda-forge/linux-64::r-cluster-2.0.6-r3.3.2_0 | |
| r-corpcor conda-forge/linux-64::r-corpcor-1.6.9-r3.3.2_0 | |
| r-deoptimr conda-forge/linux-64::r-deoptimr-1.0_8-r3.3.2_0 | |
| r-lattice conda-forge/linux-64::r-lattice-0.20_34-r3.3.2_0 | |
| r-matrixstats conda-forge/linux-64::r-matrixstats-0.52.2-r3.3.2_0 | |
| r-mvtnorm conda-forge/linux-64::r-mvtnorm-1.0_6-r3.3.2_0 | |
| r-pcapp conda-forge/linux-64::r-pcapp-1.9_61-r3.3.2_0 | |
| r-rcpp conda-forge/linux-64::r-rcpp-0.12.16-r3.3.2_0 | |
| r-robustbase conda-forge/linux-64::r-robustbase-0.92_7-r3.3.2_0 | |
| r-rrcov conda-forge/linux-64::r-rrcov-1.4_3-r3.3.2_0 | |
| readline conda-forge/linux-64::readline-6.2-0 | |
| tk conda-forge/linux-64::tk-8.5.19-2 | |
| xz conda-forge/linux-64::xz-5.2.5-h516909a_0 | |
| zlib conda-forge/linux-64::zlib-1.2.8-3 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... 10.25.100.188 - - [07/May/2020:00:07:23 +0100] "GET /api/tool_shed_repositories?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28739|app: 0|req: 80/207] 10.25.100.188 () {38 vars in 604 bytes} [Thu May 7 00:07:23 2020] GET /api/tool_shed_repositories?key=ff1fadcdba102650fb96c7f486b45d6b => generated 7780 bytes in 40 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.25.100.188 - - [07/May/2020:00:07:25 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28743|app: 0|req: 24/208] 10.25.100.188 () {42 vars in 751 bytes} [Thu May 7 00:07:25 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 131 bytes in 1924 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.25.100.188 - - [07/May/2020:00:07:27 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28737|app: 0|req: 43/209] 10.25.100.188 () {42 vars in 751 bytes} [Thu May 7 00:07:27 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 131 bytes in 679 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:07:29,527 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:31,250 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-07 00:07:31,255 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Adding new row for repository 'dropletutils_empty_drops' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:07:31,262 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:31,262 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:31,293 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-07 00:07:31,300 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops' at 2:00b41600e1c1 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:44,326 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.3+galaxy1, version: 1.0.3+galaxy1 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-07 00:07:44,327 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-07 00:07:44,353 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-07 00:07:45,284 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-07 00:07:45,285 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| done | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:07:54,968 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda clean --tarballs -y | |
| galaxy.queue_worker ERROR 2020-05-07 00:07:55,426 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-07 00:07:55,431 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-07 00:07:55,496 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:07:55,496 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-07 00:07:55,611 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:07:55,612 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,613 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:07:55,627 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:07:55,630 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:07:55,632 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-07 00:07:55,633 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:07:55,633 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,634 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-07 00:07:55,635 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:07:55,635 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,637 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools WARNING 2020-05-07 00:07:55,645 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:07:55,645 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,646 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,646 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (37.297 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,647 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,651 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,651 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,654 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,655 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,655 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,658 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,660 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,661 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,662 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,663 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,665 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,666 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,667 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,667 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,668 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,668 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,668 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,669 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,669 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,669 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,669 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,670 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,670 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,670 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,670 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,671 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.3+galaxy1, version: 1.0.3+galaxy1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,671 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,671 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,671 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,671 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,673 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,674 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,675 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,675 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:07:55,675 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (28.890 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-07 00:07:55,682 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:07:55,684 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:07:55,687 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:07:55,689 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-07 00:07:55,689 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:07:55,698 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (202.379 ms) | |
| galaxy.queue_worker INFO 2020-05-07 00:07:55,708 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-07 00:07:55,709 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-07 00:07:55,743 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (33.863 ms) | |
| Cache location: *******/galaxy/shared/_conda/pkgs | |
| Will remove the following tarballs: | |
| *******/galaxy/shared/_conda/pkgs | |
| ---------------------------------------- | |
| libopenblas-0.3.6-h5a2b251_2.tar.bz2 7.7 MB | |
| libgfortran-3.0.0-1.tar.bz2 281 KB | |
| flock-1.0-h470a237_2.tar.bz2 34 KB | |
| openblas-0.2.14-4.tar.bz2 3.6 MB | |
| _openmp_mutex-4.5-0_gnu.tar.bz2 435 KB | |
| scipy-0.16.0-np19py27_1.tar.bz2 28.2 MB | |
| blas-2.11-openblas.tar.bz2 10 KB | |
| libblas-3.8.0-11_openblas.tar.bz2 10 KB | |
| libcblas-3.8.0-11_openblas.tar.bz2 10 KB | |
| liblapacke-3.8.0-11_openblas.tar.bz2 10 KB | |
| jinja2-2.8-py36_1.tar.bz2 262 KB | |
| liblapack-3.8.0-11_openblas.tar.bz2 10 KB | |
| certifi-2020.4.5.1-py36h9f0ad1d_0.tar.bz2 151 KB | |
| python_abi-3.6-1_cp36m.tar.bz2 4 KB | |
| setuptools-46.1.3-py36h9f0ad1d_0.tar.bz2 653 KB | |
| markupsafe-1.1.1-py36h8c4c3a4_1.tar.bz2 26 KB | |
| python-3.6.10-h8356626_1011_cpython.tar.bz2 34.1 MB | |
| bioconductor-flowdensity-1.6.0-0.tar.bz2 4.4 MB | |
| r-maps-3.3.0-r36hcdcec82_1004.tar.bz2 3.4 MB | |
| r-haven-2.2.0-r36hde08347_1.tar.bz2 352 KB | |
| r-geomap-2.4_4-r36hcdcec82_1002.tar.bz2 3.2 MB | |
| r-rseis-3.9_0-r36hcdcec82_1.tar.bz2 3.5 MB | |
| r-dotcall64-1.0_0-r36h9bbef5b_1005.tar.bz2 49 KB | |
| r-nloptr-1.2.2.1-r36h0357c0b_1.tar.bz2 505 KB | |
| r-abind-1.4_5-r36h6115d3f_1003.tar.bz2 76 KB | |
| r-pbkrtest-0.4_7-r36h6115d3f_1003.tar.bz2 281 KB | |
| r-data.table-1.12.8-r36hcdcec82_1.tar.bz2 1.8 MB | |
| r-glue-1.4.0-r36hcdcec82_1.tar.bz2 144 KB | |
| r-zip-2.0.4-r36hcdcec82_1.tar.bz2 146 KB | |
| bioconductor-flowcore-1.52.0-r36he1b5a44_0.tar.bz2 7.6 MB | |
| r-fansi-0.4.1-r36hcdcec82_1.tar.bz2 196 KB | |
| r-zeallot-0.1.0-r36h6115d3f_1002.tar.bz2 62 KB | |
| r-rematch-1.0.1-r36h6115d3f_1003.tar.bz2 19 KB | |
| r-rfoc-3.4_6-r36h6115d3f_2.tar.bz2 653 KB | |
| r-cellranger-1.1.0-r36h6115d3f_1003.tar.bz2 108 KB | |
| r-rcppeigen-0.3.3.7.0-r36h0357c0b_1.tar.bz2 1.5 MB | |
| r-curl-4.3-r36hcdcec82_1.tar.bz2 702 KB | |
| r-gdata-2.18.0-r36h6115d3f_1003.tar.bz2 1.1 MB | |
| r-prettyunits-1.1.1-r36h6115d3f_1.tar.bz2 41 KB | |
| r-spam-2.5_1-r36hbf399a0_2.tar.bz2 2.6 MB | |
| r-pkgconfig-2.0.3-r36h6115d3f_1.tar.bz2 24 KB | |
| bioconductor-biobase-2.46.0-r36h516909a_0.tar.bz2 2.3 MB | |
| r-splancs-2.01_40-r36h9bbef5b_1005.tar.bz2 337 KB | |
| r-rio-0.5.16-r36h6115d3f_1002.tar.bz2 493 KB | |
| r-vctrs-0.2.4-r36hcdcec82_1.tar.bz2 894 KB | |
| r-openxlsx-4.1.5-r36h0357c0b_0.tar.bz2 1.9 MB | |
| r-cli-2.0.2-r36h6115d3f_1.tar.bz2 395 KB | |
| r-lifecycle-0.2.0-r36h6115d3f_1.tar.bz2 112 KB | |
| bioconductor-biocgenerics-0.32.0-r36_0.tar.bz2 691 KB | |
| r-gtools-3.8.2-r36hcdcec82_1.tar.bz2 333 KB | |
| r-crayon-1.3.4-r36h6115d3f_1003.tar.bz2 747 KB | |
| r-mba-0.0_9-r36h0357c0b_1004.tar.bz2 198 KB | |
| r-rpmg-2.2_3-r36h6115d3f_1.tar.bz2 212 KB | |
| r-readr-1.3.1-r36h0357c0b_1003.tar.bz2 832 KB | |
| r-hms-0.5.3-r36h6115d3f_1.tar.bz2 122 KB | |
| r-pillar-1.4.4-r36h6115d3f_0.tar.bz2 197 KB | |
| r-magrittr-1.5-r36h6115d3f_1003.tar.bz2 167 KB | |
| r-sp-1.4_1-r36hcdcec82_1.tar.bz2 1.9 MB | |
| r-backports-1.1.6-r36hcdcec82_2.tar.bz2 77 KB | |
| r-r6-2.4.1-r36h6115d3f_1.tar.bz2 63 KB | |
| r-purrr-0.3.4-r36hcdcec82_1.tar.bz2 411 KB | |
| r-sparsem-1.78-r36h9bbef5b_1.tar.bz2 1.0 MB | |
| r-gplots-3.0.3-r36h6115d3f_1.tar.bz2 595 KB | |
| r-tidyselect-1.0.0-r36h6115d3f_1.tar.bz2 221 KB | |
| r-readxl-1.3.1-r36hde08347_4.tar.bz2 856 KB | |
| r-car-3.0_7-r36h6115d3f_1.tar.bz2 1.5 MB | |
| r-tibble-3.0.1-r36hcdcec82_1.tar.bz2 382 KB | |
| r-ellipsis-0.3.0-r36hcdcec82_1.tar.bz2 47 KB | |
| bioconductor-cytolib-1.8.0-r36_0.tar.bz2 321 KB | |
| r-statmod-1.4.34-r36h6e990d7_1.tar.bz2 280 KB | |
| r-catools-1.18.0-r36h0357c0b_1.tar.bz2 223 KB | |
| r-forcats-0.5.0-r36h6115d3f_1.tar.bz2 376 KB | |
| r-lme4-1.1_23-r36h0357c0b_1.tar.bz2 4.9 MB | |
| r-rwave-2.4_8-r36hcdcec82_1002.tar.bz2 1.0 MB | |
| r-digest-0.6.25-r36h0357c0b_2.tar.bz2 199 KB | |
| r-minqa-1.2.4-r36h6786f55_1005.tar.bz2 141 KB | |
| r-rlang-0.4.6-r36hcdcec82_0.tar.bz2 1.0 MB | |
| r-matrixmodels-0.4_1-r36h6115d3f_1003.tar.bz2 354 KB | |
| r-utf8-1.1.4-r36hcdcec82_1003.tar.bz2 161 KB | |
| r-maptools-0.9_9-r36hcdcec82_1.tar.bz2 2.1 MB | |
| r-assertthat-0.2.1-r36h6115d3f_2.tar.bz2 70 KB | |
| r-stringi-1.4.6-r36h0e574ca_2.tar.bz2 783 KB | |
| r-cardata-3.0_3-r36h6115d3f_1.tar.bz2 1.8 MB | |
| r-progress-1.2.2-r36h6115d3f_2.tar.bz2 90 KB | |
| r-clipr-0.7.0-r36h6115d3f_1.tar.bz2 64 KB | |
| r-fields-10.3-r36h9bbef5b_1.tar.bz2 3.8 MB | |
| r-quantreg-5.55-r36h9bbef5b_1.tar.bz2 1.5 MB | |
| --------------------------------------------------- | |
| Total: 143.7 MB | |
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| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:07:56,189 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda list --name __bioconductor-flowdensity@1.6.0 --export > '*******/galaxy/shared/galaxy_wd/tmp/jobdepswp3zsyp2d6055eee0f70f95e6f8abc7ee51971b291b3280b9f60747625b8365674d9a7a5/__bioconductor-flowdensity@1.6.0' | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:07:58,437 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda install -y --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix *******/galaxy/shared/_cache/7717432d --file *******/galaxy/shared/galaxy_wd/tmp/jobdepswp3zsyp2d6055eee0f70f95e6f8abc7ee51971b291b3280b9f60747625b8365674d9a7a5/__bioconductor-flowdensity@1.6.0 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_cache/7717432d | |
| added / updated specs: | |
| - _libgcc_mutex==0.1=conda_forge | |
| - _openmp_mutex==4.5=1_llvm | |
| - _r-mutex==1.0.1=anacondar_1 | |
| - binutils_impl_linux-64==2.34=h53a641e_0 | |
| - binutils_linux-64==2.34=hc952b39_18 | |
| - bioconductor-biobase==2.46.0=r36h516909a_0 | |
| - bioconductor-biocgenerics==0.32.0=r36_0 | |
| - bioconductor-cytolib==1.8.0=r36_0 | |
| - bioconductor-flowcore==1.52.0=r36he1b5a44_0 | |
| - bioconductor-flowdensity==1.6.0=0 | |
| - bwidget==1.9.14=0 | |
| - bzip2==1.0.8=h516909a_2 | |
| - ca-certificates==2020.4.5.1=hecc5488_0 | |
| - cairo==1.16.0=hcf35c78_1003 | |
| - certifi==2020.4.5.1=py38h32f6830_0 | |
| - curl==7.69.1=h33f0ec9_0 | |
| - fontconfig==2.13.1=h86ecdb6_1001 | |
| - freetype==2.10.1=he06d7ca_0 | |
| - fribidi==1.0.9=h516909a_0 | |
| - gcc_impl_linux-64==7.3.0=hd420e75_5 | |
| - gcc_linux-64==7.3.0=h553295d_18 | |
| - gettext==0.19.8.1=hc5be6a0_1002 | |
| - gfortran_impl_linux-64==7.3.0=hdf63c60_5 | |
| - gfortran_linux-64==7.3.0=h553295d_18 | |
| - glib==2.58.3=py38h73cb85d_1004 | |
| - graphite2==1.3.13=he1b5a44_1001 | |
| - gsl==2.6=h294904e_0 | |
| - gxx_impl_linux-64==7.3.0=hdf63c60_5 | |
| - gxx_linux-64==7.3.0=h553295d_18 | |
| - harfbuzz==2.4.0=h9f30f68_3 | |
| - icu==64.2=he1b5a44_1 | |
| - jpeg==9c=h14c3975_1001 | |
| - krb5==1.17.1=h2fd8d38_0 | |
| - ld_impl_linux-64==2.34=h53a641e_0 | |
| - libblas==3.8.0=16_openblas | |
| - libcblas==3.8.0=16_openblas | |
| - libcurl==7.69.1=hf7181ac_0 | |
| - libedit==3.1.20170329=hf8c457e_1001 | |
| - libffi==3.2.1=he1b5a44_1007 | |
| - libgcc-ng==9.2.0=h24d8f2e_2 | |
| - libgfortran-ng==7.3.0=hdf63c60_5 | |
| - libgomp==9.2.0=h24d8f2e_2 | |
| - libiconv==1.15=h516909a_1006 | |
| - liblapack==3.8.0=16_openblas | |
| - libopenblas==0.3.9=h5ec1e0e_0 | |
| - libpng==1.6.37=hed695b0_1 | |
| - libssh2==1.8.2=h22169c7_2 | |
| - libstdcxx-ng==9.2.0=hdf63c60_2 | |
| - libtiff==4.1.0=hc7e4089_6 | |
| - libuuid==2.32.1=h14c3975_1000 | |
| - libwebp-base==1.1.0=h516909a_3 | |
| - libxcb==1.13=h14c3975_1002 | |
| - libxml2==2.9.10=hee79883_0 | |
| - llvm-openmp==10.0.0=hc9558a2_0 | |
| - lz4-c==1.9.2=he1b5a44_1 | |
| - make==4.3=h516909a_0 | |
| - ncurses==6.1=hf484d3e_1002 | |
| - openssl==1.1.1g=h516909a_0 | |
| - pango==1.42.4=h7062337_4 | |
| - pcre==8.44=he1b5a44_0 | |
| - pip==20.1=pyh9f0ad1d_0 | |
| - pixman==0.38.0=h516909a_1003 | |
| - pthread-stubs==0.4=h14c3975_1001 | |
| - python==3.8.2=he5300dc_7_cpython | |
| - python_abi==3.8=1_cp38 | |
| - r-abind==1.4_5=r36h6115d3f_1003 | |
| - r-assertthat==0.2.1=r36h6115d3f_2 | |
| - r-backports==1.1.6=r36hcdcec82_2 | |
| - r-base==3.6.3=h316533a_2 | |
| - r-bh==1.72.0_3=r36h6115d3f_1 | |
| - r-bitops==1.0_6=r36hcdcec82_1004 | |
| - r-boot==1.3_25=r36h6115d3f_1 | |
| - r-car==3.0_7=r36h6115d3f_1 | |
| - r-cardata==3.0_3=r36h6115d3f_1 | |
| - r-catools==1.18.0=r36h0357c0b_1 | |
| - r-cellranger==1.1.0=r36h6115d3f_1003 | |
| - r-class==7.3_17=r36hcdcec82_1 | |
| - r-cli==2.0.2=r36h6115d3f_1 | |
| - r-clipr==0.7.0=r36h6115d3f_1 | |
| - r-cluster==2.1.0=r36h9bbef5b_3 | |
| - r-codetools==0.2_16=r36h6115d3f_1002 | |
| - r-crayon==1.3.4=r36h6115d3f_1003 | |
| - r-curl==4.3=r36hcdcec82_1 | |
| - r-data.table==1.12.8=r36hcdcec82_1 | |
| - r-digest==0.6.25=r36h0357c0b_2 | |
| - r-dotcall64==1.0_0=r36h9bbef5b_1005 | |
| - r-ellipsis==0.3.0=r36hcdcec82_1 | |
| - r-fansi==0.4.1=r36hcdcec82_1 | |
| - r-fields==10.3=r36h9bbef5b_1 | |
| - r-forcats==0.5.0=r36h6115d3f_1 | |
| - r-foreign==0.8_76=r36hcdcec82_1 | |
| - r-gdata==2.18.0=r36h6115d3f_1003 | |
| - r-geomap==2.4_4=r36hcdcec82_1002 | |
| - r-glue==1.4.0=r36hcdcec82_1 | |
| - r-gplots==3.0.3=r36h6115d3f_1 | |
| - r-gtools==3.8.2=r36hcdcec82_1 | |
| - r-haven==2.2.0=r36hde08347_1 | |
| - r-hms==0.5.3=r36h6115d3f_1 | |
| - r-kernsmooth==2.23_17=r36hfa343cc_1 | |
| - r-lattice==0.20_41=r36hcdcec82_2 | |
| - r-lifecycle==0.2.0=r36h6115d3f_1 | |
| - r-lme4==1.1_23=r36h0357c0b_1 | |
| - r-magrittr==1.5=r36h6115d3f_1003 | |
| - r-maps==3.3.0=r36hcdcec82_1004 | |
| - r-maptools==0.9_9=r36hcdcec82_1 | |
| - r-mass==7.3_51.6=r36hcdcec82_2 | |
| - r-matrix==1.2_18=r36h7fa42b6_3 | |
| - r-matrixmodels==0.4_1=r36h6115d3f_1003 | |
| - r-matrixstats==0.56.0=r36hcdcec82_1 | |
| - r-mba==0.0_9=r36h0357c0b_1004 | |
| - r-mgcv==1.8_31=r36h7fa42b6_1 | |
| - r-minqa==1.2.4=r36h6786f55_1005 | |
| - r-nlme==3.1_147=r36h9bbef5b_1 | |
| - r-nloptr==1.2.2.1=r36h0357c0b_1 | |
| - r-nnet==7.3_14=r36hcdcec82_1 | |
| - r-openxlsx==4.1.5=r36h0357c0b_0 | |
| - r-pbkrtest==0.4_7=r36h6115d3f_1003 | |
| - r-pillar==1.4.4=r36h6115d3f_0 | |
| - r-pkgconfig==2.0.3=r36h6115d3f_1 | |
| - r-prettyunits==1.1.1=r36h6115d3f_1 | |
| - r-progress==1.2.2=r36h6115d3f_2 | |
| - r-purrr==0.3.4=r36hcdcec82_1 | |
| - r-quantreg==5.55=r36h9bbef5b_1 | |
| - r-r6==2.4.1=r36h6115d3f_1 | |
| - r-rcpp==1.0.4.6=r36h0357c0b_1 | |
| - r-rcppeigen==0.3.3.7.0=r36h0357c0b_1 | |
| - r-readr==1.3.1=r36h0357c0b_1003 | |
| - r-readxl==1.3.1=r36hde08347_4 | |
| - r-recommended==3.6=r36_1004 | |
| - r-rematch==1.0.1=r36h6115d3f_1003 | |
| - r-rfoc==3.4_6=r36h6115d3f_2 | |
| - r-rio==0.5.16=r36h6115d3f_1002 | |
| - r-rlang==0.4.6=r36hcdcec82_0 | |
| - r-rpart==4.1_15=r36hcdcec82_2 | |
| - r-rpmg==2.2_3=r36h6115d3f_1 | |
| - r-rseis==3.9_0=r36hcdcec82_1 | |
| - r-rwave==2.4_8=r36hcdcec82_1002 | |
| - r-sp==1.4_1=r36hcdcec82_1 | |
| - r-spam==2.5_1=r36hbf399a0_2 | |
| - r-sparsem==1.78=r36h9bbef5b_1 | |
| - r-spatial==7.3_12=r36hcdcec82_1 | |
| - r-splancs==2.01_40=r36h9bbef5b_1005 | |
| - r-statmod==1.4.34=r36h6e990d7_1 | |
| - r-stringi==1.4.6=r36h0e574ca_2 | |
| - r-survival==3.1_12=r36hcdcec82_1 | |
| - r-tibble==3.0.1=r36hcdcec82_1 | |
| - r-tidyselect==1.0.0=r36h6115d3f_1 | |
| - r-utf8==1.1.4=r36hcdcec82_1003 | |
| - r-vctrs==0.2.4=r36hcdcec82_1 | |
| - r-zeallot==0.1.0=r36h6115d3f_1002 | |
| - r-zip==2.0.4=r36hcdcec82_1 | |
| - r==3.6=r36_1003 | |
| - readline==8.0=hf8c457e_0 | |
| - sed==4.7=h1bed415_1000 | |
| - setuptools==46.1.3=py38h32f6830_0 | |
| - sqlite==3.30.1=hcee41ef_0 | |
| - tk==8.6.10=hed695b0_0 | |
| - tktable==2.10=h555a92e_3 | |
| - wheel==0.34.2=py_1 | |
| - xorg-kbproto==1.0.7=h14c3975_1002 | |
| - xorg-libice==1.0.10=h516909a_0 | |
| - xorg-libsm==1.2.3=h84519dc_1000 | |
| - xorg-libx11==1.6.9=h516909a_0 | |
| - xorg-libxau==1.0.9=h14c3975_0 | |
| - xorg-libxdmcp==1.1.3=h516909a_0 | |
| - xorg-libxext==1.3.4=h516909a_0 | |
| - xorg-libxrender==0.9.10=h516909a_1002 | |
| - xorg-renderproto==0.11.1=h14c3975_1002 | |
| - xorg-xextproto==7.3.0=h14c3975_1002 | |
| - xorg-xproto==7.0.31=h14c3975_1007 | |
| - xz==5.2.5=h516909a_0 | |
| - zlib==1.2.11=h516909a_1006 | |
| - zstd==1.4.4=h6597ccf_3 | |
| The following NEW packages will be INSTALLED: | |
| binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.34-h53a641e_0 | |
| binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.34-hc952b39_18 | |
| bioconductor-cyto~ bioconda/noarch::bioconductor-cytolib-1.8.0-r36_0 | |
| bioconductor-flow~ bioconda/linux-64::bioconductor-flowdensity-1.6.0-0 | |
| bwidget conda-forge/linux-64::bwidget-1.9.14-0 | |
| certifi conda-forge/linux-64::certifi-2020.4.5.1-py38h32f6830_0 | |
| fribidi conda-forge/linux-64::fribidi-1.0.9-h516909a_0 | |
| gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-7.3.0-hd420e75_5 | |
| gcc_linux-64 conda-forge/linux-64::gcc_linux-64-7.3.0-h553295d_18 | |
| gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_5 | |
| gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-7.3.0-h553295d_18 | |
| gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_5 | |
| gxx_linux-64 conda-forge/linux-64::gxx_linux-64-7.3.0-h553295d_18 | |
| krb5 conda-forge/linux-64::krb5-1.17.1-h2fd8d38_0 | |
| ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 | |
| libcurl conda-forge/linux-64::libcurl-7.69.1-hf7181ac_0 | |
| libedit conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001 | |
| libgomp conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2 | |
| liblapack conda-forge/linux-64::liblapack-3.8.0-16_openblas | |
| libssh2 conda-forge/linux-64::libssh2-1.8.2-h22169c7_2 | |
| libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000 | |
| libwebp-base conda-forge/linux-64::libwebp-base-1.1.0-h516909a_3 | |
| libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002 | |
| lz4-c conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_1 | |
| make conda-forge/linux-64::make-4.3-h516909a_0 | |
| pip conda-forge/noarch::pip-20.1-pyh9f0ad1d_0 | |
| pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001 | |
| python conda-forge/linux-64::python-3.8.2-he5300dc_7_cpython | |
| python_abi conda-forge/linux-64::python_abi-3.8-1_cp38 | |
| r conda-forge/noarch::r-3.6-r36_1003 | |
| r-abind conda-forge/noarch::r-abind-1.4_5-r36h6115d3f_1003 | |
| r-assertthat conda-forge/noarch::r-assertthat-0.2.1-r36h6115d3f_2 | |
| r-backports conda-forge/linux-64::r-backports-1.1.6-r36hcdcec82_2 | |
| r-bitops conda-forge/linux-64::r-bitops-1.0_6-r36hcdcec82_1004 | |
| r-boot conda-forge/noarch::r-boot-1.3_25-r36h6115d3f_1 | |
| r-car conda-forge/noarch::r-car-3.0_7-r36h6115d3f_1 | |
| r-cardata conda-forge/noarch::r-cardata-3.0_3-r36h6115d3f_1 | |
| r-catools conda-forge/linux-64::r-catools-1.18.0-r36h0357c0b_1 | |
| r-cellranger conda-forge/noarch::r-cellranger-1.1.0-r36h6115d3f_1003 | |
| r-class conda-forge/linux-64::r-class-7.3_17-r36hcdcec82_1 | |
| r-cli conda-forge/noarch::r-cli-2.0.2-r36h6115d3f_1 | |
| r-clipr conda-forge/noarch::r-clipr-0.7.0-r36h6115d3f_1 | |
| r-codetools conda-forge/noarch::r-codetools-0.2_16-r36h6115d3f_1002 | |
| r-crayon conda-forge/noarch::r-crayon-1.3.4-r36h6115d3f_1003 | |
| r-curl conda-forge/linux-64::r-curl-4.3-r36hcdcec82_1 | |
| r-data.table conda-forge/linux-64::r-data.table-1.12.8-r36hcdcec82_1 | |
| r-digest conda-forge/linux-64::r-digest-0.6.25-r36h0357c0b_2 | |
| r-dotcall64 conda-forge/linux-64::r-dotcall64-1.0_0-r36h9bbef5b_1005 | |
| r-ellipsis conda-forge/linux-64::r-ellipsis-0.3.0-r36hcdcec82_1 | |
| r-fansi conda-forge/linux-64::r-fansi-0.4.1-r36hcdcec82_1 | |
| r-fields conda-forge/linux-64::r-fields-10.3-r36h9bbef5b_1 | |
| r-forcats conda-forge/noarch::r-forcats-0.5.0-r36h6115d3f_1 | |
| r-foreign conda-forge/linux-64::r-foreign-0.8_76-r36hcdcec82_1 | |
| r-gdata conda-forge/noarch::r-gdata-2.18.0-r36h6115d3f_1003 | |
| r-geomap conda-forge/linux-64::r-geomap-2.4_4-r36hcdcec82_1002 | |
| r-glue conda-forge/linux-64::r-glue-1.4.0-r36hcdcec82_1 | |
| r-gplots conda-forge/noarch::r-gplots-3.0.3-r36h6115d3f_1 | |
| r-gtools conda-forge/linux-64::r-gtools-3.8.2-r36hcdcec82_1 | |
| r-haven conda-forge/linux-64::r-haven-2.2.0-r36hde08347_1 | |
| r-hms conda-forge/noarch::r-hms-0.5.3-r36h6115d3f_1 | |
| r-kernsmooth conda-forge/linux-64::r-kernsmooth-2.23_17-r36hfa343cc_1 | |
| r-lifecycle conda-forge/noarch::r-lifecycle-0.2.0-r36h6115d3f_1 | |
| r-lme4 conda-forge/linux-64::r-lme4-1.1_23-r36h0357c0b_1 | |
| r-magrittr conda-forge/noarch::r-magrittr-1.5-r36h6115d3f_1003 | |
| r-maps conda-forge/linux-64::r-maps-3.3.0-r36hcdcec82_1004 | |
| r-maptools conda-forge/linux-64::r-maptools-0.9_9-r36hcdcec82_1 | |
| r-mass conda-forge/linux-64::r-mass-7.3_51.6-r36hcdcec82_2 | |
| r-matrix conda-forge/linux-64::r-matrix-1.2_18-r36h7fa42b6_3 | |
| r-matrixmodels conda-forge/noarch::r-matrixmodels-0.4_1-r36h6115d3f_1003 | |
| r-mba conda-forge/linux-64::r-mba-0.0_9-r36h0357c0b_1004 | |
| r-mgcv conda-forge/linux-64::r-mgcv-1.8_31-r36h7fa42b6_1 | |
| r-minqa conda-forge/linux-64::r-minqa-1.2.4-r36h6786f55_1005 | |
| r-nlme conda-forge/linux-64::r-nlme-3.1_147-r36h9bbef5b_1 | |
| r-nloptr conda-forge/linux-64::r-nloptr-1.2.2.1-r36h0357c0b_1 | |
| r-nnet conda-forge/linux-64::r-nnet-7.3_14-r36hcdcec82_1 | |
| r-openxlsx conda-forge/linux-64::r-openxlsx-4.1.5-r36h0357c0b_0 | |
| r-pbkrtest conda-forge/noarch::r-pbkrtest-0.4_7-r36h6115d3f_1003 | |
| r-pillar conda-forge/noarch::r-pillar-1.4.4-r36h6115d3f_0 | |
| r-pkgconfig conda-forge/noarch::r-pkgconfig-2.0.3-r36h6115d3f_1 | |
| r-prettyunits conda-forge/noarch::r-prettyunits-1.1.1-r36h6115d3f_1 | |
| r-progress conda-forge/noarch::r-progress-1.2.2-r36h6115d3f_2 | |
| r-purrr conda-forge/linux-64::r-purrr-0.3.4-r36hcdcec82_1 | |
| r-quantreg conda-forge/linux-64::r-quantreg-5.55-r36h9bbef5b_1 | |
| r-r6 conda-forge/noarch::r-r6-2.4.1-r36h6115d3f_1 | |
| r-rcppeigen conda-forge/linux-64::r-rcppeigen-0.3.3.7.0-r36h0357c0b_1 | |
| r-readr conda-forge/linux-64::r-readr-1.3.1-r36h0357c0b_1003 | |
| r-readxl conda-forge/linux-64::r-readxl-1.3.1-r36hde08347_4 | |
| r-recommended conda-forge/noarch::r-recommended-3.6-r36_1004 | |
| r-rematch conda-forge/noarch::r-rematch-1.0.1-r36h6115d3f_1003 | |
| r-rfoc conda-forge/noarch::r-rfoc-3.4_6-r36h6115d3f_2 | |
| r-rio conda-forge/noarch::r-rio-0.5.16-r36h6115d3f_1002 | |
| r-rlang conda-forge/linux-64::r-rlang-0.4.6-r36hcdcec82_0 | |
| r-rpart conda-forge/linux-64::r-rpart-4.1_15-r36hcdcec82_2 | |
| r-rpmg conda-forge/noarch::r-rpmg-2.2_3-r36h6115d3f_1 | |
| r-rseis conda-forge/linux-64::r-rseis-3.9_0-r36hcdcec82_1 | |
| r-rwave conda-forge/linux-64::r-rwave-2.4_8-r36hcdcec82_1002 | |
| r-sp conda-forge/linux-64::r-sp-1.4_1-r36hcdcec82_1 | |
| r-spam conda-forge/linux-64::r-spam-2.5_1-r36hbf399a0_2 | |
| r-sparsem conda-forge/linux-64::r-sparsem-1.78-r36h9bbef5b_1 | |
| r-spatial conda-forge/linux-64::r-spatial-7.3_12-r36hcdcec82_1 | |
| r-splancs conda-forge/linux-64::r-splancs-2.01_40-r36h9bbef5b_1005 | |
| r-statmod conda-forge/linux-64::r-statmod-1.4.34-r36h6e990d7_1 | |
| r-stringi conda-forge/linux-64::r-stringi-1.4.6-r36h0e574ca_2 | |
| r-survival conda-forge/linux-64::r-survival-3.1_12-r36hcdcec82_1 | |
| r-tibble conda-forge/linux-64::r-tibble-3.0.1-r36hcdcec82_1 | |
| r-tidyselect conda-forge/linux-64::r-tidyselect-1.0.0-r36h6115d3f_1 | |
| r-utf8 conda-forge/linux-64::r-utf8-1.1.4-r36hcdcec82_1003 | |
| r-vctrs conda-forge/linux-64::r-vctrs-0.2.4-r36hcdcec82_1 | |
| r-zeallot conda-forge/noarch::r-zeallot-0.1.0-r36h6115d3f_1002 | |
| r-zip conda-forge/linux-64::r-zip-2.0.4-r36hcdcec82_1 | |
| sed conda-forge/linux-64::sed-4.7-h1bed415_1000 | |
| setuptools conda-forge/linux-64::setuptools-46.1.3-py38h32f6830_0 | |
| sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0 | |
| tktable conda-forge/linux-64::tktable-2.10-h555a92e_3 | |
| wheel conda-forge/noarch::wheel-0.34.2-py_1 | |
| xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002 | |
| xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0 | |
| xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000 | |
| xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0 | |
| xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0 | |
| xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0 | |
| xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0 | |
| xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002 | |
| xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002 | |
| xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002 | |
| xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007 | |
| zstd conda-forge/linux-64::zstd-1.4.4-h6597ccf_3 | |
| The following packages will be REMOVED: | |
| bioconductor-graph-1.50.0-r3.3.2_1 | |
| r-corpcor-1.6.9-r3.3.2_0 | |
| r-deoptimr-1.0_8-r3.3.2_0 | |
| r-mvtnorm-1.0_6-r3.3.2_0 | |
| r-pcapp-1.9_61-r3.3.2_0 | |
| r-robustbase-0.92_7-r3.3.2_0 | |
| r-rrcov-1.4_3-r3.3.2_0 | |
| The following packages will be UPDATED: | |
| bioconductor-biob~ 2.34.0-r3.3.2_0 --> 2.46.0-r36h516909a_0 | |
| bioconductor-bioc~ bioconda/linux-64::bioconductor-biocg~ --> bioconda/noarch::bioconductor-biocgenerics-0.32.0-r36_0 | |
| bioconductor-flow~ 1.38.2-r3.3.2_1 --> 1.52.0-r36he1b5a44_0 | |
| cairo 1.14.6-4 --> 1.16.0-hcf35c78_1003 | |
| curl 7.52.1-0 --> 7.69.1-h33f0ec9_0 | |
| fontconfig 2.12.1-6 --> 2.13.1-h86ecdb6_1001 | |
| freetype 2.7-1 --> 2.10.1-he06d7ca_0 | |
| glib 2.51.4-0 --> 2.58.3-py38h73cb85d_1004 | |
| harfbuzz 1.4.3-0 --> 2.4.0-h9f30f68_3 | |
| icu 58.2-hf484d3e_1000 --> 64.2-he1b5a44_1 | |
| libpng 1.6.28-1 --> 1.6.37-hed695b0_1 | |
| libtiff 4.0.7-0 --> 4.1.0-hc7e4089_6 | |
| libxml2 2.9.5-0 --> 2.9.10-hee79883_0 | |
| ncurses 5.9-10 --> 6.1-hf484d3e_1002 | |
| openssl 1.0.2u-h516909a_0 --> 1.1.1g-h516909a_0 | |
| pango 1.40.4-0 --> 1.42.4-h7062337_4 | |
| pixman 0.34.0-h14c3975_1003 --> 0.38.0-h516909a_1003 | |
| r-base 3.3.2-5 --> 3.6.3-h316533a_2 | |
| r-bh conda-forge/linux-64::r-bh-1.66.0_1-r~ --> conda-forge/noarch::r-bh-1.72.0_3-r36h6115d3f_1 | |
| r-cluster 2.0.6-r3.3.2_0 --> 2.1.0-r36h9bbef5b_3 | |
| r-lattice 0.20_34-r3.3.2_0 --> 0.20_41-r36hcdcec82_2 | |
| r-matrixstats 0.52.2-r3.3.2_0 --> 0.56.0-r36hcdcec82_1 | |
| r-rcpp 0.12.16-r3.3.2_0 --> 1.0.4.6-r36h0357c0b_1 | |
| readline 6.2-0 --> 8.0-hf8c457e_0 | |
| tk 8.5.19-2 --> 8.6.10-hed695b0_0 | |
| zlib 1.2.8-3 --> 1.2.11-h516909a_1006 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... galaxy.config WARNING 2020-05-07 00:08:44,360 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Waiting for toolbox reload timed out after 60 seconds | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:08:44,366 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Using dependency dropletutils-scripts version 0.0.4 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:08:44,367 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Using dependency dropletutils-scripts version 0.0.4 of type conda | |
| 10.25.100.188 - - [07/May/2020:00:07:28 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28739|app: 0|req: 81/210] 10.25.100.188 () {42 vars in 751 bytes} [Thu May 7 00:07:28 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 651 bytes in 75489 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:08:45,609 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:08:48,071 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-07 00:08:48,077 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Adding new row for repository 'dropletutils_empty_drops' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:08:48,083 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:08:48,083 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:08:48,113 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-07 00:08:48,121 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops' at 0:b4332c428c63 | |
| done | |
| Executing transaction: ...working... galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:26,097 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.3+galaxy0, version: 1.0.3+galaxy0 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-07 00:09:26,098 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-07 00:09:26,120 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-07 00:09:26,200 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-07 00:09:26,202 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-07 00:09:36,338 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-07 00:09:36,344 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-07 00:09:36,812 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:09:36,813 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-07 00:09:36,867 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:09:36,868 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,869 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:09:36,882 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:09:36,884 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:09:36,886 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-07 00:09:36,887 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:09:36,887 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,888 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-07 00:09:36,889 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:09:36,889 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,891 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools WARNING 2020-05-07 00:09:36,899 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:09:36,899 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,900 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,900 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (33.382 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,900 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,904 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,905 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,908 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,908 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,908 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,912 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,914 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,914 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,916 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,916 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,919 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,920 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,921 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,921 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,922 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,922 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,922 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,922 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,923 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,923 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,923 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,923 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,923 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,923 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,924 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,925 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,925 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,925 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,925 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,927 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,928 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,929 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,929 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:09:36,929 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (28.860 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-07 00:09:36,935 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:09:36,937 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:09:36,939 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:09:36,942 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-07 00:09:36,942 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:09:36,949 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (136.174 ms) | |
| galaxy.queue_worker INFO 2020-05-07 00:09:36,956 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-07 00:09:36,957 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-07 00:09:36,968 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (11.547 ms) | |
| galaxy.config WARNING 2020-05-07 00:10:26,140 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Waiting for toolbox reload timed out after 60 seconds | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:10:26,152 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __dropletutils-scripts@0.0.4=1 dropletutils-scripts=0.0.4=1 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| done | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_conda/envs/__dropletutils-scripts@0.0.4=1 | |
| added / updated specs: | |
| - dropletutils-scripts==0.0.4=1 | |
| The following NEW packages will be INSTALLED: | |
| _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge | |
| _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_llvm | |
| _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 | |
| binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.34-h53a641e_0 | |
| binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.34-hc952b39_18 | |
| bioconductor-beac~ bioconda/linux-64::bioconductor-beachmat-2.0.0-r36he1b5a44_1 | |
| bioconductor-biob~ bioconda/linux-64::bioconductor-biobase-2.44.0-r36h516909a_1 | |
| bioconductor-bioc~ bioconda/noarch::bioconductor-biocgenerics-0.30.0-r36_1 | |
| bioconductor-bioc~ bioconda/linux-64::bioconductor-biocparallel-1.18.0-r36he1b5a44_1 | |
| bioconductor-dela~ bioconda/linux-64::bioconductor-delayedarray-0.10.0-r36h516909a_1 | |
| bioconductor-drop~ bioconda/linux-64::bioconductor-dropletutils-1.4.2-r36he1b5a44_0 | |
| bioconductor-edger bioconda/linux-64::bioconductor-edger-3.26.5-r36he1b5a44_0 | |
| bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodb-1.20.0-r36_1 | |
| bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodbdata-1.2.2-r36_0 | |
| bioconductor-geno~ bioconda/linux-64::bioconductor-genomicranges-1.36.0-r36h516909a_1 | |
| bioconductor-hdf5~ bioconda/linux-64::bioconductor-hdf5array-1.12.1-r36h516909a_0 | |
| bioconductor-iran~ bioconda/linux-64::bioconductor-iranges-2.18.2-r36h516909a_0 | |
| bioconductor-limma bioconda/linux-64::bioconductor-limma-3.40.2-r36h516909a_0 | |
| bioconductor-rhdf5 bioconda/linux-64::bioconductor-rhdf5-2.28.0-r36he1b5a44_1 | |
| bioconductor-rhdf~ bioconda/linux-64::bioconductor-rhdf5lib-1.6.0-r36h516909a_1 | |
| bioconductor-s4ve~ bioconda/linux-64::bioconductor-s4vectors-0.22.0-r36h516909a_1 | |
| bioconductor-sing~ bioconda/noarch::bioconductor-singlecellexperiment-1.6.0-r36_1 | |
| bioconductor-summ~ bioconda/noarch::bioconductor-summarizedexperiment-1.14.0-r36_1 | |
| bioconductor-xvec~ bioconda/linux-64::bioconductor-xvector-0.24.0-r36h516909a_1 | |
| bioconductor-zlib~ bioconda/linux-64::bioconductor-zlibbioc-1.30.0-r36h516909a_1 | |
| bwidget conda-forge/linux-64::bwidget-1.9.14-0 | |
| bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_2 | |
| ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0 | |
| cairo conda-forge/linux-64::cairo-1.16.0-hcf35c78_1003 | |
| certifi conda-forge/linux-64::certifi-2020.4.5.1-py38h32f6830_0 | |
| curl conda-forge/linux-64::curl-7.69.1-h33f0ec9_0 | |
| dropletutils-scri~ bioconda/noarch::dropletutils-scripts-0.0.4-1 | |
| fontconfig conda-forge/linux-64::fontconfig-2.13.1-h86ecdb6_1001 | |
| freetype conda-forge/linux-64::freetype-2.10.1-he06d7ca_0 | |
| fribidi conda-forge/linux-64::fribidi-1.0.9-h516909a_0 | |
| gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-7.3.0-hd420e75_5 | |
| gcc_linux-64 conda-forge/linux-64::gcc_linux-64-7.3.0-h553295d_18 | |
| gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002 | |
| gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_5 | |
| gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-7.3.0-h553295d_18 | |
| glib conda-forge/linux-64::glib-2.58.3-py38h73cb85d_1004 | |
| graphite2 conda-forge/linux-64::graphite2-1.3.13-he1b5a44_1001 | |
| gsl conda-forge/linux-64::gsl-2.6-h294904e_0 | |
| gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_5 | |
| gxx_linux-64 conda-forge/linux-64::gxx_linux-64-7.3.0-h553295d_18 | |
| harfbuzz conda-forge/linux-64::harfbuzz-2.4.0-h9f30f68_3 | |
| icu conda-forge/linux-64::icu-64.2-he1b5a44_1 | |
| jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001 | |
| krb5 conda-forge/linux-64::krb5-1.17.1-h2fd8d38_0 | |
| ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 | |
| libblas conda-forge/linux-64::libblas-3.8.0-16_openblas | |
| libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas | |
| libcurl conda-forge/linux-64::libcurl-7.69.1-hf7181ac_0 | |
| libedit conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001 | |
| libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 | |
| libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2 | |
| libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5 | |
| libgomp conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2 | |
| libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1006 | |
| liblapack conda-forge/linux-64::liblapack-3.8.0-16_openblas | |
| libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0 | |
| libpng conda-forge/linux-64::libpng-1.6.37-hed695b0_1 | |
| libssh2 conda-forge/linux-64::libssh2-1.8.2-h22169c7_2 | |
| libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2 | |
| libtiff conda-forge/linux-64::libtiff-4.1.0-hc7e4089_6 | |
| libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000 | |
| libwebp-base conda-forge/linux-64::libwebp-base-1.1.0-h516909a_3 | |
| libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002 | |
| libxml2 conda-forge/linux-64::libxml2-2.9.10-hee79883_0 | |
| llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0 | |
| lz4-c conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_1 | |
| make conda-forge/linux-64::make-4.3-h516909a_0 | |
| ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002 | |
| openblas conda-forge/linux-64::openblas-0.3.9-he1df0ab_0 | |
| openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_0 | |
| pango conda-forge/linux-64::pango-1.42.4-h7062337_4 | |
| pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0 | |
| pip conda-forge/noarch::pip-20.1-pyh9f0ad1d_0 | |
| pixman conda-forge/linux-64::pixman-0.38.0-h516909a_1003 | |
| pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001 | |
| python conda-forge/linux-64::python-3.8.2-he5300dc_7_cpython | |
| python_abi conda-forge/linux-64::python_abi-3.8-1_cp38 | |
| r-base conda-forge/linux-64::r-base-3.6.3-h316533a_2 | |
| r-bh conda-forge/noarch::r-bh-1.72.0_3-r36h6115d3f_1 | |
| r-bitops conda-forge/linux-64::r-bitops-1.0_6-r36hcdcec82_1004 | |
| r-dqrng conda-forge/linux-64::r-dqrng-0.2.1-r36h0357c0b_2 | |
| r-formatr conda-forge/noarch::r-formatr-1.7-r36h6115d3f_2 | |
| r-futile.logger conda-forge/noarch::r-futile.logger-1.4.3-r36h6115d3f_1003 | |
| r-futile.options conda-forge/noarch::r-futile.options-1.0.1-r36h6115d3f_1002 | |
| r-getopt conda-forge/noarch::r-getopt-1.20.3-r36_2 | |
| r-lambda.r conda-forge/noarch::r-lambda.r-1.2.4-r36h6115d3f_1 | |
| r-lattice conda-forge/linux-64::r-lattice-0.20_41-r36hcdcec82_2 | |
| r-locfit conda-forge/linux-64::r-locfit-1.5_9.4-r36hcdcec82_1 | |
| r-matrix conda-forge/linux-64::r-matrix-1.2_18-r36h7fa42b6_3 | |
| r-matrixstats conda-forge/linux-64::r-matrixstats-0.56.0-r36hcdcec82_1 | |
| r-optparse conda-forge/noarch::r-optparse-1.6.6-r36h6115d3f_1 | |
| r-r.methodss3 conda-forge/noarch::r-r.methodss3-1.8.0-r36h6115d3f_1 | |
| r-r.oo conda-forge/noarch::r-r.oo-1.23.0-r36h6115d3f_1 | |
| r-r.utils conda-forge/noarch::r-r.utils-2.9.2-r36h6115d3f_1 | |
| r-rcpp conda-forge/linux-64::r-rcpp-1.0.4.6-r36h0357c0b_1 | |
| r-rcurl conda-forge/linux-64::r-rcurl-1.98_1.2-r36hcdcec82_1 | |
| r-sitmo conda-forge/linux-64::r-sitmo-2.0.1-r36h0357c0b_2 | |
| r-snow conda-forge/noarch::r-snow-0.4_3-r36h6115d3f_1002 | |
| r-workflowscripts~ bioconda/noarch::r-workflowscriptscommon-0.0.7-r36_0 | |
| readline conda-forge/linux-64::readline-8.0-hf8c457e_0 | |
| sed conda-forge/linux-64::sed-4.7-h1bed415_1000 | |
| setuptools conda-forge/linux-64::setuptools-46.1.3-py38h32f6830_0 | |
| sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0 | |
| tk conda-forge/linux-64::tk-8.6.10-hed695b0_0 | |
| tktable conda-forge/linux-64::tktable-2.10-h555a92e_3 | |
| wheel conda-forge/noarch::wheel-0.34.2-py_1 | |
| xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002 | |
| xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0 | |
| xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000 | |
| xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0 | |
| xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0 | |
| xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0 | |
| xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0 | |
| xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002 | |
| xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002 | |
| xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002 | |
| xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007 | |
| xz conda-forge/linux-64::xz-5.2.5-h516909a_0 | |
| zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1006 | |
| zstd conda-forge/linux-64::zstd-1.4.4-h6597ccf_3 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... | |
| ==> WARNING: A newer version of conda exists. <== | |
| current version: 4.6.14 | |
| latest version: 4.8.3 | |
| Please update conda by running | |
| $ conda update -n base conda | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:11:36,631 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda clean --tarballs -y | |
| Cache location: | |
| There are no tarballs to remove | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:11:37,614 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda list --name __r@_uv_ --export > '*******/galaxy/shared/galaxy_wd/tmp/jobdepslx0as6zzd72ce9470954fded9b6320d7553894dbc2685dfc709bc40fe22113cf16375d6a/__r@_uv_' | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:11:38,792 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda install -y --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix *******/galaxy/shared/_cache/7717432d --file *******/galaxy/shared/galaxy_wd/tmp/jobdepslx0as6zzd72ce9470954fded9b6320d7553894dbc2685dfc709bc40fe22113cf16375d6a/__r@_uv_ | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_cache/7717432d | |
| added / updated specs: | |
| - _libgcc_mutex==0.1=conda_forge | |
| - _openmp_mutex==4.5=1_llvm | |
| - _r-mutex==1.0.1=anacondar_1 | |
| - binutils_impl_linux-64==2.34=h53a641e_0 | |
| - binutils_linux-64==2.34=hc952b39_18 | |
| - bwidget==1.9.14=0 | |
| - bzip2==1.0.8=h516909a_2 | |
| - ca-certificates==2020.4.5.1=hecc5488_0 | |
| - cairo==1.16.0=hcf35c78_1003 | |
| - certifi==2020.4.5.1=py38h32f6830_0 | |
| - curl==7.69.1=h33f0ec9_0 | |
| - fontconfig==2.13.1=h86ecdb6_1001 | |
| - freetype==2.10.1=he06d7ca_0 | |
| - fribidi==1.0.9=h516909a_0 | |
| - gcc_impl_linux-64==7.3.0=hd420e75_5 | |
| - gcc_linux-64==7.3.0=h553295d_18 | |
| - gettext==0.19.8.1=hc5be6a0_1002 | |
| - gfortran_impl_linux-64==7.3.0=hdf63c60_5 | |
| - gfortran_linux-64==7.3.0=h553295d_18 | |
| - glib==2.64.2=h6f030ca_0 | |
| - graphite2==1.3.13=he1b5a44_1001 | |
| - gsl==2.6=h294904e_0 | |
| - gxx_impl_linux-64==7.3.0=hdf63c60_5 | |
| - gxx_linux-64==7.3.0=h553295d_18 | |
| - harfbuzz==2.4.0=h9f30f68_3 | |
| - icu==64.2=he1b5a44_1 | |
| - jpeg==9c=h14c3975_1001 | |
| - krb5==1.17.1=h2fd8d38_0 | |
| - ld_impl_linux-64==2.34=h53a641e_0 | |
| - libblas==3.8.0=16_openblas | |
| - libcblas==3.8.0=16_openblas | |
| - libcurl==7.69.1=hf7181ac_0 | |
| - libedit==3.1.20170329=hf8c457e_1001 | |
| - libffi==3.2.1=he1b5a44_1007 | |
| - libgcc-ng==9.2.0=h24d8f2e_2 | |
| - libgfortran-ng==7.3.0=hdf63c60_5 | |
| - libgomp==9.2.0=h24d8f2e_2 | |
| - libiconv==1.15=h516909a_1006 | |
| - liblapack==3.8.0=16_openblas | |
| - libopenblas==0.3.9=h5ec1e0e_0 | |
| - libpng==1.6.37=hed695b0_1 | |
| - libssh2==1.8.2=h22169c7_2 | |
| - libstdcxx-ng==9.2.0=hdf63c60_2 | |
| - libtiff==4.1.0=hc7e4089_6 | |
| - libuuid==2.32.1=h14c3975_1000 | |
| - libwebp-base==1.1.0=h516909a_3 | |
| - libxcb==1.13=h14c3975_1002 | |
| - libxml2==2.9.10=hee79883_0 | |
| - llvm-openmp==10.0.0=hc9558a2_0 | |
| - lz4-c==1.9.2=he1b5a44_1 | |
| - make==4.3=h516909a_0 | |
| - ncurses==6.1=hf484d3e_1002 | |
| - openssl==1.1.1g=h516909a_0 | |
| - pango==1.42.4=h7062337_4 | |
| - pcre==8.44=he1b5a44_0 | |
| - pip==20.1=pyh9f0ad1d_0 | |
| - pixman==0.38.0=h516909a_1003 | |
| - pthread-stubs==0.4=h14c3975_1001 | |
| - python==3.8.2=he5300dc_7_cpython | |
| - python_abi==3.8=1_cp38 | |
| - r-base==3.6.3=h316533a_2 | |
| - r-boot==1.3_25=r36h6115d3f_1 | |
| - r-class==7.3_17=r36hcdcec82_1 | |
| - r-cluster==2.1.0=r36h9bbef5b_3 | |
| - r-codetools==0.2_16=r36h6115d3f_1002 | |
| - r-foreign==0.8_76=r36hcdcec82_1 | |
| - r-kernsmooth==2.23_17=r36hfa343cc_1 | |
| - r-lattice==0.20_41=r36hcdcec82_2 | |
| - r-mass==7.3_51.6=r36hcdcec82_2 | |
| - r-matrix==1.2_18=r36h7fa42b6_3 | |
| - r-mgcv==1.8_31=r36h7fa42b6_1 | |
| - r-nlme==3.1_147=r36h9bbef5b_1 | |
| - r-nnet==7.3_14=r36hcdcec82_1 | |
| - r-recommended==3.6=r36_1004 | |
| - r-rpart==4.1_15=r36hcdcec82_2 | |
| - r-spatial==7.3_12=r36hcdcec82_1 | |
| - r-survival==3.1_12=r36hcdcec82_1 | |
| - r==3.6=r36_1003 | |
| - readline==8.0=hf8c457e_0 | |
| - sed==4.7=h1bed415_1000 | |
| - setuptools==46.1.3=py38h32f6830_0 | |
| - sqlite==3.30.1=hcee41ef_0 | |
| - tk==8.6.10=hed695b0_0 | |
| - tktable==2.10=h555a92e_3 | |
| - wheel==0.34.2=py_1 | |
| - xorg-kbproto==1.0.7=h14c3975_1002 | |
| - xorg-libice==1.0.10=h516909a_0 | |
| - xorg-libsm==1.2.3=h84519dc_1000 | |
| - xorg-libx11==1.6.9=h516909a_0 | |
| - xorg-libxau==1.0.9=h14c3975_0 | |
| - xorg-libxdmcp==1.1.3=h516909a_0 | |
| - xorg-libxext==1.3.4=h516909a_0 | |
| - xorg-libxrender==0.9.10=h516909a_1002 | |
| - xorg-renderproto==0.11.1=h14c3975_1002 | |
| - xorg-xextproto==7.3.0=h14c3975_1002 | |
| - xorg-xproto==7.0.31=h14c3975_1007 | |
| - xz==5.2.5=h516909a_0 | |
| - zlib==1.2.11=h516909a_1006 | |
| - zstd==1.4.4=h6597ccf_3 | |
| The following packages will be UPDATED: | |
| glib 2.58.3-py38h73cb85d_1004 --> 2.64.2-h6f030ca_0 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| ==> WARNING: A newer version of conda exists. <== | |
| current version: 4.6.14 | |
| latest version: 4.8.3 | |
| Please update conda by running | |
| $ conda update -n base conda | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:11:54,549 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda clean --tarballs -y | |
| Cache location: | |
| There are no tarballs to remove | |
| 10.25.100.188 - - [07/May/2020:00:02:23 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| Thu May 7 00:11:55 2020 - SIGPIPE: writing to a closed pipe/socket/fd (probably the client disconnected) on request /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b (ip 10.25.100.188) !!! | |
| Thu May 7 00:11:55 2020 - uwsgi_response_writev_headers_and_body_do(): Broken pipe [core/writer.c line 306] during POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b (10.25.100.188) | |
| OSError: write error | |
| [pid: 28741|app: 0|req: 63/211] 10.25.100.188 () {42 vars in 751 bytes} [Thu May 7 00:02:23 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 0 bytes in 572039 msecs (HTTP/1.1 200) 3 headers in 0 bytes (0 switches on core 0) | |
| done | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:12:04,853 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency dropletutils-scripts version 0.0.4=1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:12:04,855 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency dropletutils-scripts version 0.0.4=1 of type conda | |
| 10.25.100.188 - - [07/May/2020:00:08:44 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28743|app: 0|req: 25/212] 10.25.100.188 () {42 vars in 751 bytes} [Thu May 7 00:08:44 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 651 bytes in 199904 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| 10.25.100.188 - - [07/May/2020:00:12:05 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28737|app: 0|req: 44/213] 10.25.100.188 () {42 vars in 751 bytes} [Thu May 7 00:12:05 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 131 bytes in 644 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:12:07,282 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:09,721 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-07 00:12:09,727 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Adding new row for repository 'gtf2gene_list' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:12:09,733 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:09,733 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:09,761 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-07 00:12:09,769 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list' at 5:00ee933b08fd | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:20,426 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy5, version: 1.42.1+galaxy5 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-07 00:12:20,427 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-07 00:12:20,448 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-07 00:12:20,645 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-07 00:12:20,645 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-07 00:12:30,777 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-07 00:12:30,783 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-07 00:12:31,514 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:12:31,515 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-07 00:12:31,561 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:12:31,562 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,563 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:12:31,577 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:12:31,579 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:12:31,582 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-07 00:12:31,582 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:12:31,582 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,584 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-07 00:12:31,585 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:12:31,585 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,586 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools WARNING 2020-05-07 00:12:31,593 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:12:31,593 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,594 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,595 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (33.792 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,595 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,599 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,599 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,602 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,603 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,603 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,606 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,608 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,609 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,610 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,611 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,613 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,614 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,615 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,615 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,616 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,616 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,616 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,616 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,617 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,617 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,617 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,617 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,617 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,618 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,618 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,619 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy5, version: 1.42.1+galaxy5 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,620 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,620 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,620 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,620 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,621 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,623 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,623 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,624 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:12:31,624 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (29.064 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-07 00:12:31,631 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:12:31,633 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:12:31,635 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:12:31,637 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-07 00:12:31,637 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:12:31,645 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (130.813 ms) | |
| galaxy.queue_worker INFO 2020-05-07 00:12:31,654 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-07 00:12:31,654 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-07 00:12:31,680 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (26.519 ms) | |
| galaxy.config WARNING 2020-05-07 00:13:20,466 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Waiting for toolbox reload timed out after 60 seconds | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:13:20,478 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-f6e6a76a531c3b91ff1827ba0684329e9d85716dc0c75cb25ed9479e13ba2e5b bioconductor-rtracklayer=1.42.1 bioconductor-biostrings r-optparse | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_conda/envs/mulled-v1-f6e6a76a531c3b91ff1827ba0684329e9d85716dc0c75cb25ed9479e13ba2e5b | |
| added / updated specs: | |
| - bioconductor-biostrings | |
| - bioconductor-rtracklayer=1.42.1 | |
| - r-optparse | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| bioconductor-biobase-2.42.0| r351h14c3975_1 2.3 MB bioconda | |
| bioconductor-biocgenerics-0.28.0| r351_1 695 KB bioconda | |
| bioconductor-biocparallel-1.16.6| r351h1c2f66e_0 1.1 MB bioconda | |
| bioconductor-biostrings-2.50.2| r351h14c3975_0 13.8 MB bioconda | |
| bioconductor-delayedarray-0.8.0| r351h14c3975_0 1.6 MB bioconda | |
| bioconductor-genomeinfodb-1.18.1| r351_0 3.8 MB bioconda | |
| bioconductor-genomeinfodbdata-1.2.1| r351_0 6 KB bioconda | |
| bioconductor-genomicalignments-1.18.1| r351h14c3975_0 2.2 MB bioconda | |
| bioconductor-genomicranges-1.34.0| r351h14c3975_0 2.1 MB bioconda | |
| bioconductor-iranges-2.16.0| r351h14c3975_0 2.3 MB bioconda | |
| bioconductor-rsamtools-1.34.0| r351hf484d3e_0 3.8 MB bioconda | |
| bioconductor-rtracklayer-1.42.1| r351h9d9f1b6_1 2.7 MB bioconda | |
| bioconductor-s4vectors-0.20.1| r351h14c3975_0 2.0 MB bioconda | |
| bioconductor-summarizedexperiment-1.12.0| r351_0 2.6 MB bioconda | |
| bioconductor-xvector-0.22.0| r351h14c3975_0 711 KB bioconda | |
| bioconductor-zlibbioc-1.28.0| r351h14c3975_0 112 KB bioconda | |
| curl-7.68.0 | hf8cf82a_0 137 KB conda-forge | |
| gsl-2.5 | h294904e_1 2.7 MB conda-forge | |
| krb5-1.16.4 | h2fd8d38_0 1.4 MB conda-forge | |
| libcurl-7.68.0 | hda55be3_0 564 KB conda-forge | |
| r-base-3.5.1 | hc461eb7_1012 30.4 MB conda-forge | |
| r-bh-1.72.0_3 | r35h6115d3f_0 10.5 MB conda-forge | |
| r-bitops-1.0_6 | r35hcdcec82_1003 39 KB conda-forge | |
| r-formatr-1.7 | r35h6115d3f_1 165 KB conda-forge | |
| r-futile.logger-1.4.3 | r35h6115d3f_1002 107 KB conda-forge | |
| r-futile.options-1.0.1 | r35h6115d3f_1001 23 KB conda-forge | |
| r-getopt-1.20.3 | r35_1 39 KB conda-forge | |
| r-lambda.r-1.2.4 | r35h6115d3f_0 118 KB conda-forge | |
| r-lattice-0.20_41 | r35hcdcec82_1 1.1 MB conda-forge | |
| r-matrix-1.2_18 | r35h7fa42b6_2 3.8 MB conda-forge | |
| r-matrixstats-0.56.0 | r35hcdcec82_0 907 KB conda-forge | |
| r-optparse-1.6.6 | r35h6115d3f_0 78 KB conda-forge | |
| r-rcurl-1.98_1.2 | r35hcdcec82_0 867 KB conda-forge | |
| r-snow-0.4_3 | r35h6115d3f_1001 122 KB conda-forge | |
| r-xml-3.99_0.3 | r35hcdcec82_0 1.7 MB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 96.6 MB | |
| The following NEW packages will be INSTALLED: | |
| _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge | |
| _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_llvm | |
| _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 | |
| binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.34-h53a641e_0 | |
| binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.34-hc952b39_18 | |
| bioconductor-biob~ bioconda/linux-64::bioconductor-biobase-2.42.0-r351h14c3975_1 | |
| bioconductor-bioc~ bioconda/noarch::bioconductor-biocgenerics-0.28.0-r351_1 | |
| bioconductor-bioc~ bioconda/linux-64::bioconductor-biocparallel-1.16.6-r351h1c2f66e_0 | |
| bioconductor-bios~ bioconda/linux-64::bioconductor-biostrings-2.50.2-r351h14c3975_0 | |
| bioconductor-dela~ bioconda/linux-64::bioconductor-delayedarray-0.8.0-r351h14c3975_0 | |
| bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodb-1.18.1-r351_0 | |
| bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodbdata-1.2.1-r351_0 | |
| bioconductor-geno~ bioconda/linux-64::bioconductor-genomicalignments-1.18.1-r351h14c3975_0 | |
| bioconductor-geno~ bioconda/linux-64::bioconductor-genomicranges-1.34.0-r351h14c3975_0 | |
| bioconductor-iran~ bioconda/linux-64::bioconductor-iranges-2.16.0-r351h14c3975_0 | |
| bioconductor-rsam~ bioconda/linux-64::bioconductor-rsamtools-1.34.0-r351hf484d3e_0 | |
| bioconductor-rtra~ bioconda/linux-64::bioconductor-rtracklayer-1.42.1-r351h9d9f1b6_1 | |
| bioconductor-s4ve~ bioconda/linux-64::bioconductor-s4vectors-0.20.1-r351h14c3975_0 | |
| bioconductor-summ~ bioconda/noarch::bioconductor-summarizedexperiment-1.12.0-r351_0 | |
| bioconductor-xvec~ bioconda/linux-64::bioconductor-xvector-0.22.0-r351h14c3975_0 | |
| bioconductor-zlib~ bioconda/linux-64::bioconductor-zlibbioc-1.28.0-r351h14c3975_0 | |
| bwidget conda-forge/linux-64::bwidget-1.9.14-0 | |
| bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_2 | |
| ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0 | |
| cairo conda-forge/linux-64::cairo-1.16.0-hcf35c78_1003 | |
| certifi conda-forge/linux-64::certifi-2020.4.5.1-py38h32f6830_0 | |
| curl conda-forge/linux-64::curl-7.68.0-hf8cf82a_0 | |
| fontconfig conda-forge/linux-64::fontconfig-2.13.1-h86ecdb6_1001 | |
| freetype conda-forge/linux-64::freetype-2.10.1-he06d7ca_0 | |
| fribidi conda-forge/linux-64::fribidi-1.0.9-h516909a_0 | |
| gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-7.3.0-hd420e75_5 | |
| gcc_linux-64 conda-forge/linux-64::gcc_linux-64-7.3.0-h553295d_18 | |
| gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002 | |
| gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_5 | |
| gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-7.3.0-h553295d_18 | |
| glib conda-forge/linux-64::glib-2.58.3-py38h73cb85d_1004 | |
| graphite2 conda-forge/linux-64::graphite2-1.3.13-he1b5a44_1001 | |
| gsl conda-forge/linux-64::gsl-2.5-h294904e_1 | |
| gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_5 | |
| gxx_linux-64 conda-forge/linux-64::gxx_linux-64-7.3.0-h553295d_18 | |
| harfbuzz conda-forge/linux-64::harfbuzz-2.4.0-h9f30f68_3 | |
| icu conda-forge/linux-64::icu-64.2-he1b5a44_1 | |
| jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001 | |
| krb5 conda-forge/linux-64::krb5-1.16.4-h2fd8d38_0 | |
| ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 | |
| libblas conda-forge/linux-64::libblas-3.8.0-16_openblas | |
| libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas | |
| libcurl conda-forge/linux-64::libcurl-7.68.0-hda55be3_0 | |
| libedit conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001 | |
| libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 | |
| libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2 | |
| libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5 | |
| libgomp conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2 | |
| libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1006 | |
| liblapack conda-forge/linux-64::liblapack-3.8.0-16_openblas | |
| libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0 | |
| libpng conda-forge/linux-64::libpng-1.6.37-hed695b0_1 | |
| libssh2 conda-forge/linux-64::libssh2-1.8.2-h22169c7_2 | |
| libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2 | |
| libtiff conda-forge/linux-64::libtiff-4.1.0-hc7e4089_6 | |
| libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000 | |
| libwebp-base conda-forge/linux-64::libwebp-base-1.1.0-h516909a_3 | |
| libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002 | |
| libxml2 conda-forge/linux-64::libxml2-2.9.10-hee79883_0 | |
| llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0 | |
| lz4-c conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_1 | |
| make conda-forge/linux-64::make-4.3-h516909a_0 | |
| ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002 | |
| openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_0 | |
| pango conda-forge/linux-64::pango-1.42.4-h7062337_4 | |
| pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0 | |
| pip conda-forge/noarch::pip-20.1-pyh9f0ad1d_0 | |
| pixman conda-forge/linux-64::pixman-0.38.0-h516909a_1003 | |
| pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001 | |
| python conda-forge/linux-64::python-3.8.2-he5300dc_7_cpython | |
| python_abi conda-forge/linux-64::python_abi-3.8-1_cp38 | |
| r-base conda-forge/linux-64::r-base-3.5.1-hc461eb7_1012 | |
| r-bh conda-forge/noarch::r-bh-1.72.0_3-r35h6115d3f_0 | |
| r-bitops conda-forge/linux-64::r-bitops-1.0_6-r35hcdcec82_1003 | |
| r-formatr conda-forge/noarch::r-formatr-1.7-r35h6115d3f_1 | |
| r-futile.logger conda-forge/noarch::r-futile.logger-1.4.3-r35h6115d3f_1002 | |
| r-futile.options conda-forge/noarch::r-futile.options-1.0.1-r35h6115d3f_1001 | |
| r-getopt conda-forge/noarch::r-getopt-1.20.3-r35_1 | |
| r-lambda.r conda-forge/noarch::r-lambda.r-1.2.4-r35h6115d3f_0 | |
| r-lattice conda-forge/linux-64::r-lattice-0.20_41-r35hcdcec82_1 | |
| r-matrix conda-forge/linux-64::r-matrix-1.2_18-r35h7fa42b6_2 | |
| r-matrixstats conda-forge/linux-64::r-matrixstats-0.56.0-r35hcdcec82_0 | |
| r-optparse conda-forge/noarch::r-optparse-1.6.6-r35h6115d3f_0 | |
| r-rcurl conda-forge/linux-64::r-rcurl-1.98_1.2-r35hcdcec82_0 | |
| r-snow conda-forge/noarch::r-snow-0.4_3-r35h6115d3f_1001 | |
| r-xml conda-forge/linux-64::r-xml-3.99_0.3-r35hcdcec82_0 | |
| readline conda-forge/linux-64::readline-8.0-hf8c457e_0 | |
| setuptools conda-forge/linux-64::setuptools-46.1.3-py38h32f6830_0 | |
| sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0 | |
| tk conda-forge/linux-64::tk-8.6.10-hed695b0_0 | |
| tktable conda-forge/linux-64::tktable-2.10-h555a92e_3 | |
| wheel conda-forge/noarch::wheel-0.34.2-py_1 | |
| xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002 | |
| xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0 | |
| xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000 | |
| xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0 | |
| xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0 | |
| xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0 | |
| xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0 | |
| xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002 | |
| xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002 | |
| xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002 | |
| xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007 | |
| xz conda-forge/linux-64::xz-5.2.5-h516909a_0 | |
| zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1006 | |
| zstd conda-forge/linux-64::zstd-1.4.4-h6597ccf_3 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:16:40,403 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Using dependency bioconductor-rtracklayer version 1.42.1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:16:40,403 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Using dependency bioconductor-biostrings version None of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:16:40,404 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Using dependency r-optparse version None of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:16:40,405 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Using dependency bioconductor-rtracklayer version 1.42.1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:16:40,405 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Using dependency bioconductor-biostrings version None of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:16:40,405 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Using dependency r-optparse version None of type conda | |
| 10.25.100.188 - - [07/May/2020:00:12:06 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28739|app: 0|req: 82/214] 10.25.100.188 () {42 vars in 751 bytes} [Thu May 7 00:12:06 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 630 bytes in 273772 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:16:41,748 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:16:43,383 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-07 00:16:43,389 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Adding new row for repository 'gtf2gene_list' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:16:43,395 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:16:43,396 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:16:43,426 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-07 00:16:43,434 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list' at 0:040d4b3a19d5 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:16:54,019 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy0, version: 1.42.1+galaxy0 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-07 00:16:54,020 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-07 00:16:54,049 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-07 00:16:54,058 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-07 00:16:54,058 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-07 00:17:04,196 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-07 00:17:04,200 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-07 00:17:04,635 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:17:04,635 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-07 00:17:04,742 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:17:04,742 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,744 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:17:04,759 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:17:04,762 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:17:04,765 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-07 00:17:04,765 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:17:04,766 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,767 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-07 00:17:04,768 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:17:04,768 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,770 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools WARNING 2020-05-07 00:17:04,776 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:17:04,776 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,777 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,778 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (37.060 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,778 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,782 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,782 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,785 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,786 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,786 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,790 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,791 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,792 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,793 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,794 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,797 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,798 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,798 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,799 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,800 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,800 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,800 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,800 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,801 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,801 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,801 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,801 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,801 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,801 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,802 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,804 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,804 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,804 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,804 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,806 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,807 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,808 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,808 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:17:04,808 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (30.452 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-07 00:17:04,815 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:17:04,817 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:17:04,820 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:17:04,822 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-07 00:17:04,822 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:17:04,832 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (196.973 ms) | |
| galaxy.queue_worker INFO 2020-05-07 00:17:04,842 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-07 00:17:04,843 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-07 00:17:04,855 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (12.502 ms) | |
| galaxy.config WARNING 2020-05-07 00:17:54,065 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Waiting for toolbox reload timed out after 60 seconds | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:17:54,076 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __bioconductor-rtracklayer@1.42.1 bioconductor-rtracklayer=1.42.1 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_conda/envs/__bioconductor-rtracklayer@1.42.1 | |
| added / updated specs: | |
| - bioconductor-rtracklayer=1.42.1 | |
| The following NEW packages will be INSTALLED: | |
| _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge | |
| _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_llvm | |
| _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 | |
| binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.34-h53a641e_0 | |
| binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.34-hc952b39_18 | |
| bioconductor-biob~ bioconda/linux-64::bioconductor-biobase-2.42.0-r351h14c3975_1 | |
| bioconductor-bioc~ bioconda/noarch::bioconductor-biocgenerics-0.28.0-r351_1 | |
| bioconductor-bioc~ bioconda/linux-64::bioconductor-biocparallel-1.16.6-r351h1c2f66e_0 | |
| bioconductor-bios~ bioconda/linux-64::bioconductor-biostrings-2.50.2-r351h14c3975_0 | |
| bioconductor-dela~ bioconda/linux-64::bioconductor-delayedarray-0.8.0-r351h14c3975_0 | |
| bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodb-1.18.1-r351_0 | |
| bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodbdata-1.2.1-r351_0 | |
| bioconductor-geno~ bioconda/linux-64::bioconductor-genomicalignments-1.18.1-r351h14c3975_0 | |
| bioconductor-geno~ bioconda/linux-64::bioconductor-genomicranges-1.34.0-r351h14c3975_0 | |
| bioconductor-iran~ bioconda/linux-64::bioconductor-iranges-2.16.0-r351h14c3975_0 | |
| bioconductor-rsam~ bioconda/linux-64::bioconductor-rsamtools-1.34.0-r351hf484d3e_0 | |
| bioconductor-rtra~ bioconda/linux-64::bioconductor-rtracklayer-1.42.1-r351h9d9f1b6_1 | |
| bioconductor-s4ve~ bioconda/linux-64::bioconductor-s4vectors-0.20.1-r351h14c3975_0 | |
| bioconductor-summ~ bioconda/noarch::bioconductor-summarizedexperiment-1.12.0-r351_0 | |
| bioconductor-xvec~ bioconda/linux-64::bioconductor-xvector-0.22.0-r351h14c3975_0 | |
| bioconductor-zlib~ bioconda/linux-64::bioconductor-zlibbioc-1.28.0-r351h14c3975_0 | |
| bwidget conda-forge/linux-64::bwidget-1.9.14-0 | |
| bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_2 | |
| ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0 | |
| cairo conda-forge/linux-64::cairo-1.16.0-hcf35c78_1003 | |
| certifi conda-forge/linux-64::certifi-2020.4.5.1-py38h32f6830_0 | |
| curl conda-forge/linux-64::curl-7.68.0-hf8cf82a_0 | |
| fontconfig conda-forge/linux-64::fontconfig-2.13.1-h86ecdb6_1001 | |
| freetype conda-forge/linux-64::freetype-2.10.1-he06d7ca_0 | |
| fribidi conda-forge/linux-64::fribidi-1.0.9-h516909a_0 | |
| gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-7.3.0-hd420e75_5 | |
| gcc_linux-64 conda-forge/linux-64::gcc_linux-64-7.3.0-h553295d_18 | |
| gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002 | |
| gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_5 | |
| gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-7.3.0-h553295d_18 | |
| glib conda-forge/linux-64::glib-2.58.3-py38h73cb85d_1004 | |
| graphite2 conda-forge/linux-64::graphite2-1.3.13-he1b5a44_1001 | |
| gsl conda-forge/linux-64::gsl-2.5-h294904e_1 | |
| gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_5 | |
| gxx_linux-64 conda-forge/linux-64::gxx_linux-64-7.3.0-h553295d_18 | |
| harfbuzz conda-forge/linux-64::harfbuzz-2.4.0-h9f30f68_3 | |
| icu conda-forge/linux-64::icu-64.2-he1b5a44_1 | |
| jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001 | |
| krb5 conda-forge/linux-64::krb5-1.16.4-h2fd8d38_0 | |
| ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 | |
| libblas conda-forge/linux-64::libblas-3.8.0-16_openblas | |
| libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas | |
| libcurl conda-forge/linux-64::libcurl-7.68.0-hda55be3_0 | |
| libedit conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001 | |
| libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 | |
| libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2 | |
| libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5 | |
| libgomp conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2 | |
| libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1006 | |
| liblapack conda-forge/linux-64::liblapack-3.8.0-16_openblas | |
| libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0 | |
| libpng conda-forge/linux-64::libpng-1.6.37-hed695b0_1 | |
| libssh2 conda-forge/linux-64::libssh2-1.8.2-h22169c7_2 | |
| libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2 | |
| libtiff conda-forge/linux-64::libtiff-4.1.0-hc7e4089_6 | |
| libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000 | |
| libwebp-base conda-forge/linux-64::libwebp-base-1.1.0-h516909a_3 | |
| libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002 | |
| libxml2 conda-forge/linux-64::libxml2-2.9.10-hee79883_0 | |
| llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0 | |
| lz4-c conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_1 | |
| make conda-forge/linux-64::make-4.3-h516909a_0 | |
| ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002 | |
| openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_0 | |
| pango conda-forge/linux-64::pango-1.42.4-h7062337_4 | |
| pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0 | |
| pip conda-forge/noarch::pip-20.1-pyh9f0ad1d_0 | |
| pixman conda-forge/linux-64::pixman-0.38.0-h516909a_1003 | |
| pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001 | |
| python conda-forge/linux-64::python-3.8.2-he5300dc_7_cpython | |
| python_abi conda-forge/linux-64::python_abi-3.8-1_cp38 | |
| r-base conda-forge/linux-64::r-base-3.5.1-hc461eb7_1012 | |
| r-bh conda-forge/noarch::r-bh-1.72.0_3-r35h6115d3f_0 | |
| r-bitops conda-forge/linux-64::r-bitops-1.0_6-r35hcdcec82_1003 | |
| r-formatr conda-forge/noarch::r-formatr-1.7-r35h6115d3f_1 | |
| r-futile.logger conda-forge/noarch::r-futile.logger-1.4.3-r35h6115d3f_1002 | |
| r-futile.options conda-forge/noarch::r-futile.options-1.0.1-r35h6115d3f_1001 | |
| r-lambda.r conda-forge/noarch::r-lambda.r-1.2.4-r35h6115d3f_0 | |
| r-lattice conda-forge/linux-64::r-lattice-0.20_41-r35hcdcec82_1 | |
| r-matrix conda-forge/linux-64::r-matrix-1.2_18-r35h7fa42b6_2 | |
| r-matrixstats conda-forge/linux-64::r-matrixstats-0.56.0-r35hcdcec82_0 | |
| r-rcurl conda-forge/linux-64::r-rcurl-1.98_1.2-r35hcdcec82_0 | |
| r-snow conda-forge/noarch::r-snow-0.4_3-r35h6115d3f_1001 | |
| r-xml conda-forge/linux-64::r-xml-3.99_0.3-r35hcdcec82_0 | |
| readline conda-forge/linux-64::readline-8.0-hf8c457e_0 | |
| setuptools conda-forge/linux-64::setuptools-46.1.3-py38h32f6830_0 | |
| sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0 | |
| tk conda-forge/linux-64::tk-8.6.10-hed695b0_0 | |
| tktable conda-forge/linux-64::tktable-2.10-h555a92e_3 | |
| wheel conda-forge/noarch::wheel-0.34.2-py_1 | |
| xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002 | |
| xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0 | |
| xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000 | |
| xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0 | |
| xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0 | |
| xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0 | |
| xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0 | |
| xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002 | |
| xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002 | |
| xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002 | |
| xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007 | |
| xz conda-forge/linux-64::xz-5.2.5-h516909a_0 | |
| zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1006 | |
| zstd conda-forge/linux-64::zstd-1.4.4-h6597ccf_3 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:19:56,776 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency bioconductor-rtracklayer version 1.42.1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:19:56,778 [p:28741,w:3,m:0] [uWSGIWorker3Core0] Using dependency bioconductor-rtracklayer version 1.42.1 of type conda | |
| 10.25.100.188 - - [07/May/2020:00:16:40 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28741|app: 0|req: 64/215] 10.25.100.188 () {42 vars in 751 bytes} [Thu May 7 00:16:40 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 630 bytes in 195795 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:19:58,120 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:19:59,646 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-07 00:19:59,652 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Adding new row for repository 'gtf2gene_list' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:19:59,659 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:19:59,659 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:19:59,692 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-07 00:19:59,700 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list' at 6:1a642de6db01 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:10,027 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy6, version: 1.42.1+galaxy6 into tool panel.... | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-07 00:20:10,028 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-07 00:20:10,057 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-07 00:20:10,700 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-07 00:20:10,700 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-07 00:20:20,840 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-07 00:20:20,845 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-07 00:20:21,002 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:20:21,003 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-07 00:20:21,059 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:20:21,060 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,061 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:20:21,075 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:20:21,078 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:20:21,080 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-07 00:20:21,081 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:20:21,081 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,082 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-07 00:20:21,083 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:20:21,083 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,085 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools WARNING 2020-05-07 00:20:21,093 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:20:21,093 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,094 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,094 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (35.108 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,094 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,098 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,098 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,103 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,103 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,103 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,107 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,109 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,109 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,110 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,111 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,114 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,114 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,115 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,115 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,116 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,116 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,117 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,117 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,117 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,117 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,118 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,118 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,118 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,118 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,118 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,121 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy6, version: 1.42.1+galaxy6 into tool panel. | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,121 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,122 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,122 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,122 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,123 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,124 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,125 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,125 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:20:21,125 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (31.456 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-07 00:20:21,132 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:20:21,134 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:20:21,136 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:20:21,139 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-07 00:20:21,139 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:20:21,148 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (145.691 ms) | |
| galaxy.queue_worker INFO 2020-05-07 00:20:21,158 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-07 00:20:21,158 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2020-05-07 00:20:21,188 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (29.818 ms) | |
| galaxy.config WARNING 2020-05-07 00:21:10,075 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Waiting for toolbox reload timed out after 60 seconds | |
| galaxy.tool_util.deps.conda_util DEBUG 2020-05-07 00:21:10,096 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Executing command: *******/galaxy/shared/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-827534ec7721c4d7abc7ec7eb28d957e9a7e0257efe0d008674642904cb09fe3 bioconductor-rtracklayer=1.42.1 bioconductor-biostrings=2.50.2 r-optparse=1.6.4 | |
| Collecting package metadata: ...working... done | |
| Solving environment: ...working... done | |
| ## Package Plan ## | |
| environment location: *******/galaxy/shared/_conda/envs/mulled-v1-827534ec7721c4d7abc7ec7eb28d957e9a7e0257efe0d008674642904cb09fe3 | |
| added / updated specs: | |
| - bioconductor-biostrings=2.50.2 | |
| - bioconductor-rtracklayer=1.42.1 | |
| - r-optparse=1.6.4 | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| r-optparse-1.6.4 | r35h6115d3f_0 77 KB conda-forge | |
| ------------------------------------------------------------ | |
| Total: 77 KB | |
| The following NEW packages will be INSTALLED: | |
| _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge | |
| _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_llvm | |
| _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 | |
| binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.34-h53a641e_0 | |
| binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.34-hc952b39_18 | |
| bioconductor-biob~ bioconda/linux-64::bioconductor-biobase-2.42.0-r351h14c3975_1 | |
| bioconductor-bioc~ bioconda/noarch::bioconductor-biocgenerics-0.28.0-r351_1 | |
| bioconductor-bioc~ bioconda/linux-64::bioconductor-biocparallel-1.16.6-r351h1c2f66e_0 | |
| bioconductor-bios~ bioconda/linux-64::bioconductor-biostrings-2.50.2-r351h14c3975_0 | |
| bioconductor-dela~ bioconda/linux-64::bioconductor-delayedarray-0.8.0-r351h14c3975_0 | |
| bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodb-1.18.1-r351_0 | |
| bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodbdata-1.2.1-r351_0 | |
| bioconductor-geno~ bioconda/linux-64::bioconductor-genomicalignments-1.18.1-r351h14c3975_0 | |
| bioconductor-geno~ bioconda/linux-64::bioconductor-genomicranges-1.34.0-r351h14c3975_0 | |
| bioconductor-iran~ bioconda/linux-64::bioconductor-iranges-2.16.0-r351h14c3975_0 | |
| bioconductor-rsam~ bioconda/linux-64::bioconductor-rsamtools-1.34.0-r351hf484d3e_0 | |
| bioconductor-rtra~ bioconda/linux-64::bioconductor-rtracklayer-1.42.1-r351h9d9f1b6_1 | |
| bioconductor-s4ve~ bioconda/linux-64::bioconductor-s4vectors-0.20.1-r351h14c3975_0 | |
| bioconductor-summ~ bioconda/noarch::bioconductor-summarizedexperiment-1.12.0-r351_0 | |
| bioconductor-xvec~ bioconda/linux-64::bioconductor-xvector-0.22.0-r351h14c3975_0 | |
| bioconductor-zlib~ bioconda/linux-64::bioconductor-zlibbioc-1.28.0-r351h14c3975_0 | |
| bwidget conda-forge/linux-64::bwidget-1.9.14-0 | |
| bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_2 | |
| ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0 | |
| cairo conda-forge/linux-64::cairo-1.16.0-hcf35c78_1003 | |
| certifi conda-forge/linux-64::certifi-2020.4.5.1-py38h32f6830_0 | |
| curl conda-forge/linux-64::curl-7.68.0-hf8cf82a_0 | |
| fontconfig conda-forge/linux-64::fontconfig-2.13.1-h86ecdb6_1001 | |
| freetype conda-forge/linux-64::freetype-2.10.1-he06d7ca_0 | |
| fribidi conda-forge/linux-64::fribidi-1.0.9-h516909a_0 | |
| gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-7.3.0-hd420e75_5 | |
| gcc_linux-64 conda-forge/linux-64::gcc_linux-64-7.3.0-h553295d_18 | |
| gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002 | |
| gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_5 | |
| gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-7.3.0-h553295d_18 | |
| glib conda-forge/linux-64::glib-2.58.3-py38h73cb85d_1004 | |
| graphite2 conda-forge/linux-64::graphite2-1.3.13-he1b5a44_1001 | |
| gsl conda-forge/linux-64::gsl-2.5-h294904e_1 | |
| gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_5 | |
| gxx_linux-64 conda-forge/linux-64::gxx_linux-64-7.3.0-h553295d_18 | |
| harfbuzz conda-forge/linux-64::harfbuzz-2.4.0-h9f30f68_3 | |
| icu conda-forge/linux-64::icu-64.2-he1b5a44_1 | |
| jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001 | |
| krb5 conda-forge/linux-64::krb5-1.16.4-h2fd8d38_0 | |
| ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 | |
| libblas conda-forge/linux-64::libblas-3.8.0-16_openblas | |
| libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas | |
| libcurl conda-forge/linux-64::libcurl-7.68.0-hda55be3_0 | |
| libedit conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001 | |
| libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 | |
| libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2 | |
| libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5 | |
| libgomp conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2 | |
| libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1006 | |
| liblapack conda-forge/linux-64::liblapack-3.8.0-16_openblas | |
| libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0 | |
| libpng conda-forge/linux-64::libpng-1.6.37-hed695b0_1 | |
| libssh2 conda-forge/linux-64::libssh2-1.8.2-h22169c7_2 | |
| libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2 | |
| libtiff conda-forge/linux-64::libtiff-4.1.0-hc7e4089_6 | |
| libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000 | |
| libwebp-base conda-forge/linux-64::libwebp-base-1.1.0-h516909a_3 | |
| libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002 | |
| libxml2 conda-forge/linux-64::libxml2-2.9.10-hee79883_0 | |
| llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0 | |
| lz4-c conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_1 | |
| make conda-forge/linux-64::make-4.3-h516909a_0 | |
| ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002 | |
| openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_0 | |
| pango conda-forge/linux-64::pango-1.42.4-h7062337_4 | |
| pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0 | |
| pip conda-forge/noarch::pip-20.1-pyh9f0ad1d_0 | |
| pixman conda-forge/linux-64::pixman-0.38.0-h516909a_1003 | |
| pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001 | |
| python conda-forge/linux-64::python-3.8.2-he5300dc_7_cpython | |
| python_abi conda-forge/linux-64::python_abi-3.8-1_cp38 | |
| r-base conda-forge/linux-64::r-base-3.5.1-hc461eb7_1012 | |
| r-bh conda-forge/noarch::r-bh-1.72.0_3-r35h6115d3f_0 | |
| r-bitops conda-forge/linux-64::r-bitops-1.0_6-r35hcdcec82_1003 | |
| r-formatr conda-forge/noarch::r-formatr-1.7-r35h6115d3f_1 | |
| r-futile.logger conda-forge/noarch::r-futile.logger-1.4.3-r35h6115d3f_1002 | |
| r-futile.options conda-forge/noarch::r-futile.options-1.0.1-r35h6115d3f_1001 | |
| r-getopt conda-forge/noarch::r-getopt-1.20.3-r35_1 | |
| r-lambda.r conda-forge/noarch::r-lambda.r-1.2.4-r35h6115d3f_0 | |
| r-lattice conda-forge/linux-64::r-lattice-0.20_41-r35hcdcec82_1 | |
| r-matrix conda-forge/linux-64::r-matrix-1.2_18-r35h7fa42b6_2 | |
| r-matrixstats conda-forge/linux-64::r-matrixstats-0.56.0-r35hcdcec82_0 | |
| r-optparse conda-forge/noarch::r-optparse-1.6.4-r35h6115d3f_0 | |
| r-rcurl conda-forge/linux-64::r-rcurl-1.98_1.2-r35hcdcec82_0 | |
| r-snow conda-forge/noarch::r-snow-0.4_3-r35h6115d3f_1001 | |
| r-xml conda-forge/linux-64::r-xml-3.99_0.3-r35hcdcec82_0 | |
| readline conda-forge/linux-64::readline-8.0-hf8c457e_0 | |
| setuptools conda-forge/linux-64::setuptools-46.1.3-py38h32f6830_0 | |
| sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0 | |
| tk conda-forge/linux-64::tk-8.6.10-hed695b0_0 | |
| tktable conda-forge/linux-64::tktable-2.10-h555a92e_3 | |
| wheel conda-forge/noarch::wheel-0.34.2-py_1 | |
| xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002 | |
| xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0 | |
| xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000 | |
| xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0 | |
| xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0 | |
| xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0 | |
| xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0 | |
| xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002 | |
| xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002 | |
| xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002 | |
| xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007 | |
| xz conda-forge/linux-64::xz-5.2.5-h516909a_0 | |
| zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1006 | |
| zstd conda-forge/linux-64::zstd-1.4.4-h6597ccf_3 | |
| Preparing transaction: ...working... done | |
| Verifying transaction: ...working... done | |
| Executing transaction: ...working... done | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:22:57,482 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency bioconductor-rtracklayer version 1.42.1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:22:57,482 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency bioconductor-biostrings version 2.50.2 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:22:57,483 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency r-optparse version 1.6.4 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:22:57,484 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency bioconductor-rtracklayer version 1.42.1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:22:57,484 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency bioconductor-biostrings version 2.50.2 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:22:57,485 [p:28743,w:4,m:0] [uWSGIWorker4Core0] Using dependency r-optparse version 1.6.4 of type conda | |
| 10.25.100.188 - - [07/May/2020:00:19:57 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28743|app: 0|req: 26/216] 10.25.100.188 () {42 vars in 751 bytes} [Thu May 7 00:19:57 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 630 bytes in 180035 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:22:58,861 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:00,594 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-07 00:23:00,599 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Adding new row for repository 'gtf2gene_list' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:23:00,606 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:00,606 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:00,631 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-07 00:23:00,639 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list' at 1:247b439a78f7 | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-07 00:23:15,956 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-07 00:23:15,990 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-07 00:23:16,280 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-07 00:23:16,281 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-07 00:23:26,422 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-07 00:23:26,427 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-07 00:23:27,217 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:23:27,217 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-07 00:23:27,272 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:23:27,272 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,274 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:23:27,288 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:23:27,290 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:23:27,293 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-07 00:23:27,293 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:23:27,294 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,295 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-07 00:23:27,296 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:23:27,296 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,298 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools WARNING 2020-05-07 00:23:27,301 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:23:27,301 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,302 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,302 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (31.619 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,302 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,306 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,307 [p:28737,w:1,m:0] [Thread-1] Loading section: Collection Operations | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,310 [p:28737,w:1,m:0] [Thread-1] Loading section: Expression Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,310 [p:28737,w:1,m:0] [Thread-1] Loading section: Lift-Over | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,310 [p:28737,w:1,m:0] [Thread-1] Loading section: Text Manipulation | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,314 [p:28737,w:1,m:0] [Thread-1] Loading section: Convert Formats | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,316 [p:28737,w:1,m:0] [Thread-1] Loading section: Filter and Sort | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,316 [p:28737,w:1,m:0] [Thread-1] Loaded label: GFF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,317 [p:28737,w:1,m:0] [Thread-1] Loading section: Join, Subtract and Group | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,318 [p:28737,w:1,m:0] [Thread-1] Loading section: Fetch Alignments/Sequences | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,321 [p:28737,w:1,m:0] [Thread-1] Loading section: Operate on Genomic Intervals | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,322 [p:28737,w:1,m:0] [Thread-1] Loading section: Statistics | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,322 [p:28737,w:1,m:0] [Thread-1] Loading section: Graph/Display Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,323 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Association | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,324 [p:28737,w:1,m:0] [Thread-1] Loading section: Get scRNAseq data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,324 [p:28737,w:1,m:0] [Thread-1] Loading section: Seurat | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,324 [p:28737,w:1,m:0] [Thread-1] Loading section: SC3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,324 [p:28737,w:1,m:0] [Thread-1] Loading section: Scanpy | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,325 [p:28737,w:1,m:0] [Thread-1] Loading section: Monocle3 | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,325 [p:28737,w:1,m:0] [Thread-1] Loading section: SCMap | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,325 [p:28737,w:1,m:0] [Thread-1] Loading section: SCPred | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,325 [p:28737,w:1,m:0] [Thread-1] Loading section: Garnett | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,325 [p:28737,w:1,m:0] [Thread-1] Loading section: CellTypeScan | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,325 [p:28737,w:1,m:0] [Thread-1] Loading section: SCCAF | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,325 [p:28737,w:1,m:0] [Thread-1] Loading section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,327 [p:28737,w:1,m:0] [Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy1, version: 1.42.1+galaxy1 into tool panel.... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,330 [p:28737,w:1,m:0] [Thread-1] Loading section: RNA-Seq | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,330 [p:28737,w:1,m:0] [Thread-1] Loading section: Util | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,330 [p:28737,w:1,m:0] [Thread-1] Loading section: Upload FlowFiles | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,330 [p:28737,w:1,m:0] [Thread-1] Loading section: FCS File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,331 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Text File Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,333 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Analysis Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,333 [p:28737,w:1,m:0] [Thread-1] Loading section: Flow Visualization Tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,334 [p:28737,w:1,m:0] [Thread-1] Loading section: Phenotype Correlation Analysis | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:27,334 [p:28737,w:1,m:0] [Thread-1] Loading tool panel finished (31.297 ms) | |
| galaxy.datatypes.registry DEBUG 2020-05-07 00:23:27,340 [p:28737,w:1,m:0] [Thread-1] Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:23:27,343 [p:28737,w:1,m:0] [Thread-1] Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:23:27,345 [p:28737,w:1,m:0] [Thread-1] Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2020-05-07 00:23:27,347 [p:28737,w:1,m:0] [Thread-1] Loaded data fetch tool: __DATA_FETCH__ | |
| galaxy.queue_worker INFO 2020-05-07 00:23:27,347 [p:28737,w:1,m:0] [Thread-1] Queuing async task rebuild_toolbox_search_index for main.web.1. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:23:27,357 [p:28737,w:1,m:0] [Thread-1] Toolbox reload (139.623 ms) | |
| galaxy.queue_worker INFO 2020-05-07 00:23:27,366 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now. | |
| galaxy.tools.search DEBUG 2020-05-07 00:23:27,366 [p:28737,w:1,m:0] [Thread-1] Starting to build toolbox index. | |
| galaxy.config DEBUG 2020-05-07 00:23:27,427 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Finished waiting for toolbox reload (11437.823 ms) | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:23:27,441 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Using dependency bioconductor-rtracklayer version 1.42.1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:23:27,441 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Using dependency bioconductor-biostrings version None of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:23:27,441 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Using dependency r-optparse version None of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:23:27,444 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Using dependency bioconductor-rtracklayer version 1.42.1 of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:23:27,445 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Using dependency bioconductor-biostrings version None of type conda | |
| galaxy.tool_util.deps DEBUG 2020-05-07 00:23:27,445 [p:28737,w:1,m:0] [uWSGIWorker1Core0] Using dependency r-optparse version None of type conda | |
| 10.25.100.188 - - [07/May/2020:00:22:58 +0100] "POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b HTTP/1.1" 200 - "-" "python-requests/2.23.0" | |
| [pid: 28737|app: 0|req: 45/217] 10.25.100.188 () {42 vars in 751 bytes} [Thu May 7 00:22:58 2020] POST /api/tool_shed_repositories/new/install_repository_revision?key=ff1fadcdba102650fb96c7f486b45d6b => generated 630 bytes in 29366 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) | |
| galaxy.tools.search DEBUG 2020-05-07 00:23:27,500 [p:28737,w:1,m:0] [Thread-1] Toolbox index finished (133.839 ms) | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:23:28,556 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Creating repository dependency objects... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:30,234 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.util.repository_util DEBUG 2020-05-07 00:23:30,240 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Adding new row for repository 'gtf2gene_list' in the tool_shed_repository table, status set to 'New'. | |
| galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2020-05-07 00:23:30,246 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Building repository dependency relationships... | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:30,247 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:30,278 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Appending to tool panel section: Single Cell Utils and Viz | |
| galaxy.tool_shed.galaxy_install.install_manager INFO 2020-05-07 00:23:30,285 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list' at 4:b6354c917ef9 | |
| galaxy.tools.toolbox.integrated_panel DEBUG 2020-05-07 00:23:44,088 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Writing integrated tool panel config file to '*******/galaxy/shared/galaxy-gxa-mutable-data/config/integrated_tool_panel.xml' | |
| galaxy.config DEBUG 2020-05-07 00:23:44,124 [p:28739,w:2,m:0] [uWSGIWorker2Core0] Waiting for toolbox reload | |
| galaxy.tools.toolbox.watcher DEBUG 2020-05-07 00:23:44,589 [p:28743,w:4,m:0] [Thread-2] The file '*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml' has changes. | |
| galaxy.queue_worker INFO 2020-05-07 00:23:44,590 [p:28743,w:4,m:0] [Thread-2] Queuing sync task reload_toolbox for main.web.4. | |
| galaxy.queue_worker ERROR 2020-05-07 00:23:54,736 [p:28743,w:4,m:0] [Thread-2] Error waiting for task: '{'task': 'reload_toolbox', 'kwargs': {}}' sent with routing key 'control.main.web.4@********' | |
| Traceback (most recent call last): | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 963, in drain_events | |
| get(self._deliver, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 1001, in _drain_channel | |
| return channel.drain_events(callback=callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 745, in drain_events | |
| return self._poll(self.cycle, callback, timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 402, in _poll | |
| return cycle.get(callback) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/utils/scheduling.py", line 56, in get | |
| return self.fun(resource, callback, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver | |
| message = self._get(queue) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get | |
| raise Empty() | |
| queue.Empty | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/queue_worker.py", line 131, in send_task | |
| self.connection.drain_events(timeout=timeout) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/connection.py", line 323, in drain_events | |
| return self.transport.drain_events(self.connection, **kwargs) | |
| File "*******/galaxy/server/venv_20.01/lib64/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events | |
| raise socket.timeout() | |
| socket.timeout | |
| galaxy.queue_worker INFO 2020-05-07 00:23:54,738 [p:28743,w:4,m:0] [Thread-2] Sending reload_toolbox control task. | |
| galaxy.queue_worker INFO 2020-05-07 00:23:55,296 [p:28737,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'reload_toolbox' task, executing now. | |
| galaxy.queue_worker DEBUG 2020-05-07 00:23:55,296 [p:28737,w:1,m:0] [Thread-1] Executing toolbox reload on 'main.web.1' | |
| galaxy.tools WARNING 2020-05-07 00:23:55,338 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:23:55,338 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:55,340 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/galaxy-20.01/config/tool_conf.xml.sample is None | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:23:55,353 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/codingSnps.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:23:55,355 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/add_scores.loc' | |
| galaxy.tools.toolbox.base ERROR 2020-05-07 00:23:55,357 [p:28737,w:1,m:0] [Thread-1] Error reading tool configuration file from path 'phenotype_association/sift.xml': [Errno 2] No such file or directory: '*******/galaxy/server/galaxy-20.01/tool-data/sift_db.loc' | |
| galaxy.tools WARNING 2020-05-07 00:23:55,358 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:23:55,358 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:55,359 [p:28737,w:1,m:0] [Thread-1] Tool path for tool configuration *******/galaxy/server/config_20.01/tool_conf_cyto-sc.xml is None | |
| galaxy.tools WARNING 2020-05-07 00:23:55,360 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:23:55,360 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:55,362 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools WARNING 2020-05-07 00:23:55,370 [p:28737,w:1,m:0] [Thread-1] The default shed tool config file (*******/galaxy/shared/galaxy-gxa-mutable-data/config/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file | |
| galaxy.tools.toolbox.base INFO 2020-05-07 00:23:55,370 [p:28737,w:1,m:0] [Thread-1] Parsing the tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:55,370 [p:28737,w:1,m:0] [Thread-1] Tool path for shed tool configuration *******/galaxy/shared/galaxy-gxa-mutable-data/config/migrated_tools_conf.xml is *******/galaxy/shared/galaxy-gxa-mutable-data/shed_tools | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:55,371 [p:28737,w:1,m:0] [Thread-1] Reading tools from config files finished (33.370 ms) | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:55,371 [p:28737,w:1,m:0] [Thread-1] Loading section: Get Data | |
| galaxy.tools.toolbox.base DEBUG 2020-05-07 00:23:55,375 [p:28737,w:1,m:0] [Thread-1] Loading section: Send Da |
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