root@bioinfo-wstation-01 /mnt/work/galaxy/galaxy # sudo sh ./run.sh
Some eggs are out of date, attempting to fetch...
Warning: pbr (a dependent egg of sqlalchemy-migrate) cannot be fetched
Fetch successful.
python path is: /mnt/work/galaxy/galaxy/eggs/Babel-1.3-py2.7.egg, /mnt/work/galaxy/galaxy/eggs/pytz-2013.9-py2.7.egg, /mnt/work/galaxy/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/Mako-0.4.1-py2.7.egg, /mnt/work/galaxy/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/kombu-3.0.13-py2.7.egg, /mnt/work/galaxy/galaxy/eggs/anyjson-0.3.3-py2.7.egg, /mnt/work/galaxy/galaxy/eggs/WebHelpers-1.3-py2.7.egg, /mnt/work/galaxy/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/WebOb-0.8.5-py2.7.egg, /mnt/work/galaxy/galaxy/eggs/Routes-2.1-py2.7.egg, /mnt/work/galaxy/galaxy/eggs/repoze.lru-0.6-py2.7.egg, /mnt/work/galaxy/galaxy/eggs/amqp-1.4.5-py2.7.egg, /mnt/work/galaxy/galaxy/eggs/pexpect-2.4-py2.7.egg, /mnt/work/galaxy/galaxy/eggs/wchartype-0.1-py2.7.egg, /mnt/work/galaxy/galaxy/eggs/docutils-0.7-py2.7.egg, /mnt/work/galaxy/galaxy/eggs/PasteDeploy-1.5.0-py2.7.egg, /mnt/work/galaxy/galaxy/eggs/Paste-1.7.5.1-py2.7.egg, /mnt/work/galaxy/galaxy/lib, /usr/local/lib/python2.7/dist-packages/bx_python-0.7.2-py2.7-linux-x86_64.egg, /usr/local/lib/python2.7/dist-packages/MySQL_python-1.2.5-py2.7-linux-x86_64.egg, /usr/local/lib/python2.7/dist-packages/distribute-0.7.3-py2.7.egg, /usr/local/lib/python2.7/dist-packages/Cactus-2.3.1-py2.7.egg, /usr/local/lib/python2.7/dist-packages/Markdown-2.5.1-py2.7.egg, /usr/local/lib/python2.7/dist-packages/boto-2.34.0-py2.7.egg, /usr/local/lib/python2.7/dist-packages/Django-1.5.5-py2.7.egg, /usr/lib/python2.7, /usr/lib/python2.7/plat-linux2, /usr/lib/python2.7/lib-tk, /usr/lib/python2.7/lib-old, /usr/lib/python2.7/lib-dynload, /root/.local/lib/python2.7/site-packages, /usr/local/lib/python2.7/dist-packages, /usr/lib/python2.7/dist-packages/PIL, /usr/lib/python2.7/dist-packages/gtk-2.0, /usr/lib/pymodules/python2.7, /usr/lib/python2.7/dist-packages
tool_shed.tool_shed_registry DEBUG 2015-03-23 02:13:38,249 Loading references to tool sheds from ./config/tool_sheds_conf.xml.sample
tool_shed.tool_shed_registry DEBUG 2015-03-23 02:13:38,250 Loaded reference to tool shed: Galaxy main tool shed
tool_shed.tool_shed_registry DEBUG 2015-03-23 02:13:38,250 Loaded reference to tool shed: Galaxy test tool shed
galaxy.app DEBUG 2015-03-23 02:13:38,250 Using "galaxy.ini" config file: /mnt/work/galaxy/galaxy/config/galaxy.ini.sample
galaxy.eggs WARNING 2015-03-23 02:13:38,465 Warning: pbr (a dependent egg of sqlalchemy-migrate) cannot be fetched
migrate.versioning.repository DEBUG 2015-03-23 02:13:38,589 Loading repository lib/galaxy/model/migrate...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,589 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,589 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,589 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,590 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Loading script lib/galaxy/model/migrate/versions/0014_pages.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Loading script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Script lib/galaxy/model/migrate/versions/0019_request_library_folder.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Loading script lib/galaxy/model/migrate/versions/0020_library_upload_job.py...
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migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,591 Loading script lib/galaxy/model/migrate/versions/0021_user_prefs.py...
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migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,592 Loading script lib/galaxy/model/migrate/versions/0022_visualization_tables.py...
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migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,592 Loading script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py...
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migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,592 Loading script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py...
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migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,592 Loading script lib/galaxy/model/migrate/versions/0026_cloud_tables.py...
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migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,592 Loading script lib/galaxy/model/migrate/versions/0027_request_events.py...
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migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,592 Loading script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py...
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migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,592 Loading script lib/galaxy/model/migrate/versions/0029_user_actions.py...
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migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,665 Script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,665 Loading script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,665 Script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,665 Loading script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,665 Script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,665 Loading script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,666 Script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,666 Loading script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,666 Script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,666 Loading script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py...
migrate.versioning.script.base DEBUG 2015-03-23 02:13:38,666 Script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py loaded successfully
migrate.versioning.repository DEBUG 2015-03-23 02:13:38,666 Repository lib/tool_shed/galaxy_install/migrate loaded successfully
migrate.versioning.repository DEBUG 2015-03-23 02:13:38,666 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))])
tool_shed.galaxy_install.migrate.check DEBUG 2015-03-23 02:13:38,668 pysqlite>=2 egg successfully loaded for sqlite dialect
tool_shed.galaxy_install.migrate.check INFO 2015-03-23 02:13:38,682 At migrate_tools version 12
galaxy.model.orm DEBUG 2015-03-23 02:13:38,685 pysqlite>=2 egg successfully loaded for sqlite dialect
galaxy.config INFO 2015-03-23 02:13:38,695 Install database targetting Galaxy's database configuration.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,721 Loading datatypes from ./config/datatypes_conf.xml.sample
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,722 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,722 Retrieved datatype module galaxy.datatypes.assembly from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,722 Retrieved datatype module galaxy.datatypes.text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,722 Retrieved datatype module galaxy.datatypes.data from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,722 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,722 Retrieved datatype module galaxy.datatypes.sequence from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,722 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,722 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,722 Retrieved datatype module galaxy.datatypes.interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,722 Retrieved datatype module galaxy.datatypes.interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,722 Retrieved datatype module galaxy.datatypes.interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,723 Retrieved datatype module galaxy.datatypes.interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,723 Retrieved datatype module galaxy.datatypes.interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,723 Retrieved datatype module galaxy.datatypes.chrominfo from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,723 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,723 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,723 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,723 Retrieved datatype module galaxy.datatypes.interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,723 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,723 Retrieved datatype module galaxy.datatypes.interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,723 Retrieved datatype module galaxy.datatypes.ngsindex from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,724 Retrieved datatype module galaxy.datatypes.ngsindex from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,724 Retrieved datatype module galaxy.datatypes.sequence from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,724 Retrieved datatype module galaxy.datatypes.data from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,724 Retrieved datatype module galaxy.datatypes.data from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,724 Retrieved datatype module galaxy.datatypes.sequence from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,724 Retrieved datatype module galaxy.datatypes.sequence from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,724 Retrieved datatype module galaxy.datatypes.sequence from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,724 Retrieved datatype module galaxy.datatypes.sequence from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,724 Retrieved datatype module galaxy.datatypes.sequence from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,724 Retrieved datatype module galaxy.datatypes.sequence from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,724 Retrieved datatype module galaxy.datatypes.sequence from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,724 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,725 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,725 Retrieved datatype module galaxy.datatypes.tracks from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,725 Retrieved datatype module galaxy.datatypes.interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,725 Retrieved datatype module galaxy.datatypes.interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,725 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,725 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,725 Retrieved datatype module galaxy.datatypes.interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,725 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,725 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,725 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,725 Retrieved datatype module galaxy.datatypes.interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,726 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,726 Retrieved datatype module galaxy.datatypes.data from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,726 Retrieved datatype module galaxy.datatypes.data from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,726 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,726 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,726 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,726 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,726 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,726 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,727 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,727 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,727 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,727 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,727 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,727 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,727 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,727 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,727 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,727 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,727 Retrieved datatype module galaxy.datatypes.sequence from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,727 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,727 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,728 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,728 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,728 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,728 Retrieved datatype module galaxy.datatypes.sequence from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,728 Retrieved datatype module galaxy.datatypes.sequence from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,728 Retrieved datatype module galaxy.datatypes.sequence from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,728 Retrieved datatype module galaxy.datatypes.interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,728 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,728 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,728 Retrieved datatype module galaxy.datatypes.text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,728 Retrieved datatype module galaxy.datatypes.xml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,728 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,729 Retrieved datatype module galaxy.datatypes.qualityscore from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,729 Retrieved datatype module galaxy.datatypes.qualityscore from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,729 Retrieved datatype module galaxy.datatypes.qualityscore from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,729 Retrieved datatype module galaxy.datatypes.qualityscore from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,729 Retrieved datatype module galaxy.datatypes.qualityscore from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,729 Retrieved datatype module galaxy.datatypes.assembly from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,729 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,729 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,729 Retrieved datatype module galaxy.datatypes.assembly from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,729 Retrieved datatype module galaxy.datatypes.text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,729 Retrieved datatype module galaxy.datatypes.text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,729 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,730 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,730 Retrieved datatype module galaxy.datatypes.images from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,730 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,730 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,730 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,730 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,730 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,730 Retrieved datatype module galaxy.datatypes.data from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,730 Retrieved datatype module galaxy.datatypes.data from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,730 Retrieved datatype module galaxy.datatypes.xml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,730 Retrieved datatype module galaxy.datatypes.xml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,730 Retrieved datatype module galaxy.datatypes.xml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,731 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,731 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,731 Retrieved datatype module galaxy.datatypes.assembly from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,731 Retrieved datatype module galaxy.datatypes.interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,731 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,731 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,731 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,731 Retrieved datatype module galaxy.datatypes.xml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,731 Retrieved datatype module galaxy.datatypes.data from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,731 Retrieved datatype module galaxy.datatypes.data from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,732 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,732 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,732 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,732 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,732 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,732 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,732 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,732 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,732 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,732 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,732 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,733 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,733 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,733 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,733 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,733 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,733 Retrieved datatype module galaxy.datatypes.genetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,733 Retrieved datatype module galaxy.datatypes.tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,733 Retrieved datatype module galaxy.datatypes.text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,733 Retrieved datatype module galaxy.datatypes.text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,733 Retrieved datatype module galaxy.datatypes.graph from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,733 Retrieved datatype module galaxy.datatypes.graph from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,733 Retrieved datatype module galaxy.datatypes.graph from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Retrieved datatype module galaxy.datatypes.binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,734 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.images:Html'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,735 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.text:Json'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.images:Png'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.images:Im'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,736 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,737 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,737 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,737 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,737 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,737 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,737 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,737 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,737 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,737 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 2015-03-23 02:13:38,737 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,737 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,737 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:38,737 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt
galaxy.tools.data DEBUG 2015-03-23 02:13:38,770 Loaded tool data table 'all_fasta'
galaxy.tools.data DEBUG 2015-03-23 02:13:38,770 Loaded tool data table 'bfast_indexes'
galaxy.tools.data WARNING 2015-03-23 02:13:38,770 Cannot find index file 'tool-data/blastdb_p.loc' for tool data table 'blastdb_p'
galaxy.tools.data DEBUG 2015-03-23 02:13:38,770 Loaded tool data table 'blastdb_p'
galaxy.tools.data WARNING 2015-03-23 02:13:38,770 Cannot find index file 'tool-data/bwa_index.loc' for tool data table 'bwa_indexes'
galaxy.tools.data DEBUG 2015-03-23 02:13:38,770 Loaded tool data table 'bwa_indexes'
galaxy.tools.data WARNING 2015-03-23 02:13:38,771 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color'
galaxy.tools.data DEBUG 2015-03-23 02:13:38,771 Loaded tool data table 'bwa_indexes_color'
galaxy.tools.data DEBUG 2015-03-23 02:13:38,771 Loaded tool data table 'indexed_maf_files'
galaxy.tools.data DEBUG 2015-03-23 02:13:38,771 Loaded tool data table 'ngs_sim_fasta'
galaxy.tools.data DEBUG 2015-03-23 02:13:38,771 Loaded tool data table 'perm_base_indexes'
galaxy.tools.data DEBUG 2015-03-23 02:13:38,771 Loaded tool data table 'perm_color_indexes'
galaxy.tools.data DEBUG 2015-03-23 02:13:38,771 Loaded tool data table 'picard_indexes'
galaxy.tools.data DEBUG 2015-03-23 02:13:38,771 Loaded tool data table 'srma_indexes'
galaxy.tools.data DEBUG 2015-03-23 02:13:38,772 Loaded tool data table 'mosaik_indexes'
galaxy.tools.data DEBUG 2015-03-23 02:13:38,772 Loaded tool data table 'twobit'
galaxy.tools.data DEBUG 2015-03-23 02:13:38,984 Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/mnt/work/galaxy/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-mej24_".
galaxy.tools.data WARNING 2015-03-23 02:13:38,984 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 2015-03-23 02:13:38,987 Loaded tool data table 'igv_broad_genomes'
galaxy.jobs WARNING 2015-03-23 02:13:38,996 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/mnt/work/galaxy/galaxy/config/galaxy.ini.sample" instead
galaxy.jobs DEBUG 2015-03-23 02:13:38,996 Loading job configuration from /mnt/work/galaxy/galaxy/config/galaxy.ini.sample
galaxy.jobs DEBUG 2015-03-23 02:13:38,996 Done loading job configuration
beaker.container DEBUG 2015-03-23 02:13:39,006 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache
galaxy.tools.toolbox.base INFO 2015-03-23 02:13:39,008 Parsing the tool configuration ./config/tool_conf.xml.sample
galaxy.tools.toolbox.base INFO 2015-03-23 02:13:39,118 Parsing the tool configuration ./config/shed_tool_conf.xml
galaxy.tools.toolbox.base INFO 2015-03-23 02:13:39,119 Parsing the tool configuration ./config/migrated_tools_conf.xml
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,119 Loading section: Get Data
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,119 Loaded tool id: upload1, version: 1.1.4 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,119 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,119 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,119 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,119 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,119 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,119 Loaded tool id: biomart, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,119 Loaded tool id: biomart_test, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,120 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,120 Loaded tool id: gramenemart, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,120 Loaded tool id: modENCODEfly, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,120 Loaded tool id: flymine, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,120 Loaded tool id: flymine_test, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,120 Loaded tool id: modmine, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,120 Loaded tool id: mousemine, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,120 Loaded tool id: ratmine, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,120 Loaded tool id: yeastmine, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,120 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,120 Loaded tool id: modENCODEworm, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,120 Loaded tool id: wormbase, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,121 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,121 Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,121 Loaded tool id: eupathdb, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,121 Loaded tool id: hbvar, version: 2.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,121 Loaded tool id: genomespace_file_browser_prod, version: 0.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,121 Loaded tool id: genomespace_importer, version: 0.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,121 Loaded tool id: fix_errors, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,121 Loading section: Send Data
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,121 Loaded tool id: genomespace_exporter, version: 0.0.2 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,121 Loading section: Lift-Over
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,121 Loaded tool id: liftOver1, version: 1.0.3 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,121 Loading section: Text Manipulation
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,121 Loaded tool id: addValue, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,121 Loaded tool id: cat1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,122 Loaded tool id: Cut1, version: 1.0.2 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,122 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,122 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,122 Loaded tool id: createInterval, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,122 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,122 Loaded tool id: Paste1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,122 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,122 Loaded tool id: random_lines1, version: 2.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,122 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,122 Loaded tool id: Show tail1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,122 Loaded tool id: trimmer, version: 0.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,122 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,122 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,123 Loading section: Filter and Sort
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,123 Loaded tool id: Filter1, version: 1.1.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,123 Loaded tool id: sort1, version: 1.0.3 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,123 Loaded tool id: Grep1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,123 Loaded label: GFF
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,123 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,123 Loaded tool id: gff_filter_by_attribute, version: 0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,123 Loaded tool id: gff_filter_by_feature_count, version: 0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,123 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,123 Loading section: Join, Subtract and Group
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,123 Loaded tool id: join1, version: 2.0.2 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,123 Loaded tool id: comp1, version: 1.0.2 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,123 Loaded tool id: Grouping1, version: 2.1.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,123 Loading section: Convert Formats
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,124 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,124 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,124 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,124 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,124 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,124 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,124 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,124 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,124 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,124 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,124 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,124 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,124 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,125 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,125 Loading section: Extract Features
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,125 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,125 Loading section: Fetch Sequences
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,125 Loaded tool id: Extract genomic DNA 1, version: 2.2.3 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,125 Loading section: Fetch Alignments
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,125 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,125 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,125 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,125 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,125 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,125 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,125 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,126 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,126 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,126 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,126 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,126 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,126 Loading section: Statistics
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,126 Loaded tool id: Summary_Statistics1, version: 1.1.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,126 Loaded tool id: Count1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,126 Loading section: Graph/Display Data
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,126 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,126 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-03-23 02:13:39,126 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel..
tool_shed.galaxy_install.update_repository_manager INFO 2015-03-23 02:13:40,066 Update repository manager restarter starting up...
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,070 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,072 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,101 Loaded display application 'igv_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,102 Loaded display application 'igb_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,102 Loaded display application 'igb_bed' for datatype 'bed', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,103 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,104 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,104 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,106 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,107 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,110 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,110 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,114 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,119 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,120 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,121 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,123 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,148 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,149 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,150 Loaded display application 'igb_wig' for datatype 'wig', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,173 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False.
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,173 Adding inherited display application 'ensembl_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,174 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,174 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,174 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,174 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,174 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,174 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,174 Adding inherited display application 'ensembl_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,174 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,174 Adding inherited display application 'rviewer_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,174 Adding inherited display application 'ensembl_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,174 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,174 Adding inherited display application 'rviewer_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,175 Adding inherited display application 'ensembl_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,175 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,175 Adding inherited display application 'rviewer_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,175 Adding inherited display application 'ensembl_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,175 Adding inherited display application 'ensembl_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,175 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,175 Adding inherited display application 'rviewer_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,175 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,175 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,175 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,176 Loaded converter: CONVERTER_Bam_Bai_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,177 Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,177 Loaded converter: CONVERTER_bed_to_gff_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,178 Loaded converter: CONVERTER_bed_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,179 Loaded converter: CONVERTER_bed_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,179 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,180 Loaded converter: CONVERTER_bed_to_fli_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,180 Loaded converter: CONVERTER_bedgraph_to_bigwig
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,181 Loaded converter: CONVERTER_len_to_linecount
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,182 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,182 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,183 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,184 Loaded converter: CONVERTER_fasta_to_tabular
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,184 Loaded converter: CONVERTER_fasta_to_bowtie_base_index
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,185 Loaded converter: CONVERTER_fasta_to_bowtie_color_index
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,186 Loaded converter: CONVERTER_fasta_to_2bit
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,186 Loaded converter: CONVERTER_fasta_to_len
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,187 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,187 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,188 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,189 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,189 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,190 Loaded converter: CONVERTER_gff_to_bed_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,190 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,191 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,192 Loaded converter: CONVERTER_gff_to_fli_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,192 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,193 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,194 Loaded converter: CONVERTER_interval_to_bed_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,194 Loaded converter: CONVERTER_interval_to_bedstrict_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,195 Loaded converter: CONVERTER_interval_to_bed6_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,195 Loaded converter: CONVERTER_interval_to_bed12_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,196 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,197 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,197 Loaded converter: CONVERTER_interval_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,198 Loaded converter: CONVERTER_picard_interval_list_to_bed6
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,199 Loaded converter: CONVERTER_maf_to_fasta_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,199 Loaded converter: CONVERTER_maf_to_interval_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,200 Loaded converter: CONVERTER_encodepeak_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,200 Loaded converter: CONVERTER_encodepeak_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,201 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,202 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,203 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,204 Loaded converter: CONVERTER_sam_to_bam
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,204 Loaded converter: CONVERTER_sam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,205 Loaded converter: tabular_to_dbnsfp
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,205 Loaded converter: CONVERTER_vcf_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,206 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,207 Loaded converter: CONVERTER_vcf_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,207 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,208 Loaded converter: CONVERTER_wig_to_bigwig
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,208 Loaded converter: CONVERTER_wiggle_to_interval_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,209 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,210 Loaded converter: lped2fpedconvert
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,210 Loaded converter: lped2pbedconvert
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,211 Loaded converter: pbed2lpedconvert
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,211 Loaded converter: pbed2ldindepconvert
galaxy.datatypes.registry DEBUG 2015-03-23 02:13:40,212 Loaded external metadata tool: __SET_METADATA__
galaxy.tools.imp_exp DEBUG 2015-03-23 02:13:40,213 Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.imp_exp DEBUG 2015-03-23 02:13:40,214 Loaded history import tool: __IMPORT_HISTORY__
galaxy.web.base.pluginframework INFO 2015-03-23 02:13:40,215 VisualizationsRegistry, loaded plugin: charts
galaxy.visualization.registry INFO 2015-03-23 02:13:40,215 Visualizations plugin disabled: Circster. Skipping...
galaxy.web.base.pluginframework INFO 2015-03-23 02:13:40,216 VisualizationsRegistry, loaded plugin: graphview
galaxy.web.base.pluginframework INFO 2015-03-23 02:13:40,216 VisualizationsRegistry, loaded plugin: phyloviz
galaxy.web.base.pluginframework INFO 2015-03-23 02:13:40,217 VisualizationsRegistry, loaded plugin: scatterplot
galaxy.visualization.registry INFO 2015-03-23 02:13:40,217 Visualizations plugin disabled: Sweepster. Skipping...
galaxy.web.base.pluginframework INFO 2015-03-23 02:13:40,218 VisualizationsRegistry, loaded plugin: trackster
galaxy.jobs.manager DEBUG 2015-03-23 02:13:40,218 Starting job handler
galaxy.jobs INFO 2015-03-23 02:13:40,218 Handler 'main' will load all configured runner plugins
galaxy.jobs.runners.state_handler_factory DEBUG 2015-03-23 02:13:40,219 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs.runners DEBUG 2015-03-23 02:13:40,219 Starting 5 LocalRunner workers
galaxy.jobs DEBUG 2015-03-23 02:13:40,219 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
galaxy.jobs.runners.state_handler_factory DEBUG 2015-03-23 02:13:40,226 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs.runners DEBUG 2015-03-23 02:13:40,226 Starting 3 LWRRunner workers
galaxy.jobs.runners.lwr_client.manager INFO 2015-03-23 02:13:40,226 Setting LWR client class to standard, non-caching variant.
galaxy.jobs DEBUG 2015-03-23 02:13:40,227 Loaded job runner 'galaxy.jobs.runners.lwr:LwrJobRunner' as 'lwr'
galaxy.jobs DEBUG 2015-03-23 02:13:40,227 Legacy destination with id 'local:///', url 'local:///' converted, got params:
galaxy.jobs.handler DEBUG 2015-03-23 02:13:40,227 Loaded job runners plugins: lwr:local
galaxy.jobs.handler INFO 2015-03-23 02:13:40,227 job handler stop queue started
galaxy.jobs.handler INFO 2015-03-23 02:13:40,235 job handler queue started
galaxy.sample_tracking.external_service_types DEBUG 2015-03-23 02:13:40,236 Loaded external_service_type: Simple unknown sequencer 1.0.0
galaxy.sample_tracking.external_service_types DEBUG 2015-03-23 02:13:40,237 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0
galaxy.workflow.scheduling_manager DEBUG 2015-03-23 02:13:40,239 Starting workflow schedulers
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,257 Enabling 'userskeys' controller, class: User
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,408 Enabling 'admin_toolshed' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,408 Enabling 'admin_toolshed' controller, class: AdminToolshed
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,409 Enabling 'forms' controller, class: Forms
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,409 Enabling 'mobile' controller, class: Mobile
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,409 Enabling 'workflow' controller, class: WorkflowController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,413 Enabling 'library_common' controller, class: LibraryCommon
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,413 Enabling 'async' controller, class: ASync
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,414 Enabling 'tool_runner' controller, class: ToolRunner
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,415 Enabling 'external_service' controller, class: ExternalService
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,415 Enabling 'search' controller, class: SearchController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,415 Enabling 'error' controller, class: Error
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,417 Enabling 'history' controller, class: HistoryController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,418 Enabling 'visualization' controller, class: VisualizationController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,419 Enabling 'page' controller, class: PageController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,420 Enabling 'root' controller, class: RootController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,421 Enabling 'user' controller, class: User
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,421 Enabling 'external_services' controller, class: ExternalServiceController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,421 Enabling 'requests_common' controller, class: RequestsCommon
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,421 Enabling 'biostar' controller, class: BiostarController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,421 Enabling 'library' controller, class: Library
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,422 Enabling 'requests' controller, class: Requests
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,422 Enabling 'admin' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,422 Enabling 'tag' controller, class: TagsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,422 Enabling 'ucsc_proxy' controller, class: UCSCProxy
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,423 Enabling 'library_admin' controller, class: LibraryAdmin
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,425 Enabling 'data_manager' controller, class: DataManager
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,428 Enabling 'requests_admin' controller, class: RequestsAdmin
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,431 Enabling 'dataset' controller, class: DatasetInterface
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,432 Enabling 'request_type' controller, class: RequestType
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,476 Enabling 'cloudlaunch' controller, class: CloudController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,478 Enabling 'folder_contents' API controller, class: FolderContentsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,478 Enabling 'jobs' API controller, class: JobController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,479 Enabling 'forms' API controller, class: FormDefinitionAPIController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,479 Enabling 'datatypes' API controller, class: DatatypesController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,479 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,480 Enabling 'configuration' API controller, class: ConfigurationController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,480 Enabling 'group_users' API controller, class: GroupUsersAPIController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,481 Enabling 'groups' API controller, class: GroupAPIController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,481 Enabling 'workflows' API controller, class: WorkflowsAPIController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,481 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,481 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,489 Enabling 'search' API controller, class: SearchController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,489 Enabling 'job_files' API controller, class: JobFilesAPIController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,490 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,490 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,490 Enabling 'pages' API controller, class: PagesController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,490 Enabling 'genomes' API controller, class: GenomesController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,490 Enabling 'page_revisions' API controller, class: PageRevisionsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,491 Enabling 'visualizations' API controller, class: VisualizationsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,491 Enabling 'libraries' API controller, class: LibrariesController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,491 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,491 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,491 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,492 Enabling 'folders' API controller, class: FoldersController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,492 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,492 Enabling 'history_tags' API controller, class: HistoryTagsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,492 Enabling 'workflow_tags' API controller, class: WorkflowTagsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,492 Enabling 'datasets' API controller, class: DatasetsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,493 Enabling 'requests' API controller, class: RequestsAPIController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,493 Enabling 'quotas' API controller, class: QuotaAPIController
beaker.container DEBUG 2015-03-23 02:13:40,498 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,498 Enabling 'histories' API controller, class: HistoriesController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,498 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,499 Enabling 'library_contents' API controller, class: LibraryContentsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,499 Enabling 'tool_data' API controller, class: ToolData
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,499 Enabling 'group_roles' API controller, class: GroupRolesAPIController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,499 Enabling 'request_types' API controller, class: RequestTypeAPIController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,500 Enabling 'remote_files' API controller, class: RemoteFilesAPIController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,500 Enabling 'authenticate' API controller, class: AuthenticationController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,501 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,501 Enabling 'samples' API controller, class: SamplesAPIController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,502 Enabling 'roles' API controller, class: RoleAPIController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,502 Enabling 'users' API controller, class: UserAPIController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,502 Enabling 'metrics' API controller, class: MetricsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,502 Enabling 'history_contents' API controller, class: HistoryContentsController
galaxy.web.framework.base DEBUG 2015-03-23 02:13:40,503 Enabling 'tools' API controller, class: ToolsController
galaxy.webapps.galaxy.buildapp DEBUG 2015-03-23 02:13:40,818 Enabling 'httpexceptions' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-03-23 02:13:40,818 Enabling 'recursive' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-03-23 02:13:40,835 Enabling 'eval exceptions' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-03-23 02:13:40,836 Enabling 'trans logger' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-03-23 02:13:40,836 Enabling 'x-forwarded-host' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-03-23 02:13:40,836 Enabling 'Request ID' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-03-23 02:13:40,837 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static
galaxy.webapps.galaxy.buildapp DEBUG 2015-03-23 02:13:40,837 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static
galaxy.webapps.galaxy.buildapp DEBUG 2015-03-23 02:13:40,837 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static
galaxy.queue_worker INFO 2015-03-23 02:13:40,837 Initalizing Galaxy Queue Worker on sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE
Starting server in PID 25732.
serving on http://127.0.0.1:8080