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Created Aug 31, 2017

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Jetstream Galaxy 17.01.01 admin log
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galaxy.queue_worker INFO 2017-08-30 06:38:37,355 Initializing web0 Galaxy Queue Worker on sqlalchemy+postgresql://galaxy:********@localhost:5432/galaxy?client_encoding=utf8
tool_shed.tool_shed_registry DEBUG 2017-08-30 06:38:37,700 Loading references to tool sheds from /opt/galaxy/galaxy-app/config/tool_sheds_conf.xml
tool_shed.tool_shed_registry DEBUG 2017-08-30 06:38:37,700 Loaded reference to tool shed: Galaxy Main Tool Shed
tool_shed.tool_shed_registry DEBUG 2017-08-30 06:38:37,700 Loaded reference to tool shed: Galaxy Test Tool Shed
galaxy.app DEBUG 2017-08-30 06:38:37,707 Using "galaxy.ini" config file: /opt/galaxy/galaxy-app/config/galaxy.ini
migrate.versioning.repository DEBUG 2017-08-30 06:38:37,957 Loading repository lib/galaxy/model/migrate...
migrate.versioning.script.base DEBUG 2017-08-30 06:38:38,081 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py...
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tool_shed.galaxy_install.migrate.check INFO 2017-08-30 06:38:41,034 At migrate_tools version 12
galaxy.config INFO 2017-08-30 06:38:41,065 Install database targetting Galaxy's database configuration.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:42,596 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdzxJsSk
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:42,596 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:42,597 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:42,917 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdkWOEAT
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:42,918 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:42,918 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdkWOEAT.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:42,918 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:42,918 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdkWOEAT.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:42,996 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpd2sOort
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:42,996 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:42,996 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpd2sOort.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:42,996 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:42,997 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpd2sOort.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,105 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdpQqaMi
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,106 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,106 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdpQqaMi.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,106 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,106 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdpQqaMi.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,200 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpddkNX9j
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,201 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,201 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpddkNX9j.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,201 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,201 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpddkNX9j.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,375 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdS7SV6m
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,375 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,375 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdS7SV6m.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,376 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,376 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdS7SV6m.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,682 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdH8qHPo
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,682 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,682 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdH8qHPo.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,683 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:43,683 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdH8qHPo.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,013 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpd738n1I
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,013 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,013 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpd738n1I.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,014 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,014 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpd738n1I.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,278 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpd3AoEG1
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,278 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,278 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpd3AoEG1.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,279 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,279 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpd3AoEG1.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,547 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdreNTzI
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,548 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,548 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdreNTzI.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,548 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,548 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdreNTzI.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,808 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdV2OWkI
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,808 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,808 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdV2OWkI.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,809 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,809 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdV2OWkI.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,986 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdFuATbp
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,986 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,986 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdFuATbp.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,986 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:44,986 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdFuATbp.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,164 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdrso3px
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,164 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,165 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdrso3px.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,165 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,165 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdrso3px.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,274 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdf0ZgAM
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,274 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,274 Overriding conflicting datatype with extension 'deeptools_compute_matrix_archive', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdf0ZgAM.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,275 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,275 Overriding conflicting datatype with extension 'deeptools_coverage_matrix', using datatype from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdf0ZgAM.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,594 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdzHSazE
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,668 Exception importing proprietary code file /opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,668 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,669 Exception importing proprietary code file /opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/binary: No module named binary
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,669 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,669 Exception importing proprietary code file /opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/blast_datatypes/01b38f20197e/blast_datatypes/data: No module named data
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,669 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,670 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:45,940 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdd9QcoS
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,222 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdYd3lz2
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,222 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,223 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,223 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,223 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,223 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,224 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,224 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,224 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,224 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,225 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,225 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,225 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,225 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,225 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,226 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,226 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,226 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,226 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,227 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,227 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,227 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,227 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,228 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,228 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,228 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,228 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,228 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,229 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,229 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,229 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,229 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,230 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,230 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,230 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,230 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,230 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,231 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,231 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,231 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,231 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,232 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,232 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,232 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,232 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,233 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,233 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,233 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,233 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,233 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,234 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,234 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,234 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,234 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,234 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,235 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,235 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,235 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,235 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,235 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,236 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,236 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,236 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,236 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,237 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,237 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,237 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,237 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,238 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,238 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,238 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,238 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,238 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,239 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,239 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,239 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,239 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,240 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,240 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,240 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,240 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,240 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,241 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,241 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,241 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,241 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,241 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,242 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,242 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,243 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,243 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,243 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,243 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,244 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,244 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,244 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,244 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,733 Loading datatypes from /opt/galaxy/galaxy-app/database/tmp/tmp-toolshed-acalpdlQl8ZJ
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,733 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,783 Loading datatypes from /opt/galaxy/galaxy-app/config/datatypes_conf.xml
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,783 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,785 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,786 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,786 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,786 Overriding conflicting datatype with extension 'asn1', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,786 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,786 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,786 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,786 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,787 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,787 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,787 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,787 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,787 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,787 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,789 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,789 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,789 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,790 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,790 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,790 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,790 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,790 Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,790 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,792 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,793 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,793 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,793 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,793 Overriding conflicting datatype with extension 'data', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,793 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,793 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,793 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,794 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,794 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,794 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,794 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,794 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,794 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,794 Retrieved datatype module galaxy.datatypes.sequence:FastqGz from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,795 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerGz from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,795 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaGz from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,795 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerGz from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,795 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaGz from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,795 Retrieved datatype module galaxy.datatypes.sequence:FastqBz2 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,795 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerBz2 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,795 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaBz2 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,795 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerBz2 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,796 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaBz2 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,796 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,796 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,796 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,796 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,796 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,796 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,796 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,797 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,797 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,798 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,798 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,798 Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,798 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,799 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,799 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,799 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,799 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,800 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,800 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,800 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,800 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,800 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,801 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,801 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,801 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,801 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,802 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,802 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,802 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,802 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,802 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,803 Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,803 Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,803 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,803 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,803 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,803 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,803 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,803 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,804 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,804 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,804 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,804 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,804 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,804 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,804 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,804 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,805 Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,805 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,809 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,809 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,810 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,810 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,810 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,810 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,810 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,811 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,811 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,811 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,811 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,811 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,811 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,811 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,812 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,812 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,812 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,812 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,812 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,812 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,812 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,812 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,812 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,813 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,813 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,813 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,813 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,813 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,813 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,813 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,814 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,814 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,814 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,814 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,814 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,814 Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,814 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,815 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,815 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,815 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,815 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,815 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,815 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,815 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,815 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,815 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,816 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,816 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,816 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,816 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,816 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,816 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,816 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,816 Roadmaps is not lower case, that could cause troubles in the future. Please change it to lower case
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,817 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,817 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,817 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,817 Sequences is not lower case, that could cause troubles in the future. Please change it to lower case
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,817 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,817 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,817 Overriding conflicting datatype with extension 'snpeffdb', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,817 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,817 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,818 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,818 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,818 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,818 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,818 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,818 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,818 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,819 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,819 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,819 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,819 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,819 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,819 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,819 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,819 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,820 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,820 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,820 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,820 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,820 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,821 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,821 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,821 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,821 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,826 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,826 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,827 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,827 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,827 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,827 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,827 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,827 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,828 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,828 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,828 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,828 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,828 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,828 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,828 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,829 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,829 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,829 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,829 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,829 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,833 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,833 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,835 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,835 Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,836 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,836 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,836 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,836 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,836 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,836 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,836 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,836 Overriding conflicting datatype with extension 'btwisted', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,837 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,837 Overriding conflicting datatype with extension 'cai', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,837 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,837 Overriding conflicting datatype with extension 'charge', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,837 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,837 Overriding conflicting datatype with extension 'checktrans', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,837 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,837 Overriding conflicting datatype with extension 'chips', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,838 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,838 Overriding conflicting datatype with extension 'codcmp', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,838 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,838 Overriding conflicting datatype with extension 'coderet', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,838 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,838 Overriding conflicting datatype with extension 'compseq', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,838 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,839 Overriding conflicting datatype with extension 'cpgplot', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,839 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,839 Overriding conflicting datatype with extension 'cpgreport', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,839 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,839 Overriding conflicting datatype with extension 'cusp', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,839 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,839 Overriding conflicting datatype with extension 'cut', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,840 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,840 Overriding conflicting datatype with extension 'dan', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,840 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,840 Overriding conflicting datatype with extension 'digest', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,840 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,840 Overriding conflicting datatype with extension 'dreg', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,840 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,840 Overriding conflicting datatype with extension 'einverted', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,841 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,841 Overriding conflicting datatype with extension 'epestfind', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,841 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,841 Overriding conflicting datatype with extension 'equicktandem', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,841 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,841 Overriding conflicting datatype with extension 'est2genome', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,841 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,841 Overriding conflicting datatype with extension 'etandem', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,842 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,842 Overriding conflicting datatype with extension 'freak', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,842 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,842 Overriding conflicting datatype with extension 'fuzznuc', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,842 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,842 Overriding conflicting datatype with extension 'fuzzpro', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,842 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,842 Overriding conflicting datatype with extension 'fuzztran', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,843 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,843 Overriding conflicting datatype with extension 'garnier', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,843 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,843 Overriding conflicting datatype with extension 'geecee', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,843 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,843 Overriding conflicting datatype with extension 'helixturnhelix', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,843 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,843 Overriding conflicting datatype with extension 'hmoment', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,844 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,844 Overriding conflicting datatype with extension 'isochore', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,844 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,844 Overriding conflicting datatype with extension 'match', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,844 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,844 Overriding conflicting datatype with extension 'nametable', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,844 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,844 Overriding conflicting datatype with extension 'needle', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,845 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,845 Overriding conflicting datatype with extension 'newcpgreport', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,845 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,845 Overriding conflicting datatype with extension 'newcpgseek', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,845 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,845 Overriding conflicting datatype with extension 'noreturn', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,845 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,845 Overriding conflicting datatype with extension 'palindrome', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,846 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,846 Overriding conflicting datatype with extension 'pepcoil', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,846 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,846 Overriding conflicting datatype with extension 'pepinfo', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,846 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,846 Overriding conflicting datatype with extension 'pepstats', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,846 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,847 Overriding conflicting datatype with extension 'polydot', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,847 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,847 Overriding conflicting datatype with extension 'preg', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,847 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,847 Overriding conflicting datatype with extension 'prettyseq', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,847 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,847 Overriding conflicting datatype with extension 'primersearch', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,847 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,848 Overriding conflicting datatype with extension 'showfeat', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,848 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,848 Overriding conflicting datatype with extension 'showorf', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,848 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,848 Overriding conflicting datatype with extension 'sixpack', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,848 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,848 Overriding conflicting datatype with extension 'strider', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,848 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,849 Overriding conflicting datatype with extension 'supermatcher', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,849 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,849 Overriding conflicting datatype with extension 'syco', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,849 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,849 Overriding conflicting datatype with extension 'textsearch', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,849 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,849 Overriding conflicting datatype with extension 'vectorstrip', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,850 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,850 Overriding conflicting datatype with extension 'wobble', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,851 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,851 Overriding conflicting datatype with extension 'wordcount', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,851 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,851 Overriding conflicting datatype with extension 'dbmotif', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,851 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,851 Overriding conflicting datatype with extension 'diffseq', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,851 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,851 Overriding conflicting datatype with extension 'excel', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,852 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,852 Overriding conflicting datatype with extension 'feattable', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,852 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,852 Overriding conflicting datatype with extension 'motif', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,852 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,852 Overriding conflicting datatype with extension 'regions', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,852 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,853 Overriding conflicting datatype with extension 'seqtable', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,853 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,853 Overriding conflicting datatype with extension 'simple', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,853 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,853 Overriding conflicting datatype with extension 'table', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,853 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,853 Overriding conflicting datatype with extension 'tagseq', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,853 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,854 Overriding conflicting datatype with extension 'acedb', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,854 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,854 Overriding conflicting datatype with extension 'clustal', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,854 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,854 Overriding conflicting datatype with extension 'codata', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,854 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,854 Overriding conflicting datatype with extension 'embl', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,854 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,855 Overriding conflicting datatype with extension 'fitch', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,855 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,855 Overriding conflicting datatype with extension 'gcg', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,855 Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,855 Overriding conflicting datatype with extension 'genbank', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,855 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,855 Overriding conflicting datatype with extension 'hennig86', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,855 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,855 Overriding conflicting datatype with extension 'ig', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,856 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,856 Overriding conflicting datatype with extension 'jackknifer', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,856 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,856 Overriding conflicting datatype with extension 'jackknifernon', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,856 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,856 Overriding conflicting datatype with extension 'mega', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,856 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,856 Overriding conflicting datatype with extension 'meganon', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,857 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,857 Overriding conflicting datatype with extension 'ncbi', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,857 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,857 Overriding conflicting datatype with extension 'nexus', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,857 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,857 Overriding conflicting datatype with extension 'nexusnon', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,857 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,857 Overriding conflicting datatype with extension 'phylip', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,858 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,858 Overriding conflicting datatype with extension 'phylipnon', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,858 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,858 Overriding conflicting datatype with extension 'pir', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,858 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,858 Overriding conflicting datatype with extension 'staden', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,858 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,858 Overriding conflicting datatype with extension 'swiss', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,859 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,859 Overriding conflicting datatype with extension 'markx0', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,859 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,859 Overriding conflicting datatype with extension 'markx1', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,859 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,859 Overriding conflicting datatype with extension 'markx10', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,859 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,859 Overriding conflicting datatype with extension 'markx2', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,859 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,860 Overriding conflicting datatype with extension 'markx3', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,860 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,860 Overriding conflicting datatype with extension 'pair', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,860 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,860 Overriding conflicting datatype with extension 'score', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,860 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,860 Overriding conflicting datatype with extension 'srs', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,860 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,860 Overriding conflicting datatype with extension 'srspair', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,864 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,864 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,864 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,864 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,864 Retrieved datatype module galaxy.datatypes.binary:Cel from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,865 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,865 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,865 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,865 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,865 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,865 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,865 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,868 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,868 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,868 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,868 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,868 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,868 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,869 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,873 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,873 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,873 Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,873 Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,873 Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,873 Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,873 Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,874 Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,874 Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,874 Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,879 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,879 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,879 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,879 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,879 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,880 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,880 Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,880 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,880 Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,880 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,881 Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,881 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,881 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,881 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,881 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,881 Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,881 Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,882 Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,882 Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,882 Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,882 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,882 Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,882 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,882 Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,882 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,883 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,883 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,883 Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,883 Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,883 Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,883 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,883 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,884 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,884 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,884 Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,884 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,884 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,886 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,886 Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,888 Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,888 Overriding conflicting datatype with extension 'blastxml', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,888 Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,889 Overriding conflicting datatype with extension 'blastdbn', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,889 Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,889 Overriding conflicting datatype with extension 'blastdbp', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,889 Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,889 Overriding conflicting datatype with extension 'blastdbd', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,889 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,889 Overriding conflicting datatype with extension 'maskinfo-asn1', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,889 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,889 Overriding conflicting datatype with extension 'maskinfo-asn1-binary', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,890 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,890 Overriding conflicting datatype with extension 'pssm-asn1', using datatype from /opt/galaxy/galaxy-app/config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,890 Retrieved datatype module galaxy.datatypes.text:Smat from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,890 Loaded sniffer for datatype 'galaxy.datatypes.text:Smat'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,890 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,891 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,891 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,891 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,891 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,891 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,891 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,891 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,891 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,891 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,892 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,892 Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,892 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,892 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,892 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,892 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,892 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,892 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:MzSQlite'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:IdpDB'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:SQlite'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:H5'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Bam'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,893 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,894 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Sff'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,894 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,894 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,894 Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,894 Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,894 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,894 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,894 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,894 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,895 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,895 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,895 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,895 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,895 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,895 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,895 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,895 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,895 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,896 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,896 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,896 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,896 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,896 Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,896 Removed conflicting sniffer for datatype 'galaxy.datatypes.xml:GenericXml'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,896 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,896 Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,896 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,897 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,897 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,897 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Maf'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,897 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,897 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Lav'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,897 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,897 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:csFasta'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,897 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,897 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,897 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,897 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,897 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,897 Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,898 Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,898 Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,898 Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,898 Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,898 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fasta'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,898 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,898 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fastq'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,898 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,898 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqGz'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,898 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqBz2'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,898 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Wiggle'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Removed conflicting sniffer for datatype 'galaxy.datatypes.text:Html'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Loaded sniffer for datatype 'galaxy.datatypes.text:Html'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Axt'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Bed'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gtf'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,899 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,900 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff3'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,900 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,900 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Pileup'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,900 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,900 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Interval'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,900 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,900 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Sam'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,900 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,900 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,900 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,900 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,900 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,901 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,901 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,901 Loaded sniffer for datatype 'galaxy.datatypes.text:Json'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,901 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,901 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,901 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,901 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:CSV'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,901 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,901 Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,902 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,902 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,902 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,902 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,902 Loaded sniffer for datatype 'galaxy.datatypes.binary:Cel'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,902 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,902 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,902 Loaded sniffer for datatype 'galaxy.datatypes.images:Png'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,903 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,903 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,903 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,903 Loaded sniffer for datatype 'galaxy.datatypes.images:Im'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,903 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,903 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,903 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,903 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,904 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,904 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,904 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,904 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,904 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,904 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,904 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,904 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,905 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,905 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,905 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,905 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,905 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels'
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,923 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,926 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 2017-08-30 06:38:46,926 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,926 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,926 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt
galaxy.datatypes.registry DEBUG 2017-08-30 06:38:46,926 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt
galaxy.tools.data DEBUG 2017-08-30 06:38:49,048 Loaded 235 lines from '/galaxy/data/location/all_fasta.loc' for 'all_fasta'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,048 Loaded tool data table 'all_fasta' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,061 Loaded 5 lines from '/galaxy/data/location/bfast_indexes.loc' for 'bfast_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,061 Loaded tool data table 'bfast_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,063 Loaded 4 lines from '/galaxy/data/location/blastdb.loc' for 'blastdb'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,063 Loaded tool data table 'blastdb' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data WARNING 2017-08-30 06:38:49,065 Cannot find index file '/galaxy/data/location/blastdb_p.loc' for tool data table 'blastdb_p'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,066 Loaded tool data table 'blastdb_p' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,069 Loaded 121 lines from '/galaxy/data/location/bowtie2_indices.loc' for 'bowtie2_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,069 Loaded tool data table 'bowtie2_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,071 Loaded 16 lines from '/galaxy/data/location/bwa_mem_index.loc' for 'bwa_mem_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,071 Loaded tool data table 'bwa_mem_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,075 Loaded 201 lines from '/galaxy/data/location/bwa_index.loc' for 'bwa_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,076 Loaded tool data table 'bwa_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,078 Loaded 9 lines from '/galaxy/data/location/bwa_index_color.loc' for 'bwa_indexes_color'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,078 Loaded tool data table 'bwa_indexes_color' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,084 Loaded 24 lines from '/galaxy/data/location/maf_index.loc' for 'indexed_maf_files'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,084 Loaded tool data table 'indexed_maf_files' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,086 Loaded 3 lines from '/galaxy/data/location/ngs_sim_fasta.loc' for 'ngs_sim_fasta'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,086 Loaded tool data table 'ngs_sim_fasta' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,088 Loaded 10 lines from '/galaxy/data/location/perm_base_index.loc' for 'perm_base_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,088 Loaded tool data table 'perm_base_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,090 Loaded 10 lines from '/galaxy/data/location/perm_color_index.loc' for 'perm_color_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,091 Loaded tool data table 'perm_color_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,094 Loaded 182 lines from '/galaxy/data/location/picard_index.loc' for 'picard_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,094 Loaded tool data table 'picard_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,114 Loaded 1 lines from '/galaxy/data/location/gatk_sorted_picard_index.loc' for 'gatk_picard_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,115 Loaded tool data table 'gatk_picard_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data WARNING 2017-08-30 06:38:49,115 Cannot find index file '/galaxy/data/location/gatk_annotations.txt' for tool data table 'gatk_annotations'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,115 Loaded tool data table 'gatk_annotations' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,117 Loaded 182 lines from '/galaxy/data/location/picard_index.loc' for 'srma_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,117 Loaded tool data table 'srma_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,130 Loaded 202 lines from '/galaxy/data/location/bowtie_indices.loc' for 'tophat_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,130 Loaded tool data table 'tophat_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,135 Loaded 194 lines from '/galaxy/data/location/bowtie_indices_color.loc' for 'tophat_indexes_color'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,135 Loaded tool data table 'tophat_indexes_color' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,136 Loaded 121 lines from '/galaxy/data/location/bowtie2_indices.loc' for 'tophat2_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,136 Loaded tool data table 'tophat2_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,139 Loaded 3 lines from '/galaxy/data/location/ccat_configurations.loc' for 'ccat_configurations'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,139 Loaded tool data table 'ccat_configurations' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,141 Loaded 182 lines from '/galaxy/data/location/mosaik_index.loc' for 'mosaik_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,141 Loaded tool data table 'mosaik_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,144 Loaded 202 lines from '/galaxy/data/location/bowtie_indices.loc' for 'bowtie_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,144 Loaded tool data table 'bowtie_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,146 Loaded 194 lines from '/galaxy/data/location/bowtie_indices_color.loc' for 'bowtie_indexes_color'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,146 Loaded tool data table 'bowtie_indexes_color' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,153 Loaded 191 lines from '/galaxy/data/location/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,153 Loaded tool data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,156 Loaded 180 lines from '/galaxy/data/location/sam_fa_indices.loc' for 'sam_fa_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,157 Loaded tool data table 'sam_fa_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,223 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/annovar_index.loc' for 'annovar_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,223 Loaded tool data table 'annovar_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,231 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/tophat_fusion_blastdb.loc' for 'tophat_fusion_blastdb_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,231 Loaded tool data table 'tophat_fusion_blastdb_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,235 Loaded 178 lines from '/galaxy/data/location/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,236 Loaded tool data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,473 Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/opt/galaxy/galaxy-app/database/tmp/TTDT_URL_igv_broad_genomes-onPg0A".
galaxy.tools.data WARNING 2017-08-30 06:38:49,474 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 2017-08-30 06:38:49,475 Loaded 155 lines from '/opt/galaxy/galaxy-app/database/tmp/TTDT_URL_igv_broad_genomes-onPg0A' for 'igv_broad_genomes'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,476 Loaded tool data table 'igv_broad_genomes' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data WARNING 2017-08-30 06:38:49,481 Line 214 in tool data table 'liftOver' is invalid (HINT: '<TAB>' characters must be used to separate fields):
ce9 bruMal1 /galaxy/data/ce9/liftOver/ce9ToBruMal1.over.chain
galaxy.tools.data DEBUG 2017-08-30 06:38:49,489 Loaded 1180 lines from '/galaxy/data/location/liftOver.loc' for 'liftOver'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,499 Loaded tool data table 'liftOver' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,990 Loaded 1 lines from '/cvmfs/main.galaxyproject.org/galaxy/tool-data/bam_iobio.loc.sample' for 'bam_iobio'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,990 Loaded tool data table 'bam_iobio' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,994 Loaded 1 lines from '/cvmfs/main.galaxyproject.org/galaxy/tool-data/vcf_iobio.loc.sample' for 'vcf_iobio'
galaxy.tools.data DEBUG 2017-08-30 06:38:49,994 Loaded tool data table 'vcf_iobio' from file '/opt/galaxy/galaxy-app/config/tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,058 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/74b09c8e5f6e/all_fasta.loc' for 'all_fasta'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,058 Loading another instance of data table 'all_fasta' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,115 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/74b09c8e5f6e/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,116 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,132 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/74b09c8e5f6e/twobit.loc' for 'twobit'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,132 Loaded tool data table 'twobit' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,199 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/74b09c8e5f6e/alignseq.loc' for 'alignseq_seq'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,199 Loaded tool data table 'alignseq_seq' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,275 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/8f0137a68f02/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,275 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,463 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/6a056fb2b9c1/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,463 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,467 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/18f46b571982/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,468 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,471 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/b3589208f673/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,471 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,486 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/e94df7973bb0/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,486 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,493 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/610bbc25ed8b/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,493 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,496 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/e57bfadcab30/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,497 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,500 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/d5d57b40b29a/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,500 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,503 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/b4886e1369c4/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,503 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,508 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/87d2c75884d9/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,508 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,511 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/70bf1a5592be/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,511 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,514 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/65e0795278b4/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,515 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,518 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/17d456f4051b/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,518 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,521 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/8518a8e9ac82/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,522 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,525 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/a9d4f71dbfb0/bowtie2_indices.loc' for 'bowtie2_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,525 Loading another instance of data table 'bowtie2_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,528 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/546ada4a9f43/bwa_mem_index.loc' for 'bwa_mem_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,528 Loading another instance of data table 'bwa_mem_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,532 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/fb2e0e1dac89/blastdb.loc' for 'blastdb'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,532 Loading another instance of data table 'blastdb' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,593 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/b4427dbb6ced/bwa_index.loc' for 'bwa_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,593 Loading another instance of data table 'bwa_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,607 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/b4427dbb6ced/bwa_index_color.loc' for 'bwa_indexes_color'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,607 Loading another instance of data table 'bwa_indexes_color' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,614 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/9ca609a2a421/bowtie_indices.loc' for 'bowtie_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,614 Loading another instance of data table 'bowtie_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,655 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/lastz/60afcc2c1d05/lastz_seqs.loc' for 'lastz_seqs'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,656 Loading another instance of data table 'lastz_seqs' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,842 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/0849fa93eadb/bowtie2_indices.loc' for 'tophat2_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,843 Loading another instance of data table 'tophat2_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:50,848 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/1eb21dccc2fa/hisat2_indexes.loc' for 'hisat2_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,848 Loaded tool data table 'hisat2_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,971 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/a6dcb86af112/sam_fa_indices.loc' for 'sam_fa_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:50,971 Loading another instance of data table 'sam_fa_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:51,113 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/85d0d479f05b/sailfish_indexes.loc' for 'sailfish_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,114 Loaded tool data table 'sailfish_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,315 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/0f32ad418df8/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,315 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:51,409 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/1322b73ffe44/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,409 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:51,419 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/a1ea9af8d5f4/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,419 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:51,423 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/gffread/9f243677c4c6/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,423 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:51,494 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/1707a530e598/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,495 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:51,508 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/b2ee2bef1926/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,508 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:51,577 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat_fusion_post/f83394a2c2da/bowtie_indices.loc' for 'bowtie_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,577 Loading another instance of data table 'bowtie_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:51,585 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat_fusion_post/f83394a2c2da/tophat_fusion_blastdb.loc' for 'tophat_fusion_blastdb_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,585 Loading another instance of data table 'tophat_fusion_blastdb_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:51,678 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/881e16ad05c6/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,678 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:51,682 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/bfc4517aa037/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,683 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:51,845 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/8cfc17e27132/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,845 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:51,863 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/1ebb4ecdc1ef/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,864 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:51,945 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/890d97772e2a/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:51,945 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,138 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bamtools/ea3fc1adee75/sam_fa_indices.loc' for 'sam_fa_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,138 Loading another instance of data table 'sam_fa_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,230 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/efc56ee1ade4/picard_index.loc' for 'picard_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,231 Loading another instance of data table 'picard_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,235 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/401f29f278f0/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,236 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,251 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/046b3db333bd/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,251 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,255 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/d3f4f86a18d4/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,255 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,261 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/4dba4b988d0a/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,261 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,266 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/d485f9f1aa83/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,266 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,355 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/table_annovar/08b003ee9db7/annovar_index.loc' for 'annovar_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,355 Loading another instance of data table 'annovar_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,547 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/e09ce114d240/snpeffv_genomedb.loc' for 'snpeffv_genomedb'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,547 Loaded tool data table 'snpeffv_genomedb' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,557 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/e09ce114d240/snpeffv_regulationdb.loc' for 'snpeffv_regulationdb'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,557 Loaded tool data table 'snpeffv_regulationdb' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,582 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/e09ce114d240/snpeffv_annotations.loc' for 'snpeffv_annotations'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,582 Loaded tool data table 'snpeffv_annotations' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,598 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/e09ce114d240/snpeffv_databases.loc' for 'snpeffv_databases'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,598 Loaded tool data table 'snpeffv_databases' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,658 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/99684adf84de/fasta_indexes.loc' for 'fasta_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,658 Loading another instance of data table 'fasta_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,724 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/cfc86c3fc5c8/sam_fa_indices.loc' for 'sam_fa_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,725 Loading another instance of data table 'sam_fa_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,728 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/kraken_report/9ae975c30dde/kraken_databases.loc' for 'kraken_databases'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,728 Loaded tool data table 'kraken_databases' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,736 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/kraken_translate/b9971bca4b01/kraken_databases.loc' for 'kraken_databases'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,737 Loading another instance of data table 'kraken_databases' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,739 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/kraken_filter/fe94f318048c/kraken_databases.loc' for 'kraken_databases'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,739 Loading another instance of data table 'kraken_databases' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,742 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/kraken/b2392a9dfb01/kraken_databases.loc' for 'kraken_databases'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,743 Loading another instance of data table 'kraken_databases' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,822 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/data_manager_diamond_database_builder/ce62d0912b10/diamond_database.loc' for 'diamond_database'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,822 Loaded tool data table 'diamond_database' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,891 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/98037ef3d2a9/diamond_database.loc' for 'diamond_database'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,891 Loading another instance of data table 'diamond_database' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:52,894 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/d844fdcce44e/ncbi_taxonomy.loc' for 'ncbi_taxonomy'
galaxy.tools.data DEBUG 2017-08-30 06:38:52,894 Loaded tool data table 'ncbi_taxonomy' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2017-08-30 06:38:53,111 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/cdcc4bb60bc3/all_fasta.loc' for 'all_fasta'
galaxy.tools.data DEBUG 2017-08-30 06:38:53,111 Loading another instance of data table 'all_fasta' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:53,181 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/62d1fae3b7d3/all_fasta.loc' for 'all_fasta'
galaxy.tools.data DEBUG 2017-08-30 06:38:53,181 Loading another instance of data table 'all_fasta' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:53,231 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/table_recalibration/30e1dd77e99c/gatk_sorted_picard_index.loc' for 'gatk_picard_indexes'
galaxy.tools.data DEBUG 2017-08-30 06:38:53,231 Loading another instance of data table 'gatk_picard_indexes' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2017-08-30 06:38:53,277 Loaded 0 lines from '/opt/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/de2c5e5a206c/gene_sets.loc' for 'gene_sets'
galaxy.tools.data DEBUG 2017-08-30 06:38:53,277 Loaded tool data table 'gene_sets' from file '/opt/galaxy/galaxy-app/config/shed_tool_data_table_conf.xml'
galaxy.jobs DEBUG 2017-08-30 06:38:53,392 Loading job configuration from ./config/job_conf.xml
galaxy.jobs DEBUG 2017-08-30 06:38:53,393 Read definition for handler 'web0'
galaxy.jobs DEBUG 2017-08-30 06:38:53,393 <handlers> default set to child with id or tag 'handlers'
galaxy.jobs DEBUG 2017-08-30 06:38:53,393 <destinations> default set to child with id or tag 'slurm_cluster'
galaxy.jobs DEBUG 2017-08-30 06:38:53,394 Done loading job configuration
beaker.container DEBUG 2017-08-30 06:38:53,776 data file /opt/galaxy/galaxy-app/database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache
galaxy.tools.toolbox.base INFO 2017-08-30 06:38:55,390 Parsing the tool configuration /opt/galaxy/galaxy-app/config/tool_conf.xml
galaxy.tools.toolbox.base ERROR 2017-08-30 06:38:55,793 Error reading tool configuration file from path: extract/liftOver_wrapper.xml
galaxy.tools.toolbox.base DEBUG 2017-08-30 06:38:55,815 Loading tool Cut1 from cache
galaxy.tools.toolbox.base INFO 2017-08-30 06:38:56,043 Parsing the tool configuration /opt/galaxy/galaxy-app/config/shed_tool_conf.xml
galaxy.tools WARNING 2017-08-30 06:38:57,257 Tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3: a when tag has not been defined for 'illuminaclip (do_illuminaclip) --> no', assuming empty inputs.
galaxy.tools WARNING 2017-08-30 06:38:58,148 Tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1: a when tag has been defined for 'manipulation (manipulation_selector) --> modify_each_score', but does not appear to be selectable.
galaxy.tools.parameters.dynamic_options WARNING 2017-08-30 06:39:01,590 Data table named 'gff_gene_annotations' is required by tool but not configured
galaxy.tools WARNING 2017-08-30 06:39:01,814 Tool toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy1: a when tag has not been defined for 'samout_conditional (samout) --> False', assuming empty inputs.
galaxy.tools WARNING 2017-08-30 06:39:03,745 Tool toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1: a when tag has not been defined for 'D (seq_dictionary) --> false', assuming empty inputs.
galaxy.tools WARNING 2017-08-30 06:39:03,746 Tool toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1: a when tag has not been defined for 'i (alt_indel_snp_ratio) --> false', assuming empty inputs.
galaxy.tools WARNING 2017-08-30 06:39:03,746 Tool toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1: a when tag has not been defined for 'p (variant_filter) --> false', assuming empty inputs.
galaxy.tools WARNING 2017-08-30 06:39:03,747 Tool toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1: a when tag has not been defined for 't (mutation_rate) --> false', assuming empty inputs.
galaxy.tools WARNING 2017-08-30 06:39:04,406 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.2: a when tag has not been defined for 'rule_configuration (rules_selector) --> false', assuming empty inputs.
galaxy.tools WARNING 2017-08-30 06:39:04,420 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2: a when tag has not been defined for 'format_type (format_type_selector) --> fastq', assuming empty inputs.
galaxy.tools WARNING 2017-08-30 06:39:04,420 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2: a when tag has not been defined for 'format_type (format_type_selector) --> bed', assuming empty inputs.
galaxy.tools WARNING 2017-08-30 06:39:04,421 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2: a when tag has not been defined for 'format_type (format_type_selector) --> yaml', assuming empty inputs.
galaxy.tools WARNING 2017-08-30 06:39:04,421 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2: a when tag has not been defined for 'format_type (format_type_selector) --> json', assuming empty inputs.
galaxy.tools WARNING 2017-08-30 06:39:04,421 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2: a when tag has not been defined for 'format_type (format_type_selector) --> fasta', assuming empty inputs.
galaxy.tools WARNING 2017-08-30 06:39:04,421 Tool toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2: a when tag has been defined for 'analysis_type (analysis_type_selector) --> sort', but does not appear to be selectable.
galaxy.tools WARNING 2017-08-30 06:39:05,632 Tool toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/0.0.3: a when tag has not been defined for 'adv_options (adv_options_selector) --> false', assuming empty inputs.
galaxy.tools WARNING 2017-08-30 06:39:06,340 Tool toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/0.0.3: a when tag has not been defined for 'adv_options (adv_options_selector) --> false', assuming empty inputs.
/opt/galaxy/galaxy-app/lib/galaxy/tools/parameters/basic.py:1228: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
if elem.find( 'filter' ):
galaxy.tools WARNING 2017-08-30 06:39:13,408 Tool toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.22.1: a when tag has not been defined for 'genome (genome_choose) --> ', assuming empty inputs.
galaxy.tools WARNING 2017-08-30 06:39:13,822 Tool with id toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.22.0 declares a conditional test parameter as optional, this is invalid and will be ignored.
galaxy.tools WARNING 2017-08-30 06:39:13,822 Tool toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.22.0: a when tag has not been defined for 'addition2 (addition2_select) --> ', assuming empty inputs.
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:15,793 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/iuc/vegan_rarefaction/dd2705a31239/vegan_rarefaction/vegan_rarefaction.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 552, in _load_tool_tag_set
tool = self.load_tool(os.path.join( tool_path, path ), guid=guid, repository_id=repository_id, use_cached=False)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 737, in load_tool
if tool.tool_shed_repository or not guid:
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 453, in tool_shed_repository
installed_changeset_revision=self.installed_changeset_revision )
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2776, in _execute_and_instances
result = conn.execute(querycontext.statement, self._params)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 914, in execute
return meth(self, multiparams, params)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement
compiled_sql, distilled_params
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1146, in _execute_context
context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1341, in _handle_dbapi_exception
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1139, in _execute_context
context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 450, in do_execute
cursor.execute(statement, parameters)
OperationalError: (psycopg2.OperationalError) terminating connection due to administrator command
server closed the connection unexpectedly
This probably means the server terminated abnormally
before or while processing the request.
[SQL: 'SELECT tool_shed_repository.id AS tool_shed_repository_id, tool_shed_repository.create_time AS tool_shed_repository_create_time, tool_shed_repository.update_time AS tool_shed_repository_update_time, tool_shed_repository.tool_shed AS tool_shed_repository_tool_shed, tool_shed_repository.name AS tool_shed_repository_name, tool_shed_repository.description AS tool_shed_repository_description, tool_shed_repository.owner AS tool_shed_repository_owner, tool_shed_repository.installed_changeset_revision AS tool_shed_repository_installed_changeset_revision, tool_shed_repository.changeset_revision AS tool_shed_repository_changeset_revision, tool_shed_repository.ctx_rev AS tool_shed_repository_ctx_rev, tool_shed_repository.metadata AS tool_shed_repository_metadata, tool_shed_repository.includes_datatypes AS tool_shed_repository_includes_datatypes, tool_shed_repository.tool_shed_status AS tool_shed_repository_tool_shed_status, tool_shed_repository.deleted AS tool_shed_repository_deleted, tool_shed_repository.uninstalled AS tool_shed_repository_uninstalled, tool_shed_repository.dist_to_shed AS tool_shed_repository_dist_to_shed, tool_shed_repository.status AS tool_shed_repository_status, tool_shed_repository.error_message AS tool_shed_repository_error_message \nFROM tool_shed_repository \nWHERE tool_shed_repository.tool_shed = %(tool_shed_1)s AND tool_shed_repository.name = %(name_1)s AND tool_shed_repository.owner = %(owner_1)s AND tool_shed_repository.installed_changeset_revision = %(installed_changeset_revision_1)s \n LIMIT %(param_1)s'] [parameters: {'tool_shed_1': u'toolshed.g2.bx.psu.edu', 'name_1': u'vegan_rarefaction', 'installed_changeset_revision_1': u'dd2705a31239', 'param_1': 1, 'owner_1': u'iuc'}]
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,226 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/f11a04ed443b/taxonomy_krona_chart/taxonomy_krona_chart.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,257 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/576963db5f1b/vsearch/alignment.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,271 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/576963db5f1b/vsearch/dereplication.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,284 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/576963db5f1b/vsearch/sorting.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,292 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/576963db5f1b/vsearch/masking.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,300 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/576963db5f1b/vsearch/search.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,308 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/576963db5f1b/vsearch/shuffling.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,319 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/576963db5f1b/vsearch/chimera.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,328 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/iuc/vsearch/576963db5f1b/vsearch/clustering.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,341 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/bgruening/diamond/98037ef3d2a9/diamond/diamond_makedb.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,352 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/bgruening/diamond/98037ef3d2a9/diamond/diamond.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,363 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/d844fdcce44e/kraken2tax/kraken2tax.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,371 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/cd_hit_dup/0fb894bd8eba/cd_hit_dup/cd_hit_dup.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,380 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/linear_regression/cf431604ec3e/linear_regression/linear_regression.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,388 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/logistic_regression_vif/bd196d7c1ca9/logistic_regression_vif/logistic_regression_vif.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,396 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/partialr_square/88ef41de020d/partialr_square/partialR_square.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,404 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/rcve/7740956d197b/rcve/rcve.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,414 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/best_regression_subsets/4f33ec73e445/best_regression_subsets/best_regression_subsets.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,423 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/canonical_correlation_analysis/9bc0c48a027f/canonical_correlation_analysis/cca.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,431 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/kernel_canonical_correlation_analysis/5ce5a2adb875/kernel_canonical_correlation_analysis/kcca.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,439 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/kernel_principal_component_analysis/3d58aa83e4a3/kernel_principal_component_analysis/kpca.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,448 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/f568051cdf2e/principal_component_analysis/pca.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,460 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/cdcc4bb60bc3/meme_fimo/fimo.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,471 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/62d1fae3b7d3/meme_meme/meme.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,480 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/a3113043abb0/str_fm/profilegenerator.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,488 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/a3113043abb0/str_fm/PEsortedSAM2readprofile.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,496 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/a3113043abb0/str_fm/microsatpurity.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2074, in _wrap_pool_connect
return fn()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 376, in connect
return _ConnectionFairy._checkout(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 713, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 485, in checkout
rec.checkin()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 482, in checkout
dbapi_connection = rec.get_connection()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 563, in get_connection
self.connection = self.__connect()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/pool.py", line 607, in __connect
connection = self.__pool._invoke_creator(self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 97, in connect
return dialect.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 385, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
OperationalError: (psycopg2.OperationalError) FATAL: the database system is shutting down
FATAL: the database system is shutting down
galaxy.tools.toolbox.base ERROR 2017-08-30 06:39:16,504 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/a3113043abb0/str_fm/microsatcompat.xml
Traceback (most recent call last):
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 547, in _load_tool_tag_set
tool_shed_repository = self.get_tool_repository_from_xml_item(item, path)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/toolbox/base.py", line 613, in get_tool_repository_from_xml_item
installed_changeset_revision)
File "/opt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 289, in _get_tool_shed_repository
installed_changeset_revision=installed_changeset_revision
File "/opt/galaxy/galaxy-app/lib/tool_shed/util/repository_util.py", line 389, in get_installed_repository
return query.filter( and_( *clause_list ) ).first()
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2659, in first
ret = list(self[0:1])
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
return list(res)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
return self._execute_and_instances(context)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2774, in _execute_and_instances
close_with_result=True)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2765, in _connection_from_session
**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 893, in connection
execution_options=execution_options)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 900, in _connection_for_bind
conn = engine.contextual_connect(**kw)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2039, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 2078, in _wrap_pool_connect
e, dialect, self)
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1405, in _handle_dbapi_exception_noconnection
exc_info
File "/opt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, c