Galaxy_test_pasteur/api.log at master · fmareuil/Galaxy_test_pasteur · GitHub

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python path is: /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/Whoosh-0.3.18-py2.7.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs4.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs4.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/amqplib-0.6.1-py2.7.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.7.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs4.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg, /home/fmareuil/Travail/Galaxy/galaxy-dist/lib, /usr/lib/python2.7, /usr/lib/python2.7/plat-x86_64-linux-gnu, /usr/lib/python2.7/lib-tk, /usr/lib/python2.7/lib-old, /usr/lib/python2.7/lib-dynload, /usr/local/lib/python2.7/dist-packages, /usr/lib/python2.7/dist-packages/PILcompat, /usr/lib/python2.7/dist-packages/gtk-2.0, /usr/lib/pymodules/python2.7, /usr/lib/python2.7/dist-packages/ubuntu-sso-client, /usr/lib/python2.7/dist-packages
tool_shed.tool_shed_registry DEBUG 2014-04-18 16:36:45,397 Loading references to tool sheds from tool_sheds_conf.xml
tool_shed.tool_shed_registry DEBUG 2014-04-18 16:36:45,397 Loaded reference to tool shed: Galaxy main tool shed
tool_shed.tool_shed_registry DEBUG 2014-04-18 16:36:45,397 Loaded reference to tool shed: Galaxy test tool shed
galaxy.eggs WARNING 2014-04-18 16:36:45,655 Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetched
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migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,737 Loading script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,737 Script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py loaded successfully
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,738 Loading script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,738 Script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py loaded successfully
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,738 Loading script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,738 Script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,738 Loading script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,738 Script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py loaded successfully
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,738 Loading script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,738 Script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py loaded successfully
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,738 Loading script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,738 Script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py loaded successfully
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,738 Loading script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,738 Script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py loaded successfully
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,738 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,738 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully
migrate.versioning.repository DEBUG 2014-04-18 16:36:45,738 Repository lib/galaxy/model/migrate loaded successfully
migrate.versioning.repository DEBUG 2014-04-18 16:36:45,738 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))])
galaxy.model.migrate.check DEBUG 2014-04-18 16:36:45,742 psycopg2 egg successfully loaded for postgres dialect
/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/url.py:105: SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed from 'postgres' to 'postgresql'. The new URL format is postgresql[+driver]://<user>:<pass>@<host>/<dbname>
galaxy.model.migrate.check INFO 2014-04-18 16:36:45,907 At database version 117
migrate.versioning.repository DEBUG 2014-04-18 16:36:45,928 Loading repository lib/tool_shed/galaxy_install/migrate...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,928 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,928 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,928 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,928 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,928 Loading script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,928 Script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,928 Loading script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,928 Script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,929 Loading script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,929 Script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,929 Loading script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,929 Script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,929 Loading script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,929 Script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,929 Loading script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py...
migrate.versioning.script.base DEBUG 2014-04-18 16:36:45,929 Script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py loaded successfully
migrate.versioning.repository DEBUG 2014-04-18 16:36:45,929 Repository lib/tool_shed/galaxy_install/migrate loaded successfully
migrate.versioning.repository DEBUG 2014-04-18 16:36:45,929 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))])
tool_shed.galaxy_install.migrate.check DEBUG 2014-04-18 16:36:45,931 psycopg2 egg successfully loaded for postgres dialect
tool_shed.galaxy_install.migrate.check INFO 2014-04-18 16:36:45,958 At migrate_tools version 8
galaxy.model.mapping DEBUG 2014-04-18 16:36:45,964 psycopg2 egg successfully loaded for postgres dialect
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,985 Loading datatypes from datatypes_conf.xml
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,991 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,991 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,991 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,991 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,991 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,991 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,991 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,991 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,992 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,992 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,992 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,992 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,992 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,992 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,992 Loaded sniffer for datatype 'galaxy.datatypes.images:Html'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,992 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,992 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,992 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,992 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,992 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,992 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,993 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,993 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,993 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,993 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,993 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,993 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Png'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Im'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,995 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,995 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,995 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,995 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:45,995 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,003 Loaded tool data table 'all_fasta'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,003 Loaded tool data table 'bfast_indexes'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,003 Loaded tool data table 'blastdb'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,003 Loaded tool data table 'blastdb_p'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,003 Loaded tool data table 'bowtie2_indexes'
galaxy.tools.data WARNING 2014-04-18 16:36:46,004 Line 34 in tool data table 'bwa_indexes' is invalid (HINT: '<TAB>' characters must be used to separate fields):
mm9     mm9     /pasteur/projets/common/galaxy/projets/genomes/mm9/mm9.fa
galaxy.tools.data WARNING 2014-04-18 16:36:46,004 Line 35 in tool data table 'bwa_indexes' is invalid (HINT: '<TAB>' characters must be used to separate fields):
mm10    mm10    /pasteur/projets/common/galaxy/projets/genomes/mm10/mm10.fa
galaxy.tools.data WARNING 2014-04-18 16:36:46,004 Line 36 in tool data table 'bwa_indexes' is invalid (HINT: '<TAB>' characters must be used to separate fields):
spombe  spombe  /pasteur/services/banques/biomaj/banques/spombe/current/bwa/0.5/spombe
galaxy.tools.data WARNING 2014-04-18 16:36:46,004 Line 37 in tool data table 'bwa_indexes' is invalid (HINT: '<TAB>' characters must be used to separate fields):
pfalciparum     pfalciparum     /pasteur/services/banques/biomaj/banques/pfalciparum/current/bwa/0.5/pfalciparum
galaxy.tools.data WARNING 2014-04-18 16:36:46,004 Line 38 in tool data table 'bwa_indexes' is invalid (HINT: '<TAB>' characters must be used to separate fields):
pig             pig             /pasteur/services/banques/biomaj/banques/pig/current/bwa/0.5/pig
galaxy.tools.data WARNING 2014-04-18 16:36:46,004 Line 39 in tool data table 'bwa_indexes' is invalid (HINT: '<TAB>' characters must be used to separate fields):
yeast           yeast           /pasteur/services/banques/biomaj/banques/yeast/current/bwa/0.5/yeast
galaxy.tools.data WARNING 2014-04-18 16:36:46,004 Line 40 in tool data table 'bwa_indexes' is invalid (HINT: '<TAB>' characters must be used to separate fields):
pteropus        pteropus        /pasteur/services/banques/biomaj/banques/pteropus/current/bwa/0.5/pteropus
galaxy.tools.data WARNING 2014-04-18 16:36:46,004 Line 41 in tool data table 'bwa_indexes' is invalid (HINT: '<TAB>' characters must be used to separate fields):
pvivax          pvivax          /pasteur/services/banques/biomaj/banques/pvivax/current/bwa/0.5/pvivax
galaxy.tools.data WARNING 2014-04-18 16:36:46,004 Line 42 in tool data table 'bwa_indexes' is invalid (HINT: '<TAB>' characters must be used to separate fields):
calbicans5314   calbicans5314   /pasteur/services/banques/biomaj/banques/calbicans5314/current/bwa/0.5/calbicans5314
galaxy.tools.data WARNING 2014-04-18 16:36:46,004 Line 43 in tool data table 'bwa_indexes' is invalid (HINT: '<TAB>' characters must be used to separate fields):
calbicansWO1    calbicansWO1    /pasteur/services/banques/biomaj/banques/calbicansWO1/current/bwa/0.5/calbicansWO1
galaxy.tools.data DEBUG 2014-04-18 16:36:46,004 Loaded tool data table 'bwa_indexes'
galaxy.tools.data WARNING 2014-04-18 16:36:46,004 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,004 Loaded tool data table 'bwa_indexes_color'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,004 Loaded tool data table 'indexed_maf_files'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,004 Loaded tool data table 'ngs_sim_fasta'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,004 Loaded tool data table 'perm_base_indexes'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,005 Loaded tool data table 'perm_color_indexes'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,005 Loaded tool data table 'sam_fa_indexes'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,005 Loaded tool data table 'picard_indexes'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,005 Loaded tool data table 'gatk_picard_indexes'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,005 Loaded tool data table 'gatk_annotations'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,005 Loaded tool data table 'srma_indexes'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,005 Loaded tool data table 'tophat_indexes'
galaxy.tools.data WARNING 2014-04-18 16:36:46,005 Cannot find index file 'tool-data/bowtie_indices_color.loc' for tool data table 'tophat_indexes_color'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,005 Loaded tool data table 'tophat_indexes_color'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,005 Loaded tool data table 'tophat2_indexes'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,007 Loaded tool data table 'ccat_configurations'
galaxy.tools.data DEBUG 2014-04-18 16:36:46,007 Loaded tool data table 'mosaik_indexes'
galaxy.jobs WARNING 2014-04-18 16:36:46,007 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/home/fmareuil/Travail/Galaxy/galaxy-dist/universe_wsgi.ini" instead
galaxy.jobs DEBUG 2014-04-18 16:36:46,007 Loading job configuration from /home/fmareuil/Travail/Galaxy/galaxy-dist/universe_wsgi.ini
galaxy.jobs DEBUG 2014-04-18 16:36:46,007 Done loading job configuration
galaxy.tools INFO 2014-04-18 16:36:46,064 Parsing the tool configuration ./tool_conf.xml
galaxy.tools ERROR 2014-04-18 16:36:46,350 Error reading tool from path: test/sleep.xml
Traceback (most recent call last):
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 494, in load_tool_tag_set
    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 607, in load_tool
    tree = load_tool( config_file )
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
    tree = parse_xml(path)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 135, in parse_xml
    tree = ElementTree.parse(fname)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
    tree.parse(source, parser)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
    source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/test/sleep.xml'
galaxy.tools WARNING 2014-04-18 16:36:47,802 Tool maximal_information_based_nonparametric_exploration: a when tag has not been defined for 'master_variable_type (master_variable_type_selector) --> allPairs', assuming empty inputs.
galaxy.tools WARNING 2014-04-18 16:36:48,794 Tool fastq_manipulation: a when tag has been defined for 'manipulation (manipulation_selector) --> modify_each_score', but does not appear to be selectable.
galaxy.tools ERROR 2014-04-18 16:36:48,869 Error reading tool from path: sr_mapping/bowtie_wrapper.xml
Traceback (most recent call last):
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 494, in load_tool_tag_set
    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 607, in load_tool
    tree = load_tool( config_file )
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
    tree = parse_xml(path)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 135, in parse_xml
    tree = ElementTree.parse(fname)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
    tree.parse(source, parser)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
    source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/sr_mapping/bowtie_wrapper.xml'
galaxy.tools ERROR 2014-04-18 16:36:48,869 Error reading tool from path: sr_mapping/bowtie_color_wrapper.xml
Traceback (most recent call last):
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 494, in load_tool_tag_set
    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 607, in load_tool
    tree = load_tool( config_file )
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
    tree = parse_xml(path)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 135, in parse_xml
    tree = ElementTree.parse(fname)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
    tree.parse(source, parser)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
    source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/sr_mapping/bowtie_color_wrapper.xml'
galaxy.tools ERROR 2014-04-18 16:36:48,869 Error reading tool from path: sr_mapping/pbwa_wrapper.xml
Traceback (most recent call last):
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 494, in load_tool_tag_set
    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 607, in load_tool
    tree = load_tool( config_file )
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
    tree = parse_xml(path)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 135, in parse_xml
    tree = ElementTree.parse(fname)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
    tree.parse(source, parser)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
    source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/sr_mapping/pbwa_wrapper.xml'
docutils WARNING 2014-04-18 16:36:49,072 <string>:50: (WARNING/2) Literal block expected; none found.

galaxy.tools ERROR 2014-04-18 16:36:49,103 Error reading tool from path: samtools/sam_merge.xml
Traceback (most recent call last):
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 494, in load_tool_tag_set
    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 607, in load_tool
    tree = load_tool( config_file )
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
    tree = parse_xml(path)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 135, in parse_xml
    tree = ElementTree.parse(fname)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
    tree.parse(source, parser)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
    source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/samtools/sam_merge.xml'
galaxy.tools INFO 2014-04-18 16:36:49,638 Parsing the tool configuration ./shed_tool_conf.xml
galaxy.tools ERROR 2014-04-18 16:36:49,895 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/malex/beast/2ca3df65222b/beast/beast.xml
Traceback (most recent call last):
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 494, in load_tool_tag_set
    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 607, in load_tool
    tree = load_tool( config_file )
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
    tree = parse_xml(path)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 135, in parse_xml
    tree = ElementTree.parse(fname)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
    tree.parse(source, parser)
  File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
    source = open(source, "rb")
IOError: [Errno 2] No such file or directory: '../shed_tools/toolshed.g2.bx.psu.edu/repos/malex/beast/2ca3df65222b/beast/beast.xml'
galaxy.tools INFO 2014-04-18 16:36:50,473 Parsing the tool configuration ./migrated_tools_conf.xml
galaxy.tools DEBUG 2014-04-18 16:36:50,473 Loading section: mytools
galaxy.tools DEBUG 2014-04-18 16:36:50,473 Loading section: Get Data
galaxy.tools DEBUG 2014-04-18 16:36:50,473 Loaded tool id: upload1, version: 1.1.3 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,473 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,473 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,473 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,473 Loaded tool id: bx_browser, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,473 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,473 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,473 Loaded tool id: biomart, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,473 Loaded tool id: biomart_test, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,473 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: gramenemart, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: modENCODEfly, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: flymine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: flymine_test, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: modmine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: ratmine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: yeastmine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: modENCODEworm, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: wormbase, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: eupathdb, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: encode_db1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: epigraph_import, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: epigraph_import_test, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: hbvar, version: 2.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: genomespace_file_browser_prod, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: genomespace_importer, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,474 Loaded tool id: fix_errors, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: mpileup, version: 0.1.19 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loading section: Send Data
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: epigraph_export, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: epigraph_test_export, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: genomespace_exporter, version: 0.0.2 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loading section: ENCODE Tools
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: gencode_partition1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: random_intervals1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loading section: Lift-Over
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: liftOver1, version: 1.0.3 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loading section: Text Manipulation
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: addValue, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: Add_a_column1, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: cat1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: Cut1, version: 1.0.2 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: createInterval, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,475 Loaded tool id: Paste1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: random_lines1, version: 2.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: Show tail1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: trimmer, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: dna_filter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: tables_arithmetic_operations, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loading section: Filter and Sort
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: Filter1, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: sort1, version: 1.0.3 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: Grep1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded label: GFF
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: gff_filter_by_attribute, version: 0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: gff_filter_by_feature_count, version: 0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loading section: Join, Subtract and Group
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: join1, version: 2.0.2 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,476 Loaded tool id: comp1, version: 1.0.2 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: subtract_query1, version: 0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: Grouping1, version: 2.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: column_join, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loading section: Convert Formats
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: fasta2tab, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: tab2fasta, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: fastq_to_fasta_python, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loading section: Extract Features
galaxy.tools DEBUG 2014-04-18 16:36:50,477 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loading section: Fetch Sequences
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: Extract genomic DNA 1, version: 2.2.2 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loading section: Fetch Alignments
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loading section: Get Genomic Scores
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,478 Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.3 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: phastOdds_for_intervals, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loading section: Operate on Genomic Intervals
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: gops_intersect_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: gops_subtract_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: gops_merge_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: gops_concat_1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: gops_basecoverage_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: gops_coverage_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: gops_complement_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: gops_cluster_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: gops_join_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: get_flanks1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: flanking_features_1, version: 4.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: Annotation_Profiler_0, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loading section: Statistics
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: Summary_Statistics1, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: Count1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: cor2, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: generate_matrix_for_pca_and_lda1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: lda_analy1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,479 Loaded tool id: plot_for_lda_output1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: compute_q_values, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: maximal_information_based_nonparametric_exploration, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded label: GFF
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: count_gff_features, version: 0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loading section: Wavelet Analysis
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: dwt_var1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loading section: Graph/Display Data
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: histogram_rpy, version: 1.0.3 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: scatterplot_rpy, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: gmaj_1, version: 2.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: laj_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: build_ucsc_custom_track_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: mutation_visualize, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loading section: Regional Variation
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: winSplitter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: featureCoverage1, version: 2.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,480 Loaded tool id: wtavg, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: qualityFilter, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: cpgFilter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: getIndels_2way, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: indelRates_3way, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: substitutions1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: subRate1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: microsats_align1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: microsats_mutability1, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loading section: Multiple regression
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: LinearRegression1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: LogisticRegression, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: BestSubsetsRegression1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: rcve1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: partialRsq, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loading section: Multivariate Analysis
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: pca1, version: 1.0.2 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: cca1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: kpca1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: kcca1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loading section: Evolution
galaxy.tools DEBUG 2014-04-18 16:36:50,481 Loaded tool id: hyphy_branch_lengths_wrapper1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: hyphy_nj_tree_wrapper1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: hyphy_dnds_wrapper1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: hgv_codingSnps, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: hgv_add_scores, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loading section: Motif Tools
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: meme_meme, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: meme_fimo, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: rgweblogo3, version: 0.4 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loading section: Multiple Alignments
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: clustalw, version: 0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loading section: Metagenomic analyses
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: Fetch Taxonomic Ranks, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: t2t_report, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: Draw_phylogram, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: find_diag_hits, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: lca1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: poisson2test, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loading section: FASTA manipulation
galaxy.tools DEBUG 2014-04-18 16:36:50,482 Loaded tool id: fasta_compute_length, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded tool id: fasta_filter_by_length, version: 1.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded tool id: fasta_concatenate0, version: 0.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded tool id: fasta2tab, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded tool id: tab2fasta, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loading section: NGS: QC and manipulation
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded label: FastQC: fastq/sam/bam
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded tool id: fastqc, version: 0.52 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded label: Illumina fastq
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded tool id: fastq_paired_end_splitter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded tool id: fastq_paired_end_joiner, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded tool id: fastq_stats, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded label: Roche-454 data
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded tool id: quality_score_distribution, version: 1.0.2 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded tool id: trim_reads, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded tool id: fastq_combiner, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded label: AB-SOLiD data
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded tool id: solid2fastq, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded tool id: solid_qual_stats, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded tool id: solid_qual_boxplot, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,483 Loaded label: Generic FASTQ manipulation
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: fastq_filter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: fastq_masker_by_quality, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: fastq_paired_end_interlacer, version: 1.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: fastq_paired_end_deinterlacer, version: 1.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: fastq_manipulation, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: fastq_to_fasta_python, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: fastq_to_tabular, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: tabular_to_fastq, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loading section: NGS: Mapping
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: bowtie2, version: 0.2 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: megablast_wrapper, version: 1.2.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: megablast_xml_parser, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loading section: NGS: Indel Analysis
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: sam_indel_filter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: indel_sam2interval, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: indel_table, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: indel_analysis, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loading section: NGS: RNA Analysis
galaxy.tools DEBUG 2014-04-18 16:36:50,484 Loaded tool id: tophat, version: 1.5.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loaded tool id: tophat2, version: 0.6 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loaded tool id: tophat_color, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loaded tool id: express, version: 1.1.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loaded tool id: filter_combined_via_tracking, version: 0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loading section: NGS: SAM Tools
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loading section: NGS: GATK Tools version 2.4-9
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loading section: NGS: Peak Calling/ChIP-seq
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loaded tool id: peakcalling_macs, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loaded tool id: peakcalling_sicer, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loaded tool id: peakcalling_ccat, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loading section: NGS: Simulation
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loaded tool id: ngs_simulation, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loading section: NGS: VCF Tools
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loaded tool id: vcf2pgSnp, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loaded tool id: vcf_intersect, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loaded tool id: vcf_annotate, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loaded tool id: vcf_filter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,485 Loaded tool id: vcf_extract, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loading section: NGS: Assembly package clc 4
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loading section: NGS: BedTools
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loading section: NGS: Picard Tools
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loading section: NGS: BCF Tools
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loading section: SNP/WGA: Data; Filters
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loading section: Phenotype Association
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loaded tool id: hgv_codingSnps, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loaded tool id: hgv_add_scores, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loaded tool id: hgv_sift, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loaded tool id: hgv_david, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loaded tool id: hgv_snpFreq, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loaded tool id: freebayes_wrapper, version: 0.5.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loaded tool id: vcf2pgSnp, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,486 Loading section: Phylogeny
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loaded tool id: hyphy_branch_lengths_wrapper1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loaded tool id: hyphy_nj_tree_wrapper1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loaded tool id: hyphy_dnds_wrapper1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loaded tool id: Draw_phylogram, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loading section: Phylogeny Find Promoteur Project
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loading section: RNA-Seq URGI Tools (beta)
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loading section: ChIP-SEQ Analysis Nebula Tools, Institut Curie
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loading section: Temporary/Test
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loading section: NCBI-BLAST
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.0.17, version: 0.0.17 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.0.17, version: 0.0.17 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.0.1, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.0.10, version: 0.0.10 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.0.3, version: 0.0.3 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.0.17, version: 0.0.17 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.0.17, version: 0.0.17 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.0.17, version: 0.0.17 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info/0.0.2, version: 0.0.2 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loading section: MyTools
galaxy.tools DEBUG 2014-04-18 16:36:50,487 Loading section: NCBI-BLAST
galaxy.tools DEBUG 2014-04-18 16:36:50,488 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.0.22, version: 0.0.22 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,488 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.0.22, version: 0.0.22 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,488 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.0.22, version: 0.0.22 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,488 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.0.22, version: 0.0.22 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,488 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info/0.0.22, version: 0.0.22 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,488 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.0.22, version: 0.0.22 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,488 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.0.22, version: 0.0.22 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,488 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.0.22, version: 0.0.22 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,488 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.0.22, version: 0.0.22 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,488 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/0.0.22, version: 0.0.22 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,488 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.0.22, version: 0.0.22 into tool panel.
galaxy.tools DEBUG 2014-04-18 16:36:50,488 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.0.22, version: 0.0.22 into tool panel.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,544 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,545 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,546 Loaded display application 'igv_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,547 Loaded display application 'igb_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,547 Loaded display application 'igb_bed' for datatype 'bed', inherit=False.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,549 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,549 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,550 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,551 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,554 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,557 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,560 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,561 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,563 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,564 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,565 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,566 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,567 Loaded display application 'igb_wig' for datatype 'wig', inherit=False.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,568 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False.
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,568 Adding inherited display application 'ensembl_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,568 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,568 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,568 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,568 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,568 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,568 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,568 Adding inherited display application 'ensembl_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,568 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,568 Adding inherited display application 'rviewer_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,569 Adding inherited display application 'ensembl_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,569 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,569 Adding inherited display application 'rviewer_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,569 Adding inherited display application 'ensembl_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,569 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,569 Adding inherited display application 'rviewer_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,569 Adding inherited display application 'ensembl_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,569 Adding inherited display application 'ensembl_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,569 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,569 Adding inherited display application 'rviewer_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,569 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,569 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,569 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,573 Loaded converter: CONVERTER_Bam_Bai_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,577 Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,580 Loaded converter: CONVERTER_bed_to_gff_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,585 Loaded converter: CONVERTER_bed_to_bgzip_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,589 Loaded converter: CONVERTER_bed_to_tabix_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,592 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,595 Loaded converter: CONVERTER_bed_to_fli_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,599 Loaded converter: CONVERTER_bedgraph_to_bigwig
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,602 Loaded converter: CONVERTER_len_to_linecount
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,606 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,610 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,613 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,616 Loaded converter: CONVERTER_fasta_to_tabular
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,621 Loaded converter: CONVERTER_fasta_to_bowtie_base_index
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,625 Loaded converter: CONVERTER_fasta_to_bowtie_color_index
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,628 Loaded converter: CONVERTER_fasta_to_2bit
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,632 Loaded converter: CONVERTER_fasta_to_len
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,635 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,639 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,642 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,645 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,649 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,653 Loaded converter: CONVERTER_gff_to_bed_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,656 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,659 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,664 Loaded converter: CONVERTER_gff_to_fli_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,668 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,671 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,675 Loaded converter: CONVERTER_interval_to_bed_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,678 Loaded converter: CONVERTER_interval_to_bedstrict_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,681 Loaded converter: CONVERTER_interval_to_bed6_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,685 Loaded converter: CONVERTER_interval_to_bed12_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,688 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,692 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,696 Loaded converter: CONVERTER_interval_to_bigwig_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,699 Loaded converter: CONVERTER_picard_interval_list_to_bed6
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,702 Loaded converter: CONVERTER_maf_to_fasta_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,708 Loaded converter: CONVERTER_maf_to_interval_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,711 Loaded converter: CONVERTER_encodepeak_to_tabix_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,715 Loaded converter: CONVERTER_encodepeak_to_bgzip_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,718 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,722 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,725 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,728 Loaded converter: CONVERTER_sam_to_bam
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,732 Loaded converter: CONVERTER_sam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,736 Loaded converter: CONVERTER_vcf_to_bgzip_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,739 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,742 Loaded converter: CONVERTER_vcf_to_tabix_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,748 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,751 Loaded converter: CONVERTER_wig_to_bigwig
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,752 Loaded converter: CONVERTER_wiggle_to_interval_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,755 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,758 Loaded converter: lped2fpedconvert
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,762 Loaded converter: lped2pbedconvert
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,765 Loaded converter: pbed2lpedconvert
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,769 Loaded converter: pbed2ldindepconvert
galaxy.datatypes.registry DEBUG 2014-04-18 16:36:50,769 Loaded external metadata tool: __SET_METADATA__
galaxy.tools.imp_exp DEBUG 2014-04-18 16:36:50,770 Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.imp_exp DEBUG 2014-04-18 16:36:50,771 Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools.genome_index DEBUG 2014-04-18 16:36:50,772 Loaded genome index tool: __GENOME_INDEX__
galaxy.jobs.manager DEBUG 2014-04-18 16:36:50,772 Starting job handler
galaxy.jobs.runners DEBUG 2014-04-18 16:36:50,772 Starting 5 LocalRunner workers
galaxy.jobs DEBUG 2014-04-18 16:36:50,773 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
galaxy.jobs.runners DEBUG 2014-04-18 16:36:50,777 Starting 3 LWRRunner workers
galaxy.jobs DEBUG 2014-04-18 16:36:50,778 Loaded job runner 'galaxy.jobs.runners.lwr:LwrJobRunner' as 'lwr'
galaxy.jobs DEBUG 2014-04-18 16:36:50,778 Legacy destination with id 'local:///', url 'local:///' converted, got params:
galaxy.jobs.handler DEBUG 2014-04-18 16:36:50,778 Loaded job runners plugins: lwr:local
galaxy.jobs.handler INFO 2014-04-18 16:36:50,779 job handler stop queue started
galaxy.jobs.handler INFO 2014-04-18 16:36:50,786 job handler queue started
galaxy.sample_tracking.external_service_types DEBUG 2014-04-18 16:36:50,787 Loaded external_service_type: Simple unknown sequencer 1.0.0
galaxy.sample_tracking.external_service_types DEBUG 2014-04-18 16:36:50,788 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,790 Enabling 'error' controller, class: Error
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,794 Enabling 'data_manager' controller, class: DataManager
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,795 Enabling 'tag' controller, class: TagsController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,795 Enabling 'external_services' controller, class: ExternalServiceController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,795 Enabling 'mobile' controller, class: Mobile
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,799 Enabling 'page' controller, class: PageController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,800 Enabling 'user' controller, class: User
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,805 Enabling 'visualization' controller, class: VisualizationController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,805 Enabling 'forms' controller, class: Forms
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,957 Enabling 'admin_toolshed' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,957 Enabling 'admin_toolshed' controller, class: AdminToolshed
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,960 Enabling 'dataset' controller, class: DatasetInterface
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,961 Enabling 'biostar' controller, class: BiostarController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,961 Enabling 'library' controller, class: Library
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,961 Enabling 'library_admin' controller, class: LibraryAdmin
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,965 Enabling 'data_admin' controller, class: DataAdmin
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,966 Enabling 'tool_runner' controller, class: ToolRunner
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,966 Enabling 'ucsc_proxy' controller, class: UCSCProxy
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,977 Enabling 'requests_admin' controller, class: RequestsAdmin
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,978 Enabling 'workflow' controller, class: WorkflowController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,978 Enabling 'root' controller, class: RootController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,979 Enabling 'request_type' controller, class: RequestType
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,979 Enabling 'library_common' controller, class: LibraryCommon
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,980 Enabling 'external_service' controller, class: ExternalService
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,980 Enabling 'admin' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,980 Enabling 'async' controller, class: ASync
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,980 Enabling 'requests_common' controller, class: RequestsCommon
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,980 Enabling 'requests' controller, class: Requests
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,981 Enabling 'search' controller, class: SearchController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,982 Enabling 'history' controller, class: HistoryController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,993 Enabling 'cloudlaunch' controller, class: CloudController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,995 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,995 Enabling 'history_tags' API controller, class: HistoryTagsController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,995 Enabling 'workflow_tags' API controller, class: WorkflowTagsController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,995 Enabling 'folder_contents' API controller, class: FolderContentsController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,996 Enabling 'library_contents' API controller, class: LibraryContentsController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,996 Enabling 'quotas' API controller, class: QuotaAPIController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,996 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,996 Enabling 'datasets' API controller, class: DatasetsController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,999 Enabling 'visualizations' API controller, class: VisualizationsController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:50,999 Enabling 'forms' API controller, class: FormDefinitionAPIController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,000 Enabling 'folders' API controller, class: FoldersController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,000 Enabling 'history_contents' API controller, class: HistoryContentsController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,000 Enabling 'group_users' API controller, class: GroupUsersAPIController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,000 Enabling 'workflows' API controller, class: WorkflowsAPIController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,001 Enabling 'roles' API controller, class: RoleAPIController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,001 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,001 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,001 Enabling 'libraries' API controller, class: LibrariesController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,001 Enabling 'configuration' API controller, class: ConfigurationController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,001 Enabling 'group_roles' API controller, class: GroupRolesAPIController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,002 Enabling 'genomes' API controller, class: GenomesController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,002 Enabling 'samples' API controller, class: SamplesAPIController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,002 Enabling 'permissions' API controller, class: PermissionsController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,003 Enabling 'tools' API controller, class: ToolsController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,003 Enabling 'request_types' API controller, class: RequestTypeAPIController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,003 Enabling 'users' API controller, class: UserAPIController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,004 Enabling 'datatypes' API controller, class: DatatypesController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,004 Enabling 'groups' API controller, class: GroupAPIController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,007 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,007 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,007 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,007 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,007 Enabling 'requests' API controller, class: RequestsAPIController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,016 Enabling 'search' API controller, class: SearchController
galaxy.web.framework.base DEBUG 2014-04-18 16:36:51,018 Enabling 'histories' API controller, class: HistoriesController
galaxy.webapps.galaxy.buildapp DEBUG 2014-04-18 16:36:51,018 app.config.api_folders: False
galaxy.webapps.galaxy.buildapp DEBUG 2014-04-18 16:36:51,253 Enabling 'httpexceptions' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2014-04-18 16:36:51,253 Enabling 'remote user' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2014-04-18 16:36:51,253 Enabling 'recursive' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2014-04-18 16:36:51,272 Enabling 'eval exceptions' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2014-04-18 16:36:51,272 Enabling 'trans logger' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2014-04-18 16:36:51,272 Enabling 'x-forwarded-host' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2014-04-18 16:36:51,272 Enabling 'Request ID' middleware
Starting server in PID 9641.
serving on http://127.0.0.1:8082
galaxy.jobs.handler INFO 2014-04-18 16:37:44,743 sending stop signal to worker thread
galaxy.jobs.handler INFO 2014-04-18 16:37:44,743 job handler queue stopped
galaxy.jobs.runners INFO 2014-04-18 16:37:44,743 LWRRunner: Sending stop signal to monitor thread
galaxy.jobs.runners INFO 2014-04-18 16:37:44,743 LWRRunner: Sending stop signal to 3 worker threads
galaxy.jobs.runners INFO 2014-04-18 16:37:44,743 LocalRunner: Sending stop signal to 5 worker threads
galaxy.jobs.handler INFO 2014-04-18 16:37:44,744 sending stop signal to worker thread
galaxy.jobs.handler INFO 2014-04-18 16:37:44,744 job handler stop queue stopped
Removing PID file api.pid