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python path is: /home/galaxy/galaxy/eggs/Babel-1.3-py2.7.egg, /home/galaxy/galaxy/eggs/pytz-2013.9-py2.7.egg, /home/galaxy/galaxy/eggs/mercurial-3.2.4-py2.7-linux-x86_64-ucs4.egg, /home/galaxy/galaxy/eggs/Mako-0.4.1-py2.7.egg, /home/galaxy/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg, /home/galaxy/galaxy/eggs/kombu-3.0.24-py2.7.egg, /home/galaxy/galaxy/eggs/anyjson-0.3.3-py2.7.egg, /home/galaxy/galaxy/eggs/PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg, /home/galaxy/galaxy/eggs/WebHelpers-1.3-py2.7.egg, /home/galaxy/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg, /home/galaxy/galaxy/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs4.egg, /home/galaxy/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg, /home/galaxy/galaxy/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg, /home/galaxy/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg, /home/galaxy/galaxy/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs4.egg, /home/galaxy/galaxy/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg, /home/galaxy/galaxy/eggs/WebOb-0.8.5-py2.7.egg, /home/galaxy/galaxy/eggs/Routes-2.1-py2.7.egg, /home/galaxy/galaxy/eggs/repoze.lru-0.6-py2.7.egg, /home/galaxy/galaxy/eggs/amqp-1.4.6-py2.7.egg, /home/galaxy/galaxy/eggs/pexpect-2.4-py2.7.egg, /home/galaxy/galaxy/eggs/wchartype-0.1-py2.7.egg, /home/galaxy/galaxy/eggs/docutils-0.7-py2.7.egg, /home/galaxy/galaxy/eggs/PasteDeploy-1.5.0-py2.7.egg, /home/galaxy/galaxy/eggs/Paste-1.7.5.1-py2.7.egg, /home/galaxy/galaxy/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
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migrate.versioning.script.base DEBUG 2015-07-20 09:59:25,289 Loading script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py...
migrate.versioning.script.base DEBUG 2015-07-20 09:59:25,289 Script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2015-07-20 09:59:25,290 Loading script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py...
migrate.versioning.script.base DEBUG 2015-07-20 09:59:25,290 Script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2015-07-20 09:59:25,290 Loading script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py...
migrate.versioning.script.base DEBUG 2015-07-20 09:59:25,290 Script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2015-07-20 09:59:25,290 Loading script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py...
migrate.versioning.script.base DEBUG 2015-07-20 09:59:25,290 Script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2015-07-20 09:59:25,291 Loading script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py...
migrate.versioning.script.base DEBUG 2015-07-20 09:59:25,291 Script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py loaded successfully
migrate.versioning.repository DEBUG 2015-07-20 09:59:25,291 Repository lib/tool_shed/galaxy_install/migrate loaded successfully
migrate.versioning.repository DEBUG 2015-07-20 09:59:25,291 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))])
tool_shed.galaxy_install.migrate.check DEBUG 2015-07-20 09:59:25,300 psycopg2 egg successfully loaded for postgresql dialect
tool_shed.galaxy_install.migrate.check INFO 2015-07-20 09:59:25,367 At migrate_tools version 12
galaxy.model.orm DEBUG 2015-07-20 09:59:25,375 psycopg2 egg successfully loaded for postgresql dialect
galaxy.config INFO 2015-07-20 09:59:25,427 Install database targetting Galaxy's database configuration.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,688 Loading datatypes from /home/galaxy/galaxy/database/tmp/tmp-toolshed-acalpdzcEvg3
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,694 Loaded sniffer for datatype 'galaxy.datatypes.compressed:Zip'
galaxy.datatypes.registry ERROR 2015-07-20 09:59:25,695 Error importing datatype class for 'galaxy.datatypes.compressed:Tgdb': No module named compressed
Traceback (most recent call last):
  File "/home/galaxy/galaxy/lib/galaxy/datatypes/registry.py", line 380, in load_datatype_sniffers
    module = __import__( datatype_module )
ImportError: No module named compressed
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,707 Loaded sniffer for datatype 'galaxy.datatypes.compressed:Tbz2'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,708 Loaded sniffer for datatype 'galaxy.datatypes.compressed:Fastqgz'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,708 Loaded sniffer for datatype 'galaxy.datatypes.compressed:Fastqbz2'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,738 Loading datatypes from ./config/datatypes_conf.xml
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,738 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,739 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,739 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,739 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,740 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,740 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,740 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,740 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,741 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,741 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,741 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,742 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,742 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,742 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,743 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,743 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,743 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,744 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,744 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,744 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,744 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,745 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,745 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,745 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,745 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,746 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,746 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,746 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,747 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,747 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,747 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,748 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,748 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,748 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,748 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,749 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,749 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,749 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,750 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,750 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,750 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,751 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,751 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,751 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,752 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,752 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,752 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,753 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,753 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,754 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,754 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,755 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,755 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,755 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,756 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,756 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,756 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,756 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,757 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,757 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,757 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,758 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,758 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,758 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,758 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,759 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,763 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,764 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,764 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,765 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,765 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,765 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,766 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,766 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,767 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,767 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,767 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,768 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,768 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,768 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,768 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,769 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,769 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,769 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,770 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,770 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,770 Retrieved datatype module galaxy.datatypes.proteomics:MzSQlite from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,771 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,771 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,771 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,772 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,772 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,772 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,772 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,773 Retrieved datatype module galaxy.datatypes.proteomics:IdpDB from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,773 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,773 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,774 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,774 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,775 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,775 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,775 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,776 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,776 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,776 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,776 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,777 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,777 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,777 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,778 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,778 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,778 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,778 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,779 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,779 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,779 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,780 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,780 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,780 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,780 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,781 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,781 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,781 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,782 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,782 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,782 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,783 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,783 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,783 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,784 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,784 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,784 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,785 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,785 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,785 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,785 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,786 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,786 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,786 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,787 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,787 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,787 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,788 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,788 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,789 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,789 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,789 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,790 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,790 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,790 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,791 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,791 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,791 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,792 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,792 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,792 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,793 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,793 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,793 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,794 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,794 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,794 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,794 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,795 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,795 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,795 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,796 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,796 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,796 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,796 Retrieved datatype module galaxy.datatypes.graph:Rdf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,797 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,797 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,797 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,798 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,798 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,799 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,799 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,799 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,800 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,800 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,800 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,801 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,801 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,802 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,804 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,805 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,805 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,805 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,806 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,806 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,807 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,807 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,808 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,808 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,808 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,809 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,809 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,809 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,810 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,810 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,811 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,811 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,811 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,812 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,812 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,813 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,813 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,813 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,814 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,814 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,814 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,815 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,815 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,816 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,816 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,816 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,817 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,817 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,818 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,818 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,818 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,819 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,819 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,820 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,820 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,820 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,821 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,821 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,822 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,822 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,822 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,823 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,823 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,824 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,824 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,824 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,825 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,825 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,825 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,826 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,826 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,827 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,827 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,827 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,828 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,828 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,829 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,829 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,829 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,830 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,830 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,831 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,831 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,831 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,832 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,832 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,833 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,833 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,833 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,834 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,834 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,834 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,835 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,835 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,836 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,836 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,836 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,836 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,837 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,837 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,837 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,838 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,838 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzSQlite'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,838 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,838 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,839 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,839 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,839 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,839 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,839 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,840 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,840 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,840 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,840 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,840 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,841 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,841 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,841 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,841 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,842 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,842 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,842 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,842 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,843 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,843 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,843 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,843 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,844 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,844 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,844 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,844 Loaded sniffer for datatype 'galaxy.datatypes.images:Html'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,845 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,845 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,845 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,845 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,845 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,846 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,846 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,846 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,846 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,847 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,847 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,847 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,847 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,848 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,848 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,848 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,848 Loaded sniffer for datatype 'galaxy.datatypes.text:Json'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,849 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,849 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,849 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,849 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,850 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,850 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,850 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,850 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,851 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,851 Loaded sniffer for datatype 'galaxy.datatypes.images:Png'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,851 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,851 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,852 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,852 Loaded sniffer for datatype 'galaxy.datatypes.images:Im'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,852 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,852 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,853 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,853 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,853 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,853 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,854 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,854 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,854 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,854 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,854 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,863 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,873 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,873 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,873 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,873 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:25,873 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt
galaxy.tools.data DEBUG 2015-07-20 09:59:26,245 Loaded tool data table 'all_fasta'
galaxy.tools.data DEBUG 2015-07-20 09:59:26,246 Loaded tool data table 'bfast_indexes'
galaxy.tools.data WARNING 2015-07-20 09:59:26,247 Cannot find index file 'tool-data/blastdb_p.loc' for tool data table 'blastdb_p'
galaxy.tools.data DEBUG 2015-07-20 09:59:26,247 Loaded tool data table 'blastdb_p'
galaxy.tools.data WARNING 2015-07-20 09:59:26,247 Cannot find index file 'tool-data/bwa_index.loc' for tool data table 'bwa_indexes'
galaxy.tools.data DEBUG 2015-07-20 09:59:26,248 Loaded tool data table 'bwa_indexes'
galaxy.tools.data WARNING 2015-07-20 09:59:26,248 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color'
galaxy.tools.data DEBUG 2015-07-20 09:59:26,248 Loaded tool data table 'bwa_indexes_color'
galaxy.tools.data DEBUG 2015-07-20 09:59:26,257 Loaded tool data table 'indexed_maf_files'
galaxy.tools.data DEBUG 2015-07-20 09:59:26,263 Loaded tool data table 'ngs_sim_fasta'
galaxy.tools.data DEBUG 2015-07-20 09:59:26,264 Loaded tool data table 'perm_base_indexes'
galaxy.tools.data DEBUG 2015-07-20 09:59:26,265 Loaded tool data table 'perm_color_indexes'
galaxy.tools.data DEBUG 2015-07-20 09:59:26,266 Loaded tool data table 'picard_indexes'
galaxy.tools.data DEBUG 2015-07-20 09:59:26,266 Loaded tool data table 'srma_indexes'
galaxy.tools.data DEBUG 2015-07-20 09:59:26,268 Loaded tool data table 'mosaik_indexes'
galaxy.tools.data DEBUG 2015-07-20 09:59:26,268 Loaded tool data table 'twobit'
galaxy.tools.data DEBUG 2015-07-20 09:59:26,858 Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/home/galaxy/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-2Vl9Tg".
galaxy.tools.data WARNING 2015-07-20 09:59:26,858 Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields):
<Server-Side Genome List>
galaxy.tools.data DEBUG 2015-07-20 09:59:26,862 Loaded tool data table 'igv_broad_genomes'
galaxy.tools.data DEBUG 2015-07-20 09:59:26,871 Loaded tool data table 'bowtie2_indexes'
galaxy.jobs WARNING 2015-07-20 09:59:26,906 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/home/galaxy/galaxy/config/galaxy.ini" instead
galaxy.jobs DEBUG 2015-07-20 09:59:26,907 Loading job configuration from /home/galaxy/galaxy/config/galaxy.ini
galaxy.jobs DEBUG 2015-07-20 09:59:26,907 Done loading job configuration
beaker.container DEBUG 2015-07-20 09:59:27,113 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache
galaxy.tools.toolbox.base INFO 2015-07-20 09:59:27,128 Parsing the tool configuration ./config/tool_conf.xml
galaxy.tools.toolbox.base INFO 2015-07-20 09:59:27,983 Parsing the tool configuration ./config/shed_tool_conf.xml
galaxy.tools.toolbox.base INFO 2015-07-20 09:59:28,144 Parsing the tool configuration ./config/migrated_tools_conf.xml
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,146 Loading section: Test
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,146 Loaded tool id: gunzip, version: 0.1.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,146 Loading section: Get Data
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,147 Loaded tool id: upload1, version: 1.1.4 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,147 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,147 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,148 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,148 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,148 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,149 Loaded tool id: biomart, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,149 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,149 Loaded tool id: gramenemart, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,150 Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,150 Loaded tool id: flymine, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,150 Loaded tool id: flymine_test, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,151 Loaded tool id: modmine, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,151 Loaded tool id: mousemine, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,151 Loaded tool id: ratmine, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,151 Loaded tool id: yeastmine, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,152 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,152 Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,152 Loaded tool id: wormbase, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,153 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,153 Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,153 Loaded tool id: eupathdb, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,154 Loaded tool id: hbvar, version: 2.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,154 Loaded tool id: genomespace_file_browser_prod, version: 0.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,154 Loaded tool id: genomespace_importer, version: 0.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,154 Loaded tool id: fix_errors, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,155 Loading section: Send Data
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,155 Loaded tool id: genomespace_exporter, version: 0.0.4 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,155 Loading section: Lift-Over
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,155 Loaded tool id: liftOver1, version: 1.0.3 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,156 Loading section: Text Manipulation
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,156 Loaded tool id: addValue, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,156 Loaded tool id: cat1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,156 Loaded tool id: Cut1, version: 1.0.2 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,157 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,157 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,157 Loaded tool id: createInterval, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,158 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,158 Loaded tool id: Paste1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,158 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,158 Loaded tool id: random_lines1, version: 2.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,159 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,159 Loaded tool id: Show tail1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,159 Loaded tool id: trimmer, version: 0.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,160 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,160 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,160 Loading section: Filter and Sort
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,160 Loaded tool id: Filter1, version: 1.1.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,161 Loaded tool id: sort1, version: 1.0.3 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,161 Loaded tool id: Grep1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,161 Loaded label: GFF
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,161 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,162 Loaded tool id: gff_filter_by_attribute, version: 0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,162 Loaded tool id: gff_filter_by_feature_count, version: 0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,162 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,162 Loading section: Join, Subtract and Group
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,163 Loaded tool id: join1, version: 2.0.2 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,163 Loaded tool id: comp1, version: 1.0.2 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,163 Loaded tool id: Grouping1, version: 2.1.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,164 Loading section: Convert Formats
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,164 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,164 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,164 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,165 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,165 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,165 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,166 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,166 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,166 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,166 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,167 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,167 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,167 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,168 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,168 Loading section: Extract Features
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,168 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,168 Loading section: Fetch Sequences
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,169 Loaded tool id: Extract genomic DNA 1, version: 2.2.3 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,169 Loading section: Fetch Alignments
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,169 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,169 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,170 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,170 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,170 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,170 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,171 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,171 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,171 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,172 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,172 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,172 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,173 Loading section: Statistics
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,173 Loaded tool id: Summary_Statistics1, version: 1.1.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,173 Loaded tool id: Count1, version: 1.0.2 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,173 Loading section: Graph/Display Data
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,174 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,174 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,174 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,174 Loading section: NGS QC
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,251 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.63, version: 0.63 into tool panel....
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,251 Loading section: NGS: Mapping
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,318 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.4, version: 0.4 into tool panel....
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,318 Loading section: NGS: RNA-Seq
galaxy.tools.toolbox.base DEBUG 2015-07-20 09:59:28,351 Loaded tool id: toolshed.g2.bx.psu.edu/repos/biomonika/trinityrnaseq/trinityrnaseq/0.0.1, version: 0.0.1 into tool panel....
galaxy.tools.search DEBUG 2015-07-20 09:59:28,672 Starting to build toolbox index.
galaxy.tools.search DEBUG 2015-07-20 09:59:30,490 Toolbox index finished.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,518 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,536 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,567 Loaded display application 'igv_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,568 Loaded display application 'igb_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,569 Loaded display application 'igb_bed' for datatype 'bed', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,569 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,572 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,572 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,575 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,575 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,580 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,606 Loaded display application 'igv_gff' for datatype 'gff', inherit=True.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,606 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,611 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,618 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,620 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,645 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,647 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,649 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,680 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,681 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,682 Loaded display application 'igb_wig' for datatype 'wig', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,713 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False.
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,714 Adding inherited display application 'ensembl_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,714 Adding inherited display application 'igv_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,714 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,714 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,714 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,714 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,714 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,715 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,715 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,715 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,715 Adding inherited display application 'ensembl_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,715 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,715 Adding inherited display application 'rviewer_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,715 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,715 Adding inherited display application 'ensembl_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,715 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,715 Adding inherited display application 'rviewer_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,715 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,716 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,716 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,716 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,716 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,716 Adding inherited display application 'ensembl_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,716 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,717 Adding inherited display application 'rviewer_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,717 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,717 Adding inherited display application 'ensembl_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,717 Adding inherited display application 'igv_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,717 Adding inherited display application 'ensembl_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,717 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,717 Adding inherited display application 'rviewer_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,717 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,733 Loaded converter: CONVERTER_Bam_Bai_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,735 Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,739 Loaded converter: CONVERTER_bed_to_gff_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,740 Loaded converter: CONVERTER_bed_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,742 Loaded converter: CONVERTER_bed_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,743 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,744 Loaded converter: CONVERTER_bed_to_fli_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,745 Loaded converter: CONVERTER_bedgraph_to_bigwig
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,747 Loaded converter: CONVERTER_len_to_linecount
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,748 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,749 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,750 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,755 Loaded converter: CONVERTER_fasta_to_tabular
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,756 Loaded converter: CONVERTER_fasta_to_bowtie_base_index
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,757 Loaded converter: CONVERTER_fasta_to_bowtie_color_index
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,759 Loaded converter: CONVERTER_fasta_to_2bit
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,760 Loaded converter: CONVERTER_fasta_to_len
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,761 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,762 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,763 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,763 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,764 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,765 Loaded converter: CONVERTER_gff_to_bed_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,767 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,768 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,769 Loaded converter: CONVERTER_gff_to_fli_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,769 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,770 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,771 Loaded converter: CONVERTER_interval_to_bed_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,773 Loaded converter: CONVERTER_interval_to_bedstrict_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,774 Loaded converter: CONVERTER_interval_to_bed6_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,775 Loaded converter: CONVERTER_interval_to_bed12_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,776 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,776 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,778 Loaded converter: CONVERTER_interval_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,779 Loaded converter: CONVERTER_picard_interval_list_to_bed6
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,780 Loaded converter: CONVERTER_maf_to_fasta_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,781 Loaded converter: CONVERTER_maf_to_interval_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,782 Loaded converter: CONVERTER_encodepeak_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,783 Loaded converter: CONVERTER_encodepeak_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,785 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,789 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,792 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,794 Loaded converter: CONVERTER_sam_to_bam
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,797 Loaded converter: CONVERTER_sam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,800 Loaded converter: tabular_to_dbnsfp
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,803 Loaded converter: CONVERTER_vcf_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,806 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,809 Loaded converter: CONVERTER_vcf_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,811 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,814 Loaded converter: CONVERTER_wig_to_bigwig
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,816 Loaded converter: CONVERTER_wiggle_to_interval_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,819 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,822 Loaded converter: lped2fpedconvert
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,824 Loaded converter: lped2pbedconvert
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,827 Loaded converter: pbed2lpedconvert
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,830 Loaded converter: pbed2ldindepconvert
galaxy.datatypes.registry DEBUG 2015-07-20 09:59:30,833 Loaded external metadata tool: __SET_METADATA__
galaxy.tools.imp_exp DEBUG 2015-07-20 09:59:30,838 Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.imp_exp DEBUG 2015-07-20 09:59:30,841 Loaded history import tool: __IMPORT_HISTORY__
galaxy.web.base.pluginframework INFO 2015-07-20 09:59:30,861 VisualizationsRegistry, loaded plugin: charts
galaxy.visualization.plugins.config_parser INFO 2015-07-20 09:59:30,873 Visualizations plugin disabled: Circster. Skipping...
galaxy.web.base.pluginframework INFO 2015-07-20 09:59:30,886 VisualizationsRegistry, loaded plugin: graphview
galaxy.web.base.pluginframework INFO 2015-07-20 09:59:30,890 VisualizationsRegistry, loaded plugin: phyloviz
galaxy.web.base.pluginframework INFO 2015-07-20 09:59:30,893 VisualizationsRegistry, loaded plugin: scatterplot
galaxy.visualization.plugins.config_parser INFO 2015-07-20 09:59:30,896 Visualizations plugin disabled: Sweepster. Skipping...
galaxy.web.base.pluginframework INFO 2015-07-20 09:59:30,899 VisualizationsRegistry, loaded plugin: trackster
galaxy.web.base.pluginframework INFO 2015-07-20 09:59:30,902 VisualizationsRegistry, loaded plugin: ipython
galaxy.visualization.plugins.config_parser INFO 2015-07-20 09:59:30,905 template syntax is deprecated: use entry_point instead
galaxy.web.base.pluginframework INFO 2015-07-20 09:59:30,905 VisualizationsRegistry, loaded plugin: rstudio
galaxy.jobs.manager DEBUG 2015-07-20 09:59:30,928 Starting job handler
galaxy.jobs INFO 2015-07-20 09:59:30,928 Handler 'main' will load all configured runner plugins
galaxy.jobs.runners.state_handler_factory DEBUG 2015-07-20 09:59:30,930 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs.runners DEBUG 2015-07-20 09:59:30,931 Starting 5 LocalRunner workers
galaxy.jobs DEBUG 2015-07-20 09:59:30,934 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
galaxy.jobs.runners.state_handler_factory DEBUG 2015-07-20 09:59:30,986 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs.runners DEBUG 2015-07-20 09:59:30,986 Starting 3 LWRRunner workers
galaxy.jobs.runners.lwr_client.manager INFO 2015-07-20 09:59:30,988 Setting LWR client class to standard, non-caching variant.
galaxy.jobs DEBUG 2015-07-20 09:59:30,989 Loaded job runner 'galaxy.jobs.runners.lwr:LwrJobRunner' as 'lwr'
galaxy.jobs DEBUG 2015-07-20 09:59:30,989 Legacy destination with id 'local:///', url 'local:///' converted, got params:
galaxy.jobs.handler DEBUG 2015-07-20 09:59:30,989 Loaded job runners plugins: lwr:local
galaxy.jobs.handler INFO 2015-07-20 09:59:30,991 job handler stop queue started
galaxy.jobs.handler DEBUG 2015-07-20 09:59:31,078 (64) Job runner assigned but no external ID recorded, adding to the job handler queue
galaxy.jobs.handler INFO 2015-07-20 09:59:31,104 job handler queue started
galaxy.sample_tracking.external_service_types DEBUG 2015-07-20 09:59:31,134 Loaded external_service_type: Simple unknown sequencer 1.0.0
galaxy.sample_tracking.external_service_types DEBUG 2015-07-20 09:59:31,161 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0
galaxy.workflow.scheduling_manager DEBUG 2015-07-20 09:59:31,180 Starting workflow schedulers
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,251 Enabling 'requests' controller, class: Requests
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,259 Enabling 'history' controller, class: HistoryController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,346 Enabling 'workflow' controller, class: WorkflowController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,350 Enabling 'biostar' controller, class: BiostarController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,353 Enabling 'forms' controller, class: Forms
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,364 Enabling 'admin' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,365 Enabling 'async' controller, class: ASync
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,376 Enabling 'requests_admin' controller, class: RequestsAdmin
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,380 Enabling 'user' controller, class: User
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,381 Enabling 'error' controller, class: Error
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,381 Enabling 'requests_common' controller, class: RequestsCommon
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,383 Enabling 'root' controller, class: RootController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,384 Enabling 'search' controller, class: SearchController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,385 Enabling 'mobile' controller, class: Mobile
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,386 Enabling 'userskeys' controller, class: User
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,397 Enabling 'dataset' controller, class: DatasetInterface
galaxy.web.framework.base DEBUG 2015-07-20 09:59:31,740 Enabling 'cloudlaunch' controller, class: CloudController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,354 Enabling 'admin_toolshed' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,355 Enabling 'admin_toolshed' controller, class: AdminToolshed
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,385 Enabling 'library_common' controller, class: LibraryCommon
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,392 Enabling 'library_admin' controller, class: LibraryAdmin
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,409 Enabling 'data_manager' controller, class: DataManager
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,414 Enabling 'visualization' controller, class: VisualizationController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,416 Enabling 'ucsc_proxy' controller, class: UCSCProxy
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,417 Enabling 'library' controller, class: Library
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,419 Enabling 'external_service' controller, class: ExternalService
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,422 Enabling 'tool_runner' controller, class: ToolRunner
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,423 Enabling 'external_services' controller, class: ExternalServiceController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,432 Enabling 'request_type' controller, class: RequestType
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,441 Enabling 'page' controller, class: PageController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,443 Enabling 'tag' controller, class: TagsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,458 Enabling 'folders' API controller, class: FoldersController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,460 Enabling 'authenticate' API controller, class: AuthenticationController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,462 Enabling 'groups' API controller, class: GroupAPIController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,464 Enabling 'requests' API controller, class: RequestsAPIController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,467 Enabling 'job_files' API controller, class: JobFilesAPIController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,469 Enabling 'forms' API controller, class: FormDefinitionAPIController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,471 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,471 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,475 Enabling 'history_contents' API controller, class: HistoryContentsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,478 Enabling 'samples' API controller, class: SamplesAPIController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,480 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,480 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,482 Enabling 'users' API controller, class: UserAPIController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,484 Enabling 'metrics' API controller, class: MetricsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,489 Enabling 'configuration' API controller, class: ConfigurationController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,490 Enabling 'pages' API controller, class: PagesController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,574 Enabling 'search' API controller, class: SearchController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,577 Enabling 'jobs' API controller, class: JobController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,580 Enabling 'tools' API controller, class: ToolsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,583 Enabling 'workflows' API controller, class: WorkflowsAPIController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,584 Enabling 'page_revisions' API controller, class: PageRevisionsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,586 Enabling 'genomes' API controller, class: GenomesController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,587 Enabling 'roles' API controller, class: RoleAPIController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,590 Enabling 'request_types' API controller, class: RequestTypeAPIController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,591 Enabling 'folder_contents' API controller, class: FolderContentsController
beaker.container DEBUG 2015-07-20 09:59:32,920 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,921 Enabling 'histories' API controller, class: HistoriesController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,922 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,923 Enabling 'quotas' API controller, class: QuotaAPIController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,927 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,930 Enabling 'visualizations' API controller, class: VisualizationsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,936 Enabling 'library_contents' API controller, class: LibraryContentsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,939 Enabling 'group_roles' API controller, class: GroupRolesAPIController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,941 Enabling 'datatypes' API controller, class: DatatypesController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,944 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,945 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,945 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,945 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,947 Enabling 'remote_files' API controller, class: RemoteFilesAPIController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,948 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,948 Enabling 'history_tags' API controller, class: HistoryTagsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,948 Enabling 'workflow_tags' API controller, class: WorkflowTagsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,948 Enabling 'group_users' API controller, class: GroupUsersAPIController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,949 Enabling 'datasets' API controller, class: DatasetsController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,950 Enabling 'libraries' API controller, class: LibrariesController
galaxy.web.framework.base DEBUG 2015-07-20 09:59:32,951 Enabling 'tool_data' API controller, class: ToolData
galaxy.webapps.galaxy.buildapp DEBUG 2015-07-20 09:59:33,458 Enabling 'httpexceptions' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-07-20 09:59:33,463 Enabling 'recursive' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-07-20 09:59:33,480 Enabling 'error' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-07-20 09:59:33,480 Enabling 'trans logger' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-07-20 09:59:33,481 Enabling 'x-forwarded-host' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-07-20 09:59:33,481 Enabling 'Request ID' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-07-20 09:59:33,489 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static
galaxy.webapps.galaxy.buildapp DEBUG 2015-07-20 09:59:33,489 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static
galaxy.webapps.galaxy.buildapp DEBUG 2015-07-20 09:59:33,490 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static
galaxy.webapps.galaxy.buildapp DEBUG 2015-07-20 09:59:33,490 added url, path to static middleware: /plugins/visualizations/ipython/static, ./config/plugins/interactive_environments/ipython/static
galaxy.webapps.galaxy.buildapp DEBUG 2015-07-20 09:59:33,490 added url, path to static middleware: /plugins/visualizations/rstudio/static, ./config/plugins/interactive_environments/rstudio/static
galaxy.queue_worker INFO 2015-07-20 09:59:33,490 Binding and starting galaxy control worker for main
Starting server in PID 2867.
serving on http://144.124.110.39:8080
galaxy.jobs DEBUG 2015-07-20 10:00:59,544 (64) Working directory for job is: /home/galaxy/galaxy/database/job_working_directory/000/64
galaxy.jobs.handler DEBUG 2015-07-20 10:00:59,559 (64) Dispatching to local runner
galaxy.jobs DEBUG 2015-07-20 10:06:20,173 (64) Persisting job destination (destination id: local:///)
galaxy.jobs.runners DEBUG 2015-07-20 10:06:20,621 Job [64] queued (321060.846 ms)
galaxy.jobs.handler INFO 2015-07-20 10:06:20,669 (64) Job dispatched