/Users/dtenenba/dev/galaxy-dist/eggs/boto-2.5.2-py2.7.egg/boto/pyami/config.py:75: UserWarning: Unable to load AWS_CREDENTIAL_FILE (/Users/dtenenba/Downloads/AWSCloudFormation-1.0.9/credential-file-path.template) warnings.warn('Unable to load AWS_CREDENTIAL_FILE (%s)' % full_path) python path is: /Users/dtenenba/dev/galaxy-dist/eggs/numpy-1.6.0-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/boto-2.5.2-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/mercurial-2.2.3-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/Fabric-1.4.2-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/ssh-1.7.14-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/Whoosh-0.3.18-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/pycrypto-2.5-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/amqplib-0.6.1-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/WebHelpers-0.2-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/simplejson-2.1.1-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/lib, /Library/Python/2.7/site-packages/requests-0.14.2-py2.7.egg, /Library/Python/2.7/site-packages/tornado-2.4.1-py2.7.egg, /Library/Python/2.7/site-packages/pytz-2012j-py2.7.egg, /Library/Python/2.7/site-packages/pip-1.2.1-py2.7.egg, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload, /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyObjC, /Library/Python/2.7/site-packages, /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python galaxy.tool_shed.tool_shed_registry DEBUG 2013-02-04 09:48:17,885 Loading references to tool sheds from tool_sheds_conf.xml galaxy.tool_shed.tool_shed_registry DEBUG 2013-02-04 09:48:17,885 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2013-02-04 09:48:17,885 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2013-02-04 09:48:17,905 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.model.migrate.check INFO 2013-02-04 09:48:17,922 At database version 109 galaxy.tool_shed.migrate.check DEBUG 2013-02-04 09:48:17,932 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.tool_shed.migrate.check INFO 2013-02-04 09:48:17,939 At migrate_tools version 7 galaxy.model.custom_types DEBUG 2013-02-04 09:48:17,944 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,173 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,180 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,180 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,180 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,180 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,180 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,181 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,181 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,181 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,181 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,181 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,181 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,181 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,181 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,182 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,182 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,182 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,182 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,182 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,182 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,182 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,182 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,183 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,183 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,183 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,183 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,183 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,183 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,183 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,183 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,184 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,184 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,184 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,184 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,184 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,184 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,184 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,184 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,184 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,185 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,185 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,185 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,185 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,185 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:18,185 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.tools.data DEBUG 2013-02-04 09:48:18,197 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2013-02-04 09:48:18,197 Loaded tool data table 'bfast_indexes' galaxy.tools.data DEBUG 2013-02-04 09:48:18,197 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2013-02-04 09:48:18,198 Loaded tool data table 'blastdb_p' galaxy.tools.data DEBUG 2013-02-04 09:48:18,198 Loaded tool data table 'bowtie2_indexes' galaxy.tools.data WARNING 2013-02-04 09:48:18,198 Cannot find index file '/Users/dtenenba/dev/galaxy-dist/tool-data/bwa_index.loc' for tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2013-02-04 09:48:18,198 Loaded tool data table 'bwa_indexes' galaxy.tools.data WARNING 2013-02-04 09:48:18,198 Cannot find index file '/Users/dtenenba/dev/galaxy-dist/tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2013-02-04 09:48:18,198 Loaded tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2013-02-04 09:48:18,199 Loaded tool data table 'indexed_maf_files' galaxy.tools.data DEBUG 2013-02-04 09:48:18,199 Loaded tool data table 'ngs_sim_fasta' galaxy.tools.data DEBUG 2013-02-04 09:48:18,199 Loaded tool data table 'perm_base_indexes' galaxy.tools.data DEBUG 2013-02-04 09:48:18,199 Loaded tool data table 'perm_color_indexes' galaxy.tools.data DEBUG 2013-02-04 09:48:18,199 Loaded tool data table 'sam_fa_indexes' galaxy.tools.data DEBUG 2013-02-04 09:48:18,200 Loaded tool data table 'picard_indexes' galaxy.tools.data DEBUG 2013-02-04 09:48:18,200 Loaded tool data table 'gatk_picard_indexes' galaxy.tools.data DEBUG 2013-02-04 09:48:18,200 Loaded tool data table 'gatk_annotations' galaxy.tools.data DEBUG 2013-02-04 09:48:18,200 Loaded tool data table 'srma_indexes' galaxy.tools.data WARNING 2013-02-04 09:48:18,200 Cannot find index file '/Users/dtenenba/dev/galaxy-dist/tool-data/bowtie_indices.loc' for tool data table 'tophat_indexes' galaxy.tools.data DEBUG 2013-02-04 09:48:18,200 Loaded tool data table 'tophat_indexes' galaxy.tools.data WARNING 2013-02-04 09:48:18,201 Cannot find index file '/Users/dtenenba/dev/galaxy-dist/tool-data/bowtie_indices_color.loc' for tool data table 'tophat_indexes_color' galaxy.tools.data DEBUG 2013-02-04 09:48:18,201 Loaded tool data table 'tophat_indexes_color' galaxy.tools.data DEBUG 2013-02-04 09:48:18,201 Loaded tool data table 'tophat2_indexes' galaxy.tools.data DEBUG 2013-02-04 09:48:18,201 Loaded tool data table 'ccat_configurations' galaxy.tools.data DEBUG 2013-02-04 09:48:18,201 Loaded tool data table 'mosaik_indexes' galaxy.tools INFO 2013-02-04 09:48:18,210 Parsing the tool configuration ./tool_conf.xml galaxy.tools WARNING 2013-02-04 09:48:20,050 A when tag has not been defined for 'master_variable_type (master_variable_type_selector) --> allPairs', assuming empty inputs. galaxy.tools WARNING 2013-02-04 09:48:21,406 A when tag has been defined for 'manipulation (manipulation_selector) --> modify_each_score', but does not appear to be selectable. galaxy.tools.test DEBUG 2013-02-04 09:48:21,986 Error in add_param for report_discordant_pairs: Unable to determine parameter type of test input 'report_discordant_pairs'. Ensure that the parameter exists and that any container groups are defined first. docutils WARNING 2013-02-04 09:48:22,017 :50: (WARNING/2) Literal block expected; none found. galaxy.tools.test DEBUG 2013-02-04 09:48:22,027 Error in add_param for min_coverage_intron: Unable to determine parameter type of test input 'min_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 09:48:22,030 Error in add_param for max_coverage_intron: Unable to determine parameter type of test input 'max_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 09:48:23,132 Error in add_param for force: Unable to determine parameter type of test input 'force'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 09:48:23,375 Error in add_param for input: Unable to determine parameter type of test input 'input'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 09:48:23,376 Error in add_param for group1_1: Unable to determine parameter type of test input 'group1_1'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 09:48:23,376 Error in add_param for group1_2: Unable to determine parameter type of test input 'group1_2'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 09:48:23,376 Error in add_param for group1_3: Unable to determine parameter type of test input 'group1_3'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 09:48:23,376 Error in add_param for group2_1: Unable to determine parameter type of test input 'group2_1'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 09:48:23,376 Error in add_param for group2_2: Unable to determine parameter type of test input 'group2_2'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 09:48:23,376 Error in add_param for group2_3: Unable to determine parameter type of test input 'group2_3'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools INFO 2013-02-04 09:48:23,605 Parsing the tool configuration ./migrated_tools_conf.xml galaxy.tools DEBUG 2013-02-04 09:48:23,605 Loading section: Get Data galaxy.tools DEBUG 2013-02-04 09:48:23,605 Loaded tool id: upload1, version: 1.1.3 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,605 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,606 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,606 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,606 Loaded tool id: bx_browser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,606 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,606 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,606 Loaded tool id: biomart, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,606 Loaded tool id: biomart_test, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,606 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,606 Loaded tool id: gramenemart, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,607 Loaded tool id: modENCODEfly, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,607 Loaded tool id: flymine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,607 Loaded tool id: flymine_test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,607 Loaded tool id: modmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,607 Loaded tool id: ratmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,607 Loaded tool id: yeastmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,607 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,607 Loaded tool id: modENCODEworm, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,607 Loaded tool id: wormbase, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,607 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,608 Loaded tool id: eupathdb, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,608 Loaded tool id: encode_db1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,608 Loaded tool id: epigraph_import, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,608 Loaded tool id: epigraph_import_test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,608 Loaded tool id: hbvar, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,608 Loaded tool id: genomespace_file_browser_prod, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,608 Loaded tool id: genomespace_importer, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,608 Loaded tool id: fix_errors, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,608 Loading section: Send Data galaxy.tools DEBUG 2013-02-04 09:48:23,609 Loaded tool id: epigraph_export, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,609 Loaded tool id: epigraph_test_export, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,609 Loaded tool id: genomespace_exporter, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,609 Loading section: ENCODE Tools galaxy.tools DEBUG 2013-02-04 09:48:23,609 Loaded tool id: gencode_partition1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,609 Loaded tool id: random_intervals1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,609 Loading section: Lift-Over galaxy.tools DEBUG 2013-02-04 09:48:23,609 Loaded tool id: liftOver1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,609 Loading section: Text Manipulation galaxy.tools DEBUG 2013-02-04 09:48:23,609 Loaded tool id: addValue, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,610 Loaded tool id: Add_a_column1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,610 Loaded tool id: cat1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,610 Loaded tool id: Cut1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,610 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,610 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,610 Loaded tool id: createInterval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,610 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,610 Loaded tool id: Paste1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,610 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,610 Loaded tool id: random_lines1, version: 2.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,611 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,611 Loaded tool id: Show tail1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,611 Loaded tool id: trimmer, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,611 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,611 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,611 Loaded tool id: dna_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,611 Loaded tool id: tables_arithmetic_operations, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,611 Loading section: Filter and Sort galaxy.tools DEBUG 2013-02-04 09:48:23,611 Loaded tool id: Filter1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,611 Loaded tool id: sort1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,612 Loaded tool id: Grep1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,612 Loaded label: GFF galaxy.tools DEBUG 2013-02-04 09:48:23,612 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,612 Loaded tool id: gff_filter_by_attribute, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,612 Loaded tool id: gff_filter_by_feature_count, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,612 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,612 Loading section: Join, Subtract and Group galaxy.tools DEBUG 2013-02-04 09:48:23,612 Loaded tool id: join1, version: 2.0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,612 Loaded tool id: comp1, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,612 Loaded tool id: subtract_query1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,613 Loaded tool id: Grouping1, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,613 Loaded tool id: column_join, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,613 Loading section: Convert Formats galaxy.tools DEBUG 2013-02-04 09:48:23,613 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,613 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,613 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,613 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,613 Loaded tool id: fasta2tab, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,613 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,614 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,614 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,614 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,614 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,614 Loaded tool id: tab2fasta, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,614 Loaded tool id: fastq_to_fasta_python, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,614 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,614 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,614 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,614 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,615 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,615 Loading section: Extract Features galaxy.tools DEBUG 2013-02-04 09:48:23,615 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,615 Loading section: Fetch Sequences galaxy.tools DEBUG 2013-02-04 09:48:23,615 Loaded tool id: Extract genomic DNA 1, version: 2.2.2 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,615 Loading section: Fetch Alignments galaxy.tools DEBUG 2013-02-04 09:48:23,615 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,615 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,615 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,615 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,616 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,616 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,616 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,616 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,616 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,616 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,616 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,616 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,616 Loading section: Get Genomic Scores galaxy.tools DEBUG 2013-02-04 09:48:23,617 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,617 Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.3 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,617 Loaded tool id: phastOdds_for_intervals, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,617 Loading section: Operate on Genomic Intervals galaxy.tools DEBUG 2013-02-04 09:48:23,617 Loaded tool id: gops_intersect_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,617 Loaded tool id: gops_subtract_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,617 Loaded tool id: gops_merge_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,617 Loaded tool id: gops_concat_1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,617 Loaded tool id: gops_basecoverage_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,617 Loaded tool id: gops_coverage_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,618 Loaded tool id: gops_complement_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,618 Loaded tool id: gops_cluster_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,618 Loaded tool id: gops_join_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,618 Loaded tool id: get_flanks1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,618 Loaded tool id: flanking_features_1, version: 4.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,618 Loaded tool id: Annotation_Profiler_0, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,618 Loading section: Statistics galaxy.tools DEBUG 2013-02-04 09:48:23,618 Loaded tool id: Summary_Statistics1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,618 Loaded tool id: Count1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,619 Loaded tool id: cor2, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,619 Loaded tool id: generate_matrix_for_pca_and_lda1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,619 Loaded tool id: lda_analy1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,619 Loaded tool id: plot_for_lda_output1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,619 Loaded tool id: t_test_two_samples, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,619 Loaded tool id: compute_q_values, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,619 Loaded tool id: maximal_information_based_nonparametric_exploration, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,619 Loaded label: GFF galaxy.tools DEBUG 2013-02-04 09:48:23,619 Loaded tool id: count_gff_features, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,620 Loading section: Wavelet Analysis galaxy.tools DEBUG 2013-02-04 09:48:23,620 Loaded tool id: dwt_var1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,620 Loading section: Graph/Display Data galaxy.tools DEBUG 2013-02-04 09:48:23,620 Loaded tool id: histogram_rpy, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,620 Loaded tool id: scatterplot_rpy, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,620 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,620 Loaded tool id: XY_Plot_1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,620 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,620 Loaded tool id: gmaj_1, version: 2.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,620 Loaded tool id: laj_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,621 Loaded tool id: build_ucsc_custom_track_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,621 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,621 Loaded tool id: mutation_visualize, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,621 Loading section: Regional Variation galaxy.tools DEBUG 2013-02-04 09:48:23,621 Loaded tool id: winSplitter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,621 Loaded tool id: featureCoverage1, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,621 Loaded tool id: wtavg, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,621 Loaded tool id: qualityFilter, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,621 Loaded tool id: cpgFilter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,622 Loaded tool id: getIndels_2way, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,622 Loaded tool id: indels_3way, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,622 Loaded tool id: indelRates_3way, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,622 Loaded tool id: substitutions1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,622 Loaded tool id: subRate1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,622 Loaded tool id: microsats_align1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,622 Loaded tool id: microsats_mutability1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,622 Loaded tool id: delete_overlapping_indels, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,622 Loaded tool id: compute_motifs_frequency, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,623 Loaded tool id: compute_motif_frequencies_for_all_motifs, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,623 Loaded tool id: categorize_elements_satisfying_criteria, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,623 Loaded tool id: draw_stacked_barplots, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,623 Loading section: Multiple regression galaxy.tools DEBUG 2013-02-04 09:48:23,623 Loaded tool id: LinearRegression1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,623 Loaded tool id: LogisticRegression, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,623 Loaded tool id: BestSubsetsRegression1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,623 Loaded tool id: rcve1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,623 Loaded tool id: partialRsq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,623 Loading section: Multivariate Analysis galaxy.tools DEBUG 2013-02-04 09:48:23,624 Loaded tool id: pca1, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,624 Loaded tool id: cca1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,624 Loaded tool id: kpca1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,624 Loaded tool id: kcca1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,624 Loading section: Evolution galaxy.tools DEBUG 2013-02-04 09:48:23,624 Loaded tool id: hyphy_branch_lengths_wrapper1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,624 Loaded tool id: hyphy_nj_tree_wrapper1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,624 Loaded tool id: hyphy_dnds_wrapper1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,624 Loaded tool id: mutate_snp_codon_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,624 Loaded tool id: hgv_codingSnps, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,625 Loaded tool id: hgv_add_scores, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,625 Loading section: Motif Tools galaxy.tools DEBUG 2013-02-04 09:48:23,625 Loaded tool id: meme_meme, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,625 Loaded tool id: meme_fimo, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,625 Loaded tool id: rgweblogo3, version: 0.4 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,625 Loading section: Multiple Alignments galaxy.tools DEBUG 2013-02-04 09:48:23,625 Loaded tool id: clustalw, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,625 Loading section: Metagenomic analyses galaxy.tools DEBUG 2013-02-04 09:48:23,625 Loaded tool id: Fetch Taxonomic Ranks, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,626 Loaded tool id: t2t_report, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,626 Loaded tool id: Draw_phylogram, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,626 Loaded tool id: find_diag_hits, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,626 Loaded tool id: lca1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,626 Loaded tool id: poisson2test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,626 Loading section: FASTA manipulation galaxy.tools DEBUG 2013-02-04 09:48:23,626 Loaded tool id: fasta_compute_length, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,626 Loaded tool id: fasta_filter_by_length, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,626 Loaded tool id: fasta_concatenate0, version: 0.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,627 Loaded tool id: fasta2tab, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,627 Loaded tool id: tab2fasta, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,627 Loaded tool id: cshl_fasta_formatter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,627 Loaded tool id: cshl_fasta_nucleotides_changer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,627 Loaded tool id: cshl_fastx_collapser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,627 Loading section: NGS: QC and manipulation galaxy.tools DEBUG 2013-02-04 09:48:23,627 Loaded label: FastQC: fastq/sam/bam galaxy.tools DEBUG 2013-02-04 09:48:23,627 Loaded tool id: fastqc, version: 0.51 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,627 Loaded label: Illumina fastq galaxy.tools DEBUG 2013-02-04 09:48:23,627 Loaded tool id: fastq_groomer, version: 1.0.4 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,628 Loaded tool id: fastq_paired_end_splitter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,628 Loaded tool id: fastq_paired_end_joiner, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,628 Loaded tool id: fastq_stats, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,628 Loaded label: Roche-454 data galaxy.tools DEBUG 2013-02-04 09:48:23,628 Loaded tool id: quality_score_distribution, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,628 Loaded tool id: trim_reads, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,628 Loaded tool id: fastq_combiner, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,628 Loaded label: AB-SOLiD data galaxy.tools DEBUG 2013-02-04 09:48:23,628 Loaded tool id: solid2fastq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,628 Loaded tool id: solid_qual_stats, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,629 Loaded tool id: solid_qual_boxplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,629 Loaded label: Generic FASTQ manipulation galaxy.tools DEBUG 2013-02-04 09:48:23,629 Loaded tool id: fastq_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,629 Loaded tool id: fastq_trimmer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,629 Loaded tool id: fastq_quality_trimmer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,629 Loaded tool id: fastq_masker_by_quality, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,629 Loaded tool id: fastq_paired_end_interlacer, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,629 Loaded tool id: fastq_paired_end_deinterlacer, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,629 Loaded tool id: fastq_manipulation, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,629 Loaded tool id: fastq_to_fasta_python, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,630 Loaded tool id: fastq_to_tabular, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,630 Loaded tool id: tabular_to_fastq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,630 Loaded label: FASTX-Toolkit for FASTQ data galaxy.tools DEBUG 2013-02-04 09:48:23,630 Loaded tool id: cshl_fastq_quality_converter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,630 Loaded tool id: cshl_fastx_quality_statistics, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,630 Loaded tool id: cshl_fastq_quality_boxplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,630 Loaded tool id: cshl_fastx_nucleotides_distribution, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,630 Loaded tool id: cshl_fastq_to_fasta, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,630 Loaded tool id: cshl_fastq_quality_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,630 Loaded tool id: cshl_fastx_artifacts_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,631 Loaded tool id: cshl_fastx_barcode_splitter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,631 Loaded tool id: cshl_fastx_clipper, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,631 Loaded tool id: cshl_fastx_collapser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,631 Loaded tool id: cshl_fastx_renamer, version: 0.0.11 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,631 Loaded tool id: cshl_fastx_reverse_complement, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,631 Loaded tool id: cshl_fastx_trimmer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,631 Loading section: NGS: Mapping galaxy.tools DEBUG 2013-02-04 09:48:23,631 Loaded tool id: bowtie2, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,631 Loaded tool id: bfast_wrapper, version: 0.1.3 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,631 Loaded tool id: megablast_wrapper, version: 1.2.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,632 Loaded tool id: megablast_xml_parser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,632 Loaded tool id: PerM, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,632 Loaded tool id: srma_wrapper, version: 0.2.5 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,632 Loaded tool id: mosaik_wrapper, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,632 Loading section: NGS: Indel Analysis galaxy.tools DEBUG 2013-02-04 09:48:23,632 Loaded tool id: sam_indel_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,632 Loaded tool id: indel_sam2interval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,632 Loaded tool id: indel_table, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,632 Loaded tool id: indel_analysis, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,632 Loading section: NGS: RNA Analysis galaxy.tools DEBUG 2013-02-04 09:48:23,633 Loaded label: RNA-seq galaxy.tools DEBUG 2013-02-04 09:48:23,633 Loaded tool id: tophat, version: 1.5.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,633 Loaded tool id: tophat2, version: 0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,633 Loaded tool id: tophat_color, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,633 Loaded tool id: cufflinks, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,633 Loaded tool id: cuffcompare, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,633 Loaded tool id: cuffmerge, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,633 Loaded tool id: cuffdiff, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,633 Loaded tool id: express, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,633 Loaded label: Filtering galaxy.tools DEBUG 2013-02-04 09:48:23,634 Loaded tool id: filter_combined_via_tracking, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,634 Loading section: NGS: SAM Tools galaxy.tools DEBUG 2013-02-04 09:48:23,634 Loaded tool id: sam_bw_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,634 Loaded tool id: sam2interval, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,634 Loaded tool id: sam_to_bam, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,634 Loaded tool id: bam_to_sam, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,634 Loaded tool id: sam_merge2, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,634 Loaded tool id: samtools_mpileup, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,634 Loaded tool id: sam_pileup, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,635 Loaded tool id: pileup_parser, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,635 Loaded tool id: pileup_interval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,635 Loaded tool id: samtools_flagstat, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,635 Loaded tool id: samtools_rmdup, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,635 Loaded tool id: samtools_slice_bam, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,635 Loading section: NGS: GATK Tools (beta) galaxy.tools DEBUG 2013-02-04 09:48:23,635 Loaded label: Alignment Utilities galaxy.tools DEBUG 2013-02-04 09:48:23,635 Loaded tool id: gatk_depth_of_coverage, version: 0.0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,635 Loaded tool id: gatk_print_reads, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,635 Loaded label: Realignment galaxy.tools DEBUG 2013-02-04 09:48:23,636 Loaded tool id: gatk_realigner_target_creator, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,636 Loaded tool id: gatk_indel_realigner, version: 0.0.6 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,636 Loaded label: Base Recalibration galaxy.tools DEBUG 2013-02-04 09:48:23,636 Loaded tool id: gatk_count_covariates, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,636 Loaded tool id: gatk_table_recalibration, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,636 Loaded tool id: gatk_analyze_covariates, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,636 Loaded label: Genotyping galaxy.tools DEBUG 2013-02-04 09:48:23,636 Loaded tool id: gatk_unified_genotyper, version: 0.0.6 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,636 Loaded label: Annotation galaxy.tools DEBUG 2013-02-04 09:48:23,636 Loaded tool id: gatk_variant_annotator, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,637 Loaded label: Filtration galaxy.tools DEBUG 2013-02-04 09:48:23,637 Loaded tool id: gatk_variant_filtration, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,637 Loaded tool id: gatk_variant_select, version: 0.0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,637 Loaded label: Variant Quality Score Recalibration galaxy.tools DEBUG 2013-02-04 09:48:23,637 Loaded tool id: gatk_variant_recalibrator, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,637 Loaded tool id: gatk_variant_apply_recalibration, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,637 Loaded label: Variant Utilities galaxy.tools DEBUG 2013-02-04 09:48:23,637 Loaded tool id: gatk_validate_variants, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,637 Loaded tool id: gatk_variant_eval, version: 0.0.8 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,637 Loaded tool id: gatk_variant_combine, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,637 Loading section: NGS: Peak Calling galaxy.tools DEBUG 2013-02-04 09:48:23,638 Loaded tool id: peakcalling_macs, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,638 Loaded tool id: peakcalling_sicer, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,638 Loaded tool id: peakcalling_ccat, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,638 Loaded tool id: bed2genetrack, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,638 Loaded tool id: predict2genetrack, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,638 Loading section: NGS: Simulation galaxy.tools DEBUG 2013-02-04 09:48:23,638 Loaded tool id: ngs_simulation, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,638 Loading section: SNP/WGA: Data; Filters galaxy.tools DEBUG 2013-02-04 09:48:23,638 Loaded label: Data: Import and upload galaxy.tools DEBUG 2013-02-04 09:48:23,638 Loaded tool id: upload1, version: 1.1.3 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,639 Loaded tool id: library_access1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,639 Loaded label: Data: Filter and Clean galaxy.tools DEBUG 2013-02-04 09:48:23,639 Loaded tool id: rgClean1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,639 Loaded tool id: rgPedSub1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,639 Loaded tool id: rgLDIndep1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,639 Loaded label: Simulate galaxy.tools DEBUG 2013-02-04 09:48:23,639 Loaded tool id: fakePhe1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,639 Loaded tool id: rgfakePed1, version: 0.02 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,639 Loading section: SNP/WGA: QC; LD; Plots galaxy.tools DEBUG 2013-02-04 09:48:23,639 Loaded label: QC; Eigenstrat galaxy.tools DEBUG 2013-02-04 09:48:23,640 Loaded tool id: rgQC1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,640 Loaded tool id: rgEigPCA1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,640 Loaded label: LD; Manhattan/QQ; GRR galaxy.tools DEBUG 2013-02-04 09:48:23,640 Loaded tool id: rgHaploView1, version: 0.3 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,640 Loaded tool id: rgManQQ1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,640 Loaded tool id: rgGRR1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,640 Loading section: SNP/WGA: Statistical Models galaxy.tools DEBUG 2013-02-04 09:48:23,640 Loaded tool id: rgCaCo1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,640 Loaded tool id: rgTDT1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,641 Loaded tool id: rgGLM1, version: 0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,641 Loaded tool id: rgManQQ1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,641 Loading section: Phenotype Association galaxy.tools DEBUG 2013-02-04 09:48:23,641 Loaded tool id: hgv_codingSnps, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,641 Loaded tool id: hgv_add_scores, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,641 Loaded tool id: hgv_sift, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,641 Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,641 Loaded tool id: hgv_david, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,641 Loaded tool id: ctdBatch_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,641 Loaded tool id: hgv_funDo, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,642 Loaded tool id: hgv_snpFreq, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,642 Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,642 Loaded tool id: hgv_pass, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,642 Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,642 Loaded tool id: hgv_beam, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,642 Loaded tool id: hgv_lps, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,642 Loaded tool id: hgv_hilbertvis, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,642 Loaded tool id: freebayes_wrapper, version: 0.5.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,642 Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,643 Loaded tool id: vcf2pgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,643 Loaded tool id: dividePgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,643 Loading section: VCF Tools galaxy.tools DEBUG 2013-02-04 09:48:23,643 Loaded tool id: vcf_intersect, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,643 Loaded tool id: vcf_annotate, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,643 Loaded tool id: vcf_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 09:48:23,643 Loaded tool id: vcf_extract, version: 1.0.0 into tool panel. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,732 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,734 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,735 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,736 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,737 Loaded display application 'genetrack_interval' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,738 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,740 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,741 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,743 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,744 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,748 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,749 Loaded display application 'genetrack_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,754 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,761 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,762 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,764 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,766 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,768 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,769 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,770 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,772 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,772 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,772 Adding inherited display application 'genetrack_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,772 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,772 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,772 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,773 Adding inherited display application 'genetrack_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,773 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,773 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,773 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,773 Adding inherited display application 'genetrack_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,773 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,773 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,773 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,774 Adding inherited display application 'genetrack_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,774 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,774 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,774 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,774 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,774 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,775 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,775 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,775 Adding inherited display application 'genetrack_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,775 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,775 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,775 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,776 Adding inherited display application 'genetrack_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,776 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,776 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,776 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,782 Loaded converter: CONVERTER_Bam_Bai_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,788 Loaded converter: CONVERTER_bam_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,793 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,798 Loaded converter: CONVERTER_interval_to_coverage_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,804 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,810 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,815 Loaded converter: CONVERTER_bed_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,820 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,825 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,832 Loaded converter: CONVERTER_bed_to_genetrack_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,837 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,843 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,848 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,853 Loaded converter: CONVERTER_interval_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,858 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,863 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,868 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,872 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,878 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,883 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,889 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,896 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,901 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,906 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,911 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,916 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,920 Loaded converter: CONVERTER_gff_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,925 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,930 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,935 Loaded converter: CONVERTER_gff_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,940 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,945 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,949 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,956 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,961 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,966 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,971 Loaded converter: CONVERTER_interval_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,976 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,981 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,986 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,991 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:23,996 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,001 Loaded converter: CONVERTER_encodepeak_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,007 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,012 Loaded converter: CONVERTER_sam_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,019 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,025 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,029 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,034 Loaded converter: CONVERTER_vcf_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,039 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,040 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,045 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,050 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,056 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,061 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,066 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2013-02-04 09:48:24,068 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.imp_exp DEBUG 2013-02-04 09:48:24,069 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2013-02-04 09:48:24,070 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.genome_index DEBUG 2013-02-04 09:48:24,072 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.runners.local INFO 2013-02-04 09:48:24,073 starting workers galaxy.jobs.runners.local DEBUG 2013-02-04 09:48:24,074 5 workers ready galaxy.jobs.handler DEBUG 2013-02-04 09:48:24,074 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.runners.lwr INFO 2013-02-04 09:48:24,075 starting workers galaxy.jobs.runners.lwr DEBUG 2013-02-04 09:48:24,076 5 workers ready galaxy.jobs.handler DEBUG 2013-02-04 09:48:24,076 Loaded job runner: galaxy.jobs.runners.lwr:LwrJobRunner galaxy.jobs.handler DEBUG 2013-02-04 09:48:24,076 Job runners: local:lwr galaxy.jobs.handler INFO 2013-02-04 09:48:24,076 job handler stop queue started galaxy.jobs.manager INFO 2013-02-04 09:48:24,079 job manager queue started galaxy.jobs.manager INFO 2013-02-04 09:48:24,080 job manager stop queue started galaxy.jobs.handler INFO 2013-02-04 09:48:24,081 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2013-02-04 09:48:24,083 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2013-02-04 09:48:24,084 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 >>> /Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers ['/Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers'] galaxy.webapps.galaxy.controllers admin galaxy.webapps.galaxy.controllers.admin galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,092 Enabling 'admin' controller, class: AdminGalaxy galaxy.webapps.galaxy.controllers admin_toolshed galaxy.webapps.galaxy.controllers.admin_toolshed galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,140 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,140 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.webapps.galaxy.controllers async galaxy.webapps.galaxy.controllers.async galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,141 Enabling 'async' controller, class: ASync galaxy.webapps.galaxy.controllers cloudlaunch galaxy.webapps.galaxy.controllers.cloudlaunch galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,150 Enabling 'cloudlaunch' controller, class: CloudController galaxy.webapps.galaxy.controllers data_admin galaxy.webapps.galaxy.controllers.data_admin galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,163 Enabling 'data_admin' controller, class: DataAdmin galaxy.webapps.galaxy.controllers dataset galaxy.webapps.galaxy.controllers.dataset galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,170 Enabling 'dataset' controller, class: DatasetInterface galaxy.webapps.galaxy.controllers error galaxy.webapps.galaxy.controllers.error galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,170 Enabling 'error' controller, class: Error galaxy.webapps.galaxy.controllers external_service galaxy.webapps.galaxy.controllers.external_service galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,172 Enabling 'external_service' controller, class: ExternalService galaxy.webapps.galaxy.controllers external_services galaxy.webapps.galaxy.controllers.external_services galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,173 Enabling 'external_services' controller, class: ExternalServiceController galaxy.webapps.galaxy.controllers forms galaxy.webapps.galaxy.controllers.forms galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,174 Enabling 'forms' controller, class: Forms galaxy.webapps.galaxy.controllers history galaxy.webapps.galaxy.controllers.history galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,176 Enabling 'history' controller, class: HistoryController galaxy.webapps.galaxy.controllers library galaxy.webapps.galaxy.controllers.library galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,176 Enabling 'library' controller, class: Library galaxy.webapps.galaxy.controllers library_admin galaxy.webapps.galaxy.controllers.library_admin galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,177 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.webapps.galaxy.controllers library_common galaxy.webapps.galaxy.controllers.library_common galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,178 Enabling 'library_common' controller, class: LibraryCommon galaxy.webapps.galaxy.controllers mobile galaxy.webapps.galaxy.controllers.mobile galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,178 Enabling 'mobile' controller, class: Mobile galaxy.webapps.galaxy.controllers page galaxy.webapps.galaxy.controllers.page galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,180 Enabling 'page' controller, class: PageController galaxy.webapps.galaxy.controllers request_type galaxy.webapps.galaxy.controllers.request_type galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,181 Enabling 'request_type' controller, class: RequestType galaxy.webapps.galaxy.controllers requests galaxy.webapps.galaxy.controllers.requests galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,181 Enabling 'requests' controller, class: Requests galaxy.webapps.galaxy.controllers requests_admin galaxy.webapps.galaxy.controllers.requests_admin galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,194 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.webapps.galaxy.controllers requests_common galaxy.webapps.galaxy.controllers.requests_common galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,194 Enabling 'requests_common' controller, class: RequestsCommon galaxy.webapps.galaxy.controllers root galaxy.webapps.galaxy.controllers.root galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,195 Enabling 'root' controller, class: RootController galaxy.webapps.galaxy.controllers tag galaxy.webapps.galaxy.controllers.tag galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,196 Enabling 'tag' controller, class: TagsController galaxy.webapps.galaxy.controllers tool_runner galaxy.webapps.galaxy.controllers.tool_runner galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,197 Enabling 'tool_runner' controller, class: ToolRunner galaxy.webapps.galaxy.controllers ucsc_proxy galaxy.webapps.galaxy.controllers.ucsc_proxy galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,197 Enabling 'ucsc_proxy' controller, class: UCSCProxy galaxy.webapps.galaxy.controllers user galaxy.webapps.galaxy.controllers.user galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,198 Enabling 'user' controller, class: User galaxy.webapps.galaxy.controllers visualization galaxy.webapps.galaxy.controllers.visualization galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,199 Enabling 'visualization' controller, class: VisualizationController galaxy.webapps.galaxy.controllers workflow galaxy.webapps.galaxy.controllers.workflow galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,200 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,201 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,202 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,202 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,203 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,204 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,204 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,204 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,205 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,205 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,210 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,217 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,218 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,218 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,218 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,219 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,219 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,220 Enabling 'permissions' API controller, class: PermissionsController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,221 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,221 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,222 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,222 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,223 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,224 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,224 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,225 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2013-02-04 09:48:24,225 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 09:48:24,225 app.config.api_folders: False galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 09:48:24,460 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 09:48:24,460 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 09:48:24,462 Enabling 'print debug' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 09:48:24,502 Enabling 'eval exceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 09:48:24,502 Enabling 'trans logger' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 09:48:24,503 Enabling 'config' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 09:48:24,503 Enabling 'x-forwarded-host' middleware Starting server in PID 1504. serving on http://127.0.0.1:8080 galaxy.web.framework DEBUG 2013-02-04 09:49:30,100 Error: this request returned None from get_history(): http://localhost:8080/ 127.0.0.1 - - [04/Feb/2013:09:49:30 -0700] "GET / HTTP/1.1" 200 - "http://localhost:8080/user/login?use_panels=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:09:49:30 -0700] "GET /root/tool_menu HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:09:49:30 -0700] "GET /history HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:09:49:32 -0700] "GET /user/login HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:09:49:34 -0700] "POST /user/login?use_panels=False HTTP/1.1" 200 - "http://localhost:8080/user/login" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" galaxy.web.framework DEBUG 2013-02-04 09:49:34,097 Error: this request returned None from get_history(): http://localhost:8080/ 127.0.0.1 - - [04/Feb/2013:09:49:34 -0700] "GET / HTTP/1.1" 200 - "http://localhost:8080/user/login?use_panels=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:09:49:34 -0700] "GET /root/tool_menu HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:09:49:34 -0700] "GET /history HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:09:49:43 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:8080/root/tool_menu" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" galaxy.web.framework DEBUG 2013-02-04 09:50:43,994 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 09:50:43,994 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 09:50:43,994 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 09:50:43,994 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 09:50:43,994 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 09:50:43,994 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 09:50:43,994 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 09:50:43,995 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 09:50:43,995 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create 127.0.0.1 - - [04/Feb/2013:09:50:43 -0700] "POST /tool_runner/upload_async_create HTTP/1.1" 500 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" Debug at: http://localhost:8080/_debug/view/1360000104 127.0.0.1 - - [04/Feb/2013:09:50:44 -0700] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:09:50:44 -0700] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" galaxy.tools.actions.upload_common INFO 2013-02-04 09:50:46,200 tool upload1 created job id 10 127.0.0.1 - - [04/Feb/2013:09:50:44 -0700] "POST /tool_runner/index HTTP/1.1" 200 - "http://localhost:8080/tool_runner?tool_id=upload1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:09:50:46 -0700] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" galaxy.jobs.manager DEBUG 2013-02-04 09:50:52,143 (10) Job assigned to handler 'main' galaxy.jobs DEBUG 2013-02-04 09:50:57,240 (10) Working directory for job is: /Users/dtenenba/dev/galaxy-dist/database/job_working_directory/000/10 galaxy.jobs.handler DEBUG 2013-02-04 09:50:57,241 dispatching job 10 to local runner galaxy.jobs.handler INFO 2013-02-04 09:50:57,326 (10) Job dispatched galaxy.jobs.runners.local DEBUG 2013-02-04 09:50:57,382 Local runner: starting job 10 galaxy.jobs.runners.local DEBUG 2013-02-04 09:50:57,649 executing: python /Users/dtenenba/dev/galaxy-dist/tools/data_source/upload.py /Users/dtenenba/dev/galaxy-dist /Users/dtenenba/dev/galaxy-dist/database/tmp/tmp5KMZpt /Users/dtenenba/dev/galaxy-dist/database/tmp/tmphdNKCy 16:/Users/dtenenba/dev/galaxy-dist/database/job_working_directory/000/10/dataset_16_files:/Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_16.dat galaxy.jobs.runners.local DEBUG 2013-02-04 09:50:58,768 execution finished: python /Users/dtenenba/dev/galaxy-dist/tools/data_source/upload.py /Users/dtenenba/dev/galaxy-dist /Users/dtenenba/dev/galaxy-dist/database/tmp/tmp5KMZpt /Users/dtenenba/dev/galaxy-dist/database/tmp/tmphdNKCy 16:/Users/dtenenba/dev/galaxy-dist/database/job_working_directory/000/10/dataset_16_files:/Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_16.dat galaxy.jobs DEBUG 2013-02-04 09:50:58,822 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-02-04 09:50:59,056 job 10 ended /Users/dtenenba/dev/galaxy-dist/eggs/boto-2.5.2-py2.7.egg/boto/pyami/config.py:75: UserWarning: Unable to load AWS_CREDENTIAL_FILE (/Users/dtenenba/Downloads/AWSCloudFormation-1.0.9/credential-file-path.template) warnings.warn('Unable to load AWS_CREDENTIAL_FILE (%s)' % full_path) python path is: /Users/dtenenba/dev/galaxy-dist/eggs/numpy-1.6.0-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/boto-2.5.2-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/mercurial-2.2.3-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/Fabric-1.4.2-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/ssh-1.7.14-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/Whoosh-0.3.18-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/pycrypto-2.5-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/amqplib-0.6.1-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/WebHelpers-0.2-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/simplejson-2.1.1-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg, /Users/dtenenba/dev/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg, /Users/dtenenba/dev/galaxy-dist/lib, /Library/Python/2.7/site-packages/requests-0.14.2-py2.7.egg, /Library/Python/2.7/site-packages/tornado-2.4.1-py2.7.egg, /Library/Python/2.7/site-packages/pytz-2012j-py2.7.egg, /Library/Python/2.7/site-packages/pip-1.2.1-py2.7.egg, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload, /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyObjC, /Library/Python/2.7/site-packages, /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python galaxy.tool_shed.tool_shed_registry DEBUG 2013-02-04 10:25:28,608 Loading references to tool sheds from tool_sheds_conf.xml galaxy.tool_shed.tool_shed_registry DEBUG 2013-02-04 10:25:28,608 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2013-02-04 10:25:28,608 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2013-02-04 10:25:28,630 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.model.migrate.check INFO 2013-02-04 10:25:28,647 At database version 109 galaxy.tool_shed.migrate.check DEBUG 2013-02-04 10:25:28,658 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.tool_shed.migrate.check INFO 2013-02-04 10:25:28,665 At migrate_tools version 7 galaxy.model.custom_types DEBUG 2013-02-04 10:25:28,670 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,900 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,907 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,907 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,907 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,907 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,907 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,907 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,908 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,908 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,908 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,908 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,908 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,908 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,908 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,908 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,908 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,909 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,909 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,909 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,909 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,909 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,909 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,909 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,910 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,910 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,910 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,910 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,910 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,910 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,910 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,910 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,910 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,911 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,911 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,911 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,911 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,911 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,911 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,911 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,911 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,912 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,912 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,912 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,912 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:28,912 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.tools.data DEBUG 2013-02-04 10:25:28,924 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2013-02-04 10:25:28,924 Loaded tool data table 'bfast_indexes' galaxy.tools.data DEBUG 2013-02-04 10:25:28,925 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2013-02-04 10:25:28,925 Loaded tool data table 'blastdb_p' galaxy.tools.data DEBUG 2013-02-04 10:25:28,925 Loaded tool data table 'bowtie2_indexes' galaxy.tools.data WARNING 2013-02-04 10:25:28,925 Cannot find index file '/Users/dtenenba/dev/galaxy-dist/tool-data/bwa_index.loc' for tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2013-02-04 10:25:28,925 Loaded tool data table 'bwa_indexes' galaxy.tools.data WARNING 2013-02-04 10:25:28,925 Cannot find index file '/Users/dtenenba/dev/galaxy-dist/tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2013-02-04 10:25:28,926 Loaded tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2013-02-04 10:25:28,926 Loaded tool data table 'indexed_maf_files' galaxy.tools.data DEBUG 2013-02-04 10:25:28,926 Loaded tool data table 'ngs_sim_fasta' galaxy.tools.data DEBUG 2013-02-04 10:25:28,926 Loaded tool data table 'perm_base_indexes' galaxy.tools.data DEBUG 2013-02-04 10:25:28,926 Loaded tool data table 'perm_color_indexes' galaxy.tools.data DEBUG 2013-02-04 10:25:28,926 Loaded tool data table 'sam_fa_indexes' galaxy.tools.data DEBUG 2013-02-04 10:25:28,927 Loaded tool data table 'picard_indexes' galaxy.tools.data DEBUG 2013-02-04 10:25:28,927 Loaded tool data table 'gatk_picard_indexes' galaxy.tools.data DEBUG 2013-02-04 10:25:28,927 Loaded tool data table 'gatk_annotations' galaxy.tools.data DEBUG 2013-02-04 10:25:28,927 Loaded tool data table 'srma_indexes' galaxy.tools.data WARNING 2013-02-04 10:25:28,927 Cannot find index file '/Users/dtenenba/dev/galaxy-dist/tool-data/bowtie_indices.loc' for tool data table 'tophat_indexes' galaxy.tools.data DEBUG 2013-02-04 10:25:28,928 Loaded tool data table 'tophat_indexes' galaxy.tools.data WARNING 2013-02-04 10:25:28,928 Cannot find index file '/Users/dtenenba/dev/galaxy-dist/tool-data/bowtie_indices_color.loc' for tool data table 'tophat_indexes_color' galaxy.tools.data DEBUG 2013-02-04 10:25:28,928 Loaded tool data table 'tophat_indexes_color' galaxy.tools.data DEBUG 2013-02-04 10:25:28,928 Loaded tool data table 'tophat2_indexes' galaxy.tools.data DEBUG 2013-02-04 10:25:28,928 Loaded tool data table 'ccat_configurations' galaxy.tools.data DEBUG 2013-02-04 10:25:28,928 Loaded tool data table 'mosaik_indexes' galaxy.tools INFO 2013-02-04 10:25:28,937 Parsing the tool configuration ./tool_conf.xml galaxy.tools WARNING 2013-02-04 10:25:30,785 A when tag has not been defined for 'master_variable_type (master_variable_type_selector) --> allPairs', assuming empty inputs. galaxy.tools WARNING 2013-02-04 10:25:32,118 A when tag has been defined for 'manipulation (manipulation_selector) --> modify_each_score', but does not appear to be selectable. galaxy.tools.test DEBUG 2013-02-04 10:25:32,706 Error in add_param for report_discordant_pairs: Unable to determine parameter type of test input 'report_discordant_pairs'. Ensure that the parameter exists and that any container groups are defined first. docutils WARNING 2013-02-04 10:25:32,734 :50: (WARNING/2) Literal block expected; none found. galaxy.tools.test DEBUG 2013-02-04 10:25:32,744 Error in add_param for min_coverage_intron: Unable to determine parameter type of test input 'min_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 10:25:32,746 Error in add_param for max_coverage_intron: Unable to determine parameter type of test input 'max_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 10:25:33,828 Error in add_param for force: Unable to determine parameter type of test input 'force'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 10:25:34,071 Error in add_param for input: Unable to determine parameter type of test input 'input'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 10:25:34,071 Error in add_param for group1_1: Unable to determine parameter type of test input 'group1_1'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 10:25:34,071 Error in add_param for group1_2: Unable to determine parameter type of test input 'group1_2'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 10:25:34,071 Error in add_param for group1_3: Unable to determine parameter type of test input 'group1_3'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 10:25:34,072 Error in add_param for group2_1: Unable to determine parameter type of test input 'group2_1'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 10:25:34,072 Error in add_param for group2_2: Unable to determine parameter type of test input 'group2_2'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 10:25:34,072 Error in add_param for group2_3: Unable to determine parameter type of test input 'group2_3'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools INFO 2013-02-04 10:25:34,303 Parsing the tool configuration ./migrated_tools_conf.xml galaxy.tools DEBUG 2013-02-04 10:25:34,304 Loading section: Get Data galaxy.tools DEBUG 2013-02-04 10:25:34,304 Loaded tool id: upload1, version: 1.1.3 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,304 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,304 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,304 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,304 Loaded tool id: bx_browser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,304 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,305 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,305 Loaded tool id: biomart, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,305 Loaded tool id: biomart_test, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,305 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,305 Loaded tool id: gramenemart, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,305 Loaded tool id: modENCODEfly, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,305 Loaded tool id: flymine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,305 Loaded tool id: flymine_test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,305 Loaded tool id: modmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,305 Loaded tool id: ratmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,306 Loaded tool id: yeastmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,306 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,306 Loaded tool id: modENCODEworm, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,306 Loaded tool id: wormbase, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,306 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,306 Loaded tool id: eupathdb, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,306 Loaded tool id: encode_db1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,306 Loaded tool id: epigraph_import, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,306 Loaded tool id: epigraph_import_test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,306 Loaded tool id: hbvar, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,307 Loaded tool id: genomespace_file_browser_prod, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,307 Loaded tool id: genomespace_importer, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,307 Loaded tool id: fix_errors, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,307 Loading section: Send Data galaxy.tools DEBUG 2013-02-04 10:25:34,307 Loaded tool id: epigraph_export, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,307 Loaded tool id: epigraph_test_export, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,307 Loaded tool id: genomespace_exporter, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,307 Loading section: ENCODE Tools galaxy.tools DEBUG 2013-02-04 10:25:34,307 Loaded tool id: gencode_partition1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,308 Loaded tool id: random_intervals1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,308 Loading section: Lift-Over galaxy.tools DEBUG 2013-02-04 10:25:34,308 Loaded tool id: liftOver1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,308 Loading section: Text Manipulation galaxy.tools DEBUG 2013-02-04 10:25:34,308 Loaded tool id: addValue, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,308 Loaded tool id: Add_a_column1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,308 Loaded tool id: cat1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,308 Loaded tool id: Cut1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,308 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,309 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,309 Loaded tool id: createInterval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,309 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,309 Loaded tool id: Paste1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,309 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,309 Loaded tool id: random_lines1, version: 2.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,309 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,309 Loaded tool id: Show tail1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,309 Loaded tool id: trimmer, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,309 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,309 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,310 Loaded tool id: dna_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,310 Loaded tool id: tables_arithmetic_operations, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,310 Loading section: Filter and Sort galaxy.tools DEBUG 2013-02-04 10:25:34,310 Loaded tool id: Filter1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,310 Loaded tool id: sort1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,310 Loaded tool id: Grep1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,310 Loaded label: GFF galaxy.tools DEBUG 2013-02-04 10:25:34,310 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,310 Loaded tool id: gff_filter_by_attribute, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,310 Loaded tool id: gff_filter_by_feature_count, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,311 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,311 Loading section: Join, Subtract and Group galaxy.tools DEBUG 2013-02-04 10:25:34,311 Loaded tool id: join1, version: 2.0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,311 Loaded tool id: comp1, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,311 Loaded tool id: subtract_query1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,311 Loaded tool id: Grouping1, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,311 Loaded tool id: column_join, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,311 Loading section: Convert Formats galaxy.tools DEBUG 2013-02-04 10:25:34,311 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,311 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,312 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,312 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,312 Loaded tool id: fasta2tab, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,312 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,312 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,312 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,312 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,312 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,312 Loaded tool id: tab2fasta, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,312 Loaded tool id: fastq_to_fasta_python, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,313 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,313 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,313 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,313 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,313 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,313 Loading section: Extract Features galaxy.tools DEBUG 2013-02-04 10:25:34,313 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,313 Loading section: Fetch Sequences galaxy.tools DEBUG 2013-02-04 10:25:34,313 Loaded tool id: Extract genomic DNA 1, version: 2.2.2 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,314 Loading section: Fetch Alignments galaxy.tools DEBUG 2013-02-04 10:25:34,314 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,314 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,314 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,314 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,314 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,314 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,314 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,314 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,314 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,315 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,315 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,315 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,315 Loading section: Get Genomic Scores galaxy.tools DEBUG 2013-02-04 10:25:34,315 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,315 Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.3 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,315 Loaded tool id: phastOdds_for_intervals, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,315 Loading section: Operate on Genomic Intervals galaxy.tools DEBUG 2013-02-04 10:25:34,315 Loaded tool id: gops_intersect_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,316 Loaded tool id: gops_subtract_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,316 Loaded tool id: gops_merge_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,316 Loaded tool id: gops_concat_1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,316 Loaded tool id: gops_basecoverage_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,316 Loaded tool id: gops_coverage_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,316 Loaded tool id: gops_complement_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,316 Loaded tool id: gops_cluster_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,316 Loaded tool id: gops_join_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,316 Loaded tool id: get_flanks1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,316 Loaded tool id: flanking_features_1, version: 4.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,317 Loaded tool id: Annotation_Profiler_0, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,317 Loading section: Statistics galaxy.tools DEBUG 2013-02-04 10:25:34,317 Loaded tool id: Summary_Statistics1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,317 Loaded tool id: Count1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,317 Loaded tool id: cor2, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,317 Loaded tool id: generate_matrix_for_pca_and_lda1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,317 Loaded tool id: lda_analy1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,317 Loaded tool id: plot_for_lda_output1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,317 Loaded tool id: t_test_two_samples, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,317 Loaded tool id: compute_q_values, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,318 Loaded tool id: maximal_information_based_nonparametric_exploration, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,318 Loaded label: GFF galaxy.tools DEBUG 2013-02-04 10:25:34,318 Loaded tool id: count_gff_features, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,318 Loading section: Wavelet Analysis galaxy.tools DEBUG 2013-02-04 10:25:34,318 Loaded tool id: dwt_var1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,318 Loading section: Graph/Display Data galaxy.tools DEBUG 2013-02-04 10:25:34,318 Loaded tool id: histogram_rpy, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,318 Loaded tool id: scatterplot_rpy, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,318 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,318 Loaded tool id: XY_Plot_1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,319 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,319 Loaded tool id: gmaj_1, version: 2.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,319 Loaded tool id: laj_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,319 Loaded tool id: build_ucsc_custom_track_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,319 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,319 Loaded tool id: mutation_visualize, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,319 Loading section: Regional Variation galaxy.tools DEBUG 2013-02-04 10:25:34,319 Loaded tool id: winSplitter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,319 Loaded tool id: featureCoverage1, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,320 Loaded tool id: wtavg, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,320 Loaded tool id: qualityFilter, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,320 Loaded tool id: cpgFilter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,320 Loaded tool id: getIndels_2way, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,320 Loaded tool id: indels_3way, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,320 Loaded tool id: indelRates_3way, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,320 Loaded tool id: substitutions1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,320 Loaded tool id: subRate1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,320 Loaded tool id: microsats_align1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,321 Loaded tool id: microsats_mutability1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,321 Loaded tool id: delete_overlapping_indels, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,321 Loaded tool id: compute_motifs_frequency, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,321 Loaded tool id: compute_motif_frequencies_for_all_motifs, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,321 Loaded tool id: categorize_elements_satisfying_criteria, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,321 Loaded tool id: draw_stacked_barplots, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,321 Loading section: Multiple regression galaxy.tools DEBUG 2013-02-04 10:25:34,321 Loaded tool id: LinearRegression1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,321 Loaded tool id: LogisticRegression, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,322 Loaded tool id: BestSubsetsRegression1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,322 Loaded tool id: rcve1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,322 Loaded tool id: partialRsq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,322 Loading section: Multivariate Analysis galaxy.tools DEBUG 2013-02-04 10:25:34,322 Loaded tool id: pca1, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,322 Loaded tool id: cca1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,322 Loaded tool id: kpca1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,322 Loaded tool id: kcca1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,322 Loading section: Evolution galaxy.tools DEBUG 2013-02-04 10:25:34,323 Loaded tool id: hyphy_branch_lengths_wrapper1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,323 Loaded tool id: hyphy_nj_tree_wrapper1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,323 Loaded tool id: hyphy_dnds_wrapper1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,323 Loaded tool id: mutate_snp_codon_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,323 Loaded tool id: hgv_codingSnps, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,323 Loaded tool id: hgv_add_scores, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,323 Loading section: Motif Tools galaxy.tools DEBUG 2013-02-04 10:25:34,323 Loaded tool id: meme_meme, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,323 Loaded tool id: meme_fimo, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,323 Loaded tool id: rgweblogo3, version: 0.4 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,324 Loading section: Multiple Alignments galaxy.tools DEBUG 2013-02-04 10:25:34,324 Loaded tool id: clustalw, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,324 Loading section: Metagenomic analyses galaxy.tools DEBUG 2013-02-04 10:25:34,324 Loaded tool id: Fetch Taxonomic Ranks, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,324 Loaded tool id: t2t_report, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,324 Loaded tool id: Draw_phylogram, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,324 Loaded tool id: find_diag_hits, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,324 Loaded tool id: lca1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,324 Loaded tool id: poisson2test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,325 Loading section: FASTA manipulation galaxy.tools DEBUG 2013-02-04 10:25:34,325 Loaded tool id: fasta_compute_length, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,325 Loaded tool id: fasta_filter_by_length, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,325 Loaded tool id: fasta_concatenate0, version: 0.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,325 Loaded tool id: fasta2tab, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,325 Loaded tool id: tab2fasta, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,325 Loaded tool id: cshl_fasta_formatter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,325 Loaded tool id: cshl_fasta_nucleotides_changer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,325 Loaded tool id: cshl_fastx_collapser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,325 Loading section: NGS: QC and manipulation galaxy.tools DEBUG 2013-02-04 10:25:34,326 Loaded label: FastQC: fastq/sam/bam galaxy.tools DEBUG 2013-02-04 10:25:34,326 Loaded tool id: fastqc, version: 0.51 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,326 Loaded label: Illumina fastq galaxy.tools DEBUG 2013-02-04 10:25:34,326 Loaded tool id: fastq_groomer, version: 1.0.4 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,326 Loaded tool id: fastq_paired_end_splitter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,326 Loaded tool id: fastq_paired_end_joiner, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,326 Loaded tool id: fastq_stats, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,326 Loaded label: Roche-454 data galaxy.tools DEBUG 2013-02-04 10:25:34,326 Loaded tool id: quality_score_distribution, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,327 Loaded tool id: trim_reads, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,327 Loaded tool id: fastq_combiner, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,327 Loaded label: AB-SOLiD data galaxy.tools DEBUG 2013-02-04 10:25:34,327 Loaded tool id: solid2fastq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,327 Loaded tool id: solid_qual_stats, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,327 Loaded tool id: solid_qual_boxplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,327 Loaded label: Generic FASTQ manipulation galaxy.tools DEBUG 2013-02-04 10:25:34,327 Loaded tool id: fastq_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,327 Loaded tool id: fastq_trimmer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,327 Loaded tool id: fastq_quality_trimmer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,327 Loaded tool id: fastq_masker_by_quality, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,328 Loaded tool id: fastq_paired_end_interlacer, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,328 Loaded tool id: fastq_paired_end_deinterlacer, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,328 Loaded tool id: fastq_manipulation, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,328 Loaded tool id: fastq_to_fasta_python, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,328 Loaded tool id: fastq_to_tabular, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,328 Loaded tool id: tabular_to_fastq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,328 Loaded label: FASTX-Toolkit for FASTQ data galaxy.tools DEBUG 2013-02-04 10:25:34,328 Loaded tool id: cshl_fastq_quality_converter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,328 Loaded tool id: cshl_fastx_quality_statistics, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,328 Loaded tool id: cshl_fastq_quality_boxplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,329 Loaded tool id: cshl_fastx_nucleotides_distribution, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,329 Loaded tool id: cshl_fastq_to_fasta, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,329 Loaded tool id: cshl_fastq_quality_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,329 Loaded tool id: cshl_fastx_artifacts_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,329 Loaded tool id: cshl_fastx_barcode_splitter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,329 Loaded tool id: cshl_fastx_clipper, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,329 Loaded tool id: cshl_fastx_collapser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,329 Loaded tool id: cshl_fastx_renamer, version: 0.0.11 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,329 Loaded tool id: cshl_fastx_reverse_complement, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,329 Loaded tool id: cshl_fastx_trimmer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,330 Loading section: NGS: Mapping galaxy.tools DEBUG 2013-02-04 10:25:34,330 Loaded tool id: bowtie2, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,330 Loaded tool id: bfast_wrapper, version: 0.1.3 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,330 Loaded tool id: megablast_wrapper, version: 1.2.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,330 Loaded tool id: megablast_xml_parser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,330 Loaded tool id: PerM, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,330 Loaded tool id: srma_wrapper, version: 0.2.5 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,330 Loaded tool id: mosaik_wrapper, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,330 Loading section: NGS: Indel Analysis galaxy.tools DEBUG 2013-02-04 10:25:34,330 Loaded tool id: sam_indel_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,331 Loaded tool id: indel_sam2interval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,331 Loaded tool id: indel_table, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,331 Loaded tool id: indel_analysis, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,331 Loading section: NGS: RNA Analysis galaxy.tools DEBUG 2013-02-04 10:25:34,331 Loaded label: RNA-seq galaxy.tools DEBUG 2013-02-04 10:25:34,331 Loaded tool id: tophat, version: 1.5.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,331 Loaded tool id: tophat2, version: 0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,331 Loaded tool id: tophat_color, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,331 Loaded tool id: cufflinks, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,331 Loaded tool id: cuffcompare, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,332 Loaded tool id: cuffmerge, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,332 Loaded tool id: cuffdiff, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,332 Loaded tool id: express, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,332 Loaded label: Filtering galaxy.tools DEBUG 2013-02-04 10:25:34,332 Loaded tool id: filter_combined_via_tracking, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,332 Loading section: NGS: SAM Tools galaxy.tools DEBUG 2013-02-04 10:25:34,332 Loaded tool id: sam_bw_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,332 Loaded tool id: sam2interval, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,332 Loaded tool id: sam_to_bam, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,333 Loaded tool id: bam_to_sam, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,333 Loaded tool id: sam_merge2, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,333 Loaded tool id: samtools_mpileup, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,333 Loaded tool id: sam_pileup, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,333 Loaded tool id: pileup_parser, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,333 Loaded tool id: pileup_interval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,333 Loaded tool id: samtools_flagstat, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,333 Loaded tool id: samtools_rmdup, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,333 Loaded tool id: samtools_slice_bam, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,333 Loading section: NGS: GATK Tools (beta) galaxy.tools DEBUG 2013-02-04 10:25:34,334 Loaded label: Alignment Utilities galaxy.tools DEBUG 2013-02-04 10:25:34,334 Loaded tool id: gatk_depth_of_coverage, version: 0.0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,334 Loaded tool id: gatk_print_reads, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,334 Loaded label: Realignment galaxy.tools DEBUG 2013-02-04 10:25:34,334 Loaded tool id: gatk_realigner_target_creator, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,334 Loaded tool id: gatk_indel_realigner, version: 0.0.6 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,334 Loaded label: Base Recalibration galaxy.tools DEBUG 2013-02-04 10:25:34,334 Loaded tool id: gatk_count_covariates, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,334 Loaded tool id: gatk_table_recalibration, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,334 Loaded tool id: gatk_analyze_covariates, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,335 Loaded label: Genotyping galaxy.tools DEBUG 2013-02-04 10:25:34,335 Loaded tool id: gatk_unified_genotyper, version: 0.0.6 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,335 Loaded label: Annotation galaxy.tools DEBUG 2013-02-04 10:25:34,335 Loaded tool id: gatk_variant_annotator, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,335 Loaded label: Filtration galaxy.tools DEBUG 2013-02-04 10:25:34,335 Loaded tool id: gatk_variant_filtration, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,335 Loaded tool id: gatk_variant_select, version: 0.0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,335 Loaded label: Variant Quality Score Recalibration galaxy.tools DEBUG 2013-02-04 10:25:34,335 Loaded tool id: gatk_variant_recalibrator, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,335 Loaded tool id: gatk_variant_apply_recalibration, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,336 Loaded label: Variant Utilities galaxy.tools DEBUG 2013-02-04 10:25:34,336 Loaded tool id: gatk_validate_variants, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,336 Loaded tool id: gatk_variant_eval, version: 0.0.8 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,336 Loaded tool id: gatk_variant_combine, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,336 Loading section: NGS: Peak Calling galaxy.tools DEBUG 2013-02-04 10:25:34,336 Loaded tool id: peakcalling_macs, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,336 Loaded tool id: peakcalling_sicer, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,336 Loaded tool id: peakcalling_ccat, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,336 Loaded tool id: bed2genetrack, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,337 Loaded tool id: predict2genetrack, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,337 Loading section: NGS: Simulation galaxy.tools DEBUG 2013-02-04 10:25:34,337 Loaded tool id: ngs_simulation, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,337 Loading section: SNP/WGA: Data; Filters galaxy.tools DEBUG 2013-02-04 10:25:34,337 Loaded label: Data: Import and upload galaxy.tools DEBUG 2013-02-04 10:25:34,337 Loaded tool id: upload1, version: 1.1.3 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,337 Loaded tool id: library_access1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,337 Loaded label: Data: Filter and Clean galaxy.tools DEBUG 2013-02-04 10:25:34,337 Loaded tool id: rgClean1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,338 Loaded tool id: rgPedSub1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,338 Loaded tool id: rgLDIndep1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,338 Loaded label: Simulate galaxy.tools DEBUG 2013-02-04 10:25:34,338 Loaded tool id: fakePhe1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,338 Loaded tool id: rgfakePed1, version: 0.02 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,338 Loading section: SNP/WGA: QC; LD; Plots galaxy.tools DEBUG 2013-02-04 10:25:34,338 Loaded label: QC; Eigenstrat galaxy.tools DEBUG 2013-02-04 10:25:34,338 Loaded tool id: rgQC1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,338 Loaded tool id: rgEigPCA1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,338 Loaded label: LD; Manhattan/QQ; GRR galaxy.tools DEBUG 2013-02-04 10:25:34,339 Loaded tool id: rgHaploView1, version: 0.3 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,339 Loaded tool id: rgManQQ1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,339 Loaded tool id: rgGRR1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,339 Loading section: SNP/WGA: Statistical Models galaxy.tools DEBUG 2013-02-04 10:25:34,339 Loaded tool id: rgCaCo1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,339 Loaded tool id: rgTDT1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,339 Loaded tool id: rgGLM1, version: 0.2 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,339 Loaded tool id: rgManQQ1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,339 Loading section: Phenotype Association galaxy.tools DEBUG 2013-02-04 10:25:34,339 Loaded tool id: hgv_codingSnps, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,340 Loaded tool id: hgv_add_scores, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,340 Loaded tool id: hgv_sift, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,340 Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,340 Loaded tool id: hgv_david, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,340 Loaded tool id: ctdBatch_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,340 Loaded tool id: hgv_funDo, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,340 Loaded tool id: hgv_snpFreq, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,340 Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,340 Loaded tool id: hgv_pass, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,340 Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,341 Loaded tool id: hgv_beam, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,341 Loaded tool id: hgv_lps, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,341 Loaded tool id: hgv_hilbertvis, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,341 Loaded tool id: freebayes_wrapper, version: 0.5.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,341 Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,341 Loaded tool id: vcf2pgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,341 Loaded tool id: dividePgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,341 Loading section: VCF Tools galaxy.tools DEBUG 2013-02-04 10:25:34,341 Loaded tool id: vcf_intersect, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,341 Loaded tool id: vcf_annotate, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,342 Loaded tool id: vcf_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-02-04 10:25:34,342 Loaded tool id: vcf_extract, version: 1.0.0 into tool panel. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,433 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,435 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,437 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,438 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,438 Loaded display application 'genetrack_interval' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,439 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,441 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,442 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,444 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,445 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,450 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,450 Loaded display application 'genetrack_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,455 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,461 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,463 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,465 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,467 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,469 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,470 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,471 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,473 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,473 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,473 Adding inherited display application 'genetrack_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,473 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,473 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,473 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,474 Adding inherited display application 'genetrack_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,474 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,474 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,474 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,474 Adding inherited display application 'genetrack_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,474 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,474 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,474 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,474 Adding inherited display application 'genetrack_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,474 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,475 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,475 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,475 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,475 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,475 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,476 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,476 Adding inherited display application 'genetrack_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,476 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,476 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,476 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,476 Adding inherited display application 'genetrack_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,476 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,476 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,476 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,483 Loaded converter: CONVERTER_Bam_Bai_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,489 Loaded converter: CONVERTER_bam_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,493 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,499 Loaded converter: CONVERTER_interval_to_coverage_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,504 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,509 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,514 Loaded converter: CONVERTER_bed_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,519 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,524 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,531 Loaded converter: CONVERTER_bed_to_genetrack_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,535 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,540 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,545 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,550 Loaded converter: CONVERTER_interval_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,555 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,560 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,565 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,569 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,574 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,579 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,584 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,591 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,596 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,601 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,605 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,610 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,616 Loaded converter: CONVERTER_gff_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,621 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,625 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,630 Loaded converter: CONVERTER_gff_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,635 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,640 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,644 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,651 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,656 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,661 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,666 Loaded converter: CONVERTER_interval_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,670 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,675 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,680 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,685 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,690 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,694 Loaded converter: CONVERTER_encodepeak_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,699 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,704 Loaded converter: CONVERTER_sam_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,711 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,716 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,721 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,726 Loaded converter: CONVERTER_vcf_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,730 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,731 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,736 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,740 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,745 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,750 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,755 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2013-02-04 10:25:34,756 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.imp_exp DEBUG 2013-02-04 10:25:34,758 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2013-02-04 10:25:34,758 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.genome_index DEBUG 2013-02-04 10:25:34,760 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.runners.local INFO 2013-02-04 10:25:34,761 starting workers galaxy.jobs.runners.local DEBUG 2013-02-04 10:25:34,762 5 workers ready galaxy.jobs.handler DEBUG 2013-02-04 10:25:34,762 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.runners.lwr INFO 2013-02-04 10:25:34,763 starting workers galaxy.jobs.runners.lwr DEBUG 2013-02-04 10:25:34,764 5 workers ready galaxy.jobs.handler DEBUG 2013-02-04 10:25:34,764 Loaded job runner: galaxy.jobs.runners.lwr:LwrJobRunner galaxy.jobs.handler DEBUG 2013-02-04 10:25:34,764 Job runners: local:lwr galaxy.jobs.handler INFO 2013-02-04 10:25:34,764 job handler stop queue started galaxy.jobs.manager INFO 2013-02-04 10:25:34,767 job manager queue started galaxy.jobs.manager INFO 2013-02-04 10:25:34,767 job manager stop queue started galaxy.jobs.handler INFO 2013-02-04 10:25:34,769 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2013-02-04 10:25:34,770 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2013-02-04 10:25:34,772 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 >>> /Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers ['/Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers'] galaxy.webapps.galaxy.controllers admin galaxy.webapps.galaxy.controllers.admin galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,779 Enabling 'admin' controller, class: AdminGalaxy galaxy.webapps.galaxy.controllers admin_toolshed galaxy.webapps.galaxy.controllers.admin_toolshed galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,827 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,827 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.webapps.galaxy.controllers async galaxy.webapps.galaxy.controllers.async galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,828 Enabling 'async' controller, class: ASync galaxy.webapps.galaxy.controllers cloudlaunch galaxy.webapps.galaxy.controllers.cloudlaunch galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,838 Enabling 'cloudlaunch' controller, class: CloudController galaxy.webapps.galaxy.controllers data_admin galaxy.webapps.galaxy.controllers.data_admin galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,851 Enabling 'data_admin' controller, class: DataAdmin galaxy.webapps.galaxy.controllers dataset galaxy.webapps.galaxy.controllers.dataset galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,857 Enabling 'dataset' controller, class: DatasetInterface galaxy.webapps.galaxy.controllers error galaxy.webapps.galaxy.controllers.error galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,858 Enabling 'error' controller, class: Error galaxy.webapps.galaxy.controllers external_service galaxy.webapps.galaxy.controllers.external_service galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,860 Enabling 'external_service' controller, class: ExternalService galaxy.webapps.galaxy.controllers external_services galaxy.webapps.galaxy.controllers.external_services galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,860 Enabling 'external_services' controller, class: ExternalServiceController galaxy.webapps.galaxy.controllers forms galaxy.webapps.galaxy.controllers.forms galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,861 Enabling 'forms' controller, class: Forms galaxy.webapps.galaxy.controllers history galaxy.webapps.galaxy.controllers.history galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,863 Enabling 'history' controller, class: HistoryController galaxy.webapps.galaxy.controllers library galaxy.webapps.galaxy.controllers.library galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,864 Enabling 'library' controller, class: Library galaxy.webapps.galaxy.controllers library_admin galaxy.webapps.galaxy.controllers.library_admin galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,865 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.webapps.galaxy.controllers library_common galaxy.webapps.galaxy.controllers.library_common galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,866 Enabling 'library_common' controller, class: LibraryCommon galaxy.webapps.galaxy.controllers mobile galaxy.webapps.galaxy.controllers.mobile galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,866 Enabling 'mobile' controller, class: Mobile galaxy.webapps.galaxy.controllers page galaxy.webapps.galaxy.controllers.page galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,868 Enabling 'page' controller, class: PageController galaxy.webapps.galaxy.controllers request_type galaxy.webapps.galaxy.controllers.request_type galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,868 Enabling 'request_type' controller, class: RequestType galaxy.webapps.galaxy.controllers requests galaxy.webapps.galaxy.controllers.requests galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,869 Enabling 'requests' controller, class: Requests galaxy.webapps.galaxy.controllers requests_admin galaxy.webapps.galaxy.controllers.requests_admin galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,882 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.webapps.galaxy.controllers requests_common galaxy.webapps.galaxy.controllers.requests_common galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,882 Enabling 'requests_common' controller, class: RequestsCommon galaxy.webapps.galaxy.controllers root galaxy.webapps.galaxy.controllers.root galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,883 Enabling 'root' controller, class: RootController galaxy.webapps.galaxy.controllers tag galaxy.webapps.galaxy.controllers.tag galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,884 Enabling 'tag' controller, class: TagsController galaxy.webapps.galaxy.controllers tool_runner galaxy.webapps.galaxy.controllers.tool_runner galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,885 Enabling 'tool_runner' controller, class: ToolRunner galaxy.webapps.galaxy.controllers ucsc_proxy galaxy.webapps.galaxy.controllers.ucsc_proxy galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,886 Enabling 'ucsc_proxy' controller, class: UCSCProxy galaxy.webapps.galaxy.controllers user galaxy.webapps.galaxy.controllers.user galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,886 Enabling 'user' controller, class: User galaxy.webapps.galaxy.controllers visualization galaxy.webapps.galaxy.controllers.visualization galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,888 Enabling 'visualization' controller, class: VisualizationController galaxy.webapps.galaxy.controllers workflow galaxy.webapps.galaxy.controllers.workflow galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,888 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,889 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,890 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,890 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,891 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,892 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,892 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,892 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,893 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,893 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,898 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,905 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,905 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,906 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,906 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,906 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,907 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,908 Enabling 'permissions' API controller, class: PermissionsController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,908 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,909 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,909 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,910 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,910 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,911 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,912 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,912 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2013-02-04 10:25:34,912 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 10:25:34,913 app.config.api_folders: False galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 10:25:35,143 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 10:25:35,144 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 10:25:35,145 Enabling 'print debug' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 10:25:35,186 Enabling 'eval exceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 10:25:35,187 Enabling 'trans logger' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 10:25:35,187 Enabling 'config' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-02-04 10:25:35,187 Enabling 'x-forwarded-host' middleware Starting server in PID 1996. serving on http://127.0.0.1:8080 127.0.0.1 - - [04/Feb/2013:10:26:02 -0700] "GET /user/login HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:10:26:04 -0700] "POST /user/login?use_panels=False HTTP/1.1" 200 - "http://localhost:8080/user/login" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" galaxy.web.framework DEBUG 2013-02-04 10:26:04,732 Error: this request returned None from get_history(): http://localhost:8080/ 127.0.0.1 - - [04/Feb/2013:10:26:04 -0700] "GET / HTTP/1.1" 200 - "http://localhost:8080/user/login?use_panels=False" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:10:26:04 -0700] "GET /root/tool_menu HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:10:26:04 -0700] "GET /history HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:10:26:13 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:8080/root/tool_menu" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" galaxy.web.framework DEBUG 2013-02-04 10:26:21,402 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 10:26:21,402 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 10:26:21,402 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 10:26:21,402 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 10:26:21,402 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 10:26:21,402 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 10:26:21,403 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 10:26:21,403 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-04 10:26:21,404 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create 127.0.0.1 - - [04/Feb/2013:10:26:21 -0700] "POST /tool_runner/upload_async_create HTTP/1.1" 500 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" Debug at: http://localhost:8080/_debug/view/1360002335 127.0.0.1 - - [04/Feb/2013:10:26:21 -0700] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" galaxy.tools.actions.upload_common INFO 2013-02-04 10:26:21,569 tool upload1 created job id 11 127.0.0.1 - - [04/Feb/2013:10:26:21 -0700] "POST /tool_runner/index HTTP/1.1" 200 - "http://localhost:8080/tool_runner?tool_id=upload1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:10:26:21 -0700] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:10:26:21 -0700] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 50355) Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 323, in finish_request self.RequestHandlerClass(request, client_address, self) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 641, in __init__ self.finish() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 694, in finish self.wfile.flush() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- galaxy.jobs.manager DEBUG 2013-02-04 10:26:26,801 (11) Job assigned to handler 'main' galaxy.jobs DEBUG 2013-02-04 10:26:31,856 (11) Working directory for job is: /Users/dtenenba/dev/galaxy-dist/database/job_working_directory/000/11 galaxy.jobs.handler DEBUG 2013-02-04 10:26:31,857 dispatching job 11 to local runner galaxy.jobs.handler INFO 2013-02-04 10:26:31,900 (11) Job dispatched galaxy.jobs.runners.local DEBUG 2013-02-04 10:26:31,952 Local runner: starting job 11 galaxy.jobs.runners.local DEBUG 2013-02-04 10:26:32,075 executing: python /Users/dtenenba/dev/galaxy-dist/tools/data_source/upload.py /Users/dtenenba/dev/galaxy-dist /Users/dtenenba/dev/galaxy-dist/database/tmp/tmpiGtWWL /Users/dtenenba/dev/galaxy-dist/database/tmp/tmpkyryRT 18:/Users/dtenenba/dev/galaxy-dist/database/job_working_directory/000/11/dataset_18_files:/Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_18.dat galaxy.jobs.runners.local DEBUG 2013-02-04 10:26:33,073 execution finished: python /Users/dtenenba/dev/galaxy-dist/tools/data_source/upload.py /Users/dtenenba/dev/galaxy-dist /Users/dtenenba/dev/galaxy-dist/database/tmp/tmpiGtWWL /Users/dtenenba/dev/galaxy-dist/database/tmp/tmpkyryRT 18:/Users/dtenenba/dev/galaxy-dist/database/job_working_directory/000/11/dataset_18_files:/Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_18.dat galaxy.jobs DEBUG 2013-02-04 10:26:33,108 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-02-04 10:26:33,178 job 11 ended 127.0.0.1 - - [04/Feb/2013:10:27:07 -0700] "GET /_debug/view/1360002335 HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:10:27:07 -0700] "GET /_debug/media/jquery-1.2.1.min.js HTTP/1.1" 200 46437 "http://localhost:8080/_debug/view/1360002335" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:10:27:07 -0700] "GET /_debug/media/traceback.css HTTP/1.1" 200 9521 "http://localhost:8080/_debug/view/1360002335" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:10:27:07 -0700] "GET /_debug/media/debug.js HTTP/1.1" 200 10525 "http://localhost:8080/_debug/view/1360002335" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:10:27:07 -0700] "GET /_debug/media/plus.jpg HTTP/1.1" 200 361 "http://localhost:8080/_debug/view/1360002335" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:10:28:40 -0700] "GET /_debug/view/1360002335 HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17"