Architecture appears to be cygwin_nt-5.1-i686 UCS2 python path: /galaxy_dist/lib:/galaxy_dist/eggs/UCS2:/galaxy_dist/eggs path: /usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/cygdrive/c/WINDOWS/system32:/cygdrive/c/WINDOWS:/cygdrive/c/WINDOWS/System32/Wbem:/cygdrive/c/Program Files/ATI Technologies/ATI Control Panel:/cygdrive/c/Program Files/Common Files/Teleca Shared:/cygdrive/c/Program Files/Intuwave/Shared/mRouterRuntime:/Cheetah-2.0.1/dist/bin:/depot/apps/i686/bin:/home/universe/cygwin_nt-5.1-i686/EMBOSS-5.0.0/bin:/home/universe/cygwin_nt-5.1-i686/ImageMagick/bin:/home/universe/cygwin_nt-5.1-i686/PAML/paml3.15/bin galaxy.model.mapping DEBUG 2008-03-14 18:57:40,103 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.tools INFO 2008-03-14 18:57:40,365 parsing the tool configuration galaxy.tools DEBUG 2008-03-14 18:57:40,529 Loading tools in section: Get Data galaxy.tools DEBUG 2008-03-14 18:57:41,188 Loaded tool: upload1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:41,223 Loaded tool: ucsc_table_direct1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:41,234 Loaded tool: ucsc_table_direct_test1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:41,243 Loaded tool: ucsc_table_direct_archaea1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:41,580 Loaded tool: microbial_import1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:41,634 Loaded tool: biomart 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:41,641 Loaded tool: biomart 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:41,657 Loaded tool: encode_db1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:41,667 Loaded tool: hbvar 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:41,710 Loaded tool: fix_errors 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:41,711 Loading tools in section: Get ENCODE Data galaxy.tools DEBUG 2008-03-14 18:57:41,837 Loaded tool: encode_import_chromatin_and_chromosomes1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:41,947 Loaded tool: encode_import_genes_and_transcripts1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:42,057 Loaded tool: encode_import_multi-species_sequence_analysis1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:42,173 Loaded tool: encode_import_transcription_regulation1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:42,286 Loaded tool: encode_import_all_latest_datasets1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:42,394 Loaded tool: encode_import_gencode1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:42,395 Loading tools in section: ENCODE Tools galaxy.tools DEBUG 2008-03-14 18:57:42,526 Loaded tool: gencode_partition1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:42,620 Loaded tool: random_intervals1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:42,620 Loading tools in section: Lift-Over galaxy.tools DEBUG 2008-03-14 18:57:42,727 Loaded tool: liftOver1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:42,727 Loading tools in section: Text Manipulation galaxy.tools DEBUG 2008-03-14 18:57:42,859 Loaded tool: addValue 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:42,953 Loaded tool: Add a column1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:43,007 Loaded tool: cat1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:43,054 Loaded tool: Condense characters1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:43,099 Loaded tool: Convert characters1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:43,142 Loaded tool: createInterval 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:43,240 Loaded tool: Cut1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:43,274 Loaded tool: ChangeCase1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:43,319 Loaded tool: Paste1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:43,353 Loaded tool: Remove beginning1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:43,380 Loaded tool: Show beginning1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:43,439 Loaded tool: Show tail1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:43,439 Loading tools in section: Filter and Sort galaxy.tools DEBUG 2008-03-14 18:57:43,616 Loaded tool: Filter1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:43,675 Loaded tool: sort1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:43,901 Loaded tool: Grep1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:43,901 Loading tools in section: Join, Subtract and Group galaxy.tools DEBUG 2008-03-14 18:57:43,972 Loaded tool: join1 2.0.0 galaxy.tools DEBUG 2008-03-14 18:57:44,047 Loaded tool: comp1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:44,176 Loaded tool: subtract_query1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:44,260 Loaded tool: Grouping1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:44,260 Loading tools in section: Convert Formats galaxy.tools DEBUG 2008-03-14 18:57:44,364 Loaded tool: axt_to_concat_fasta 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:44,467 Loaded tool: axt_to_fasta 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:44,608 Loaded tool: axt_to_lav_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:44,665 Loaded tool: bed2gff1 2.0.0 galaxy.tools DEBUG 2008-03-14 18:57:44,727 Loaded tool: fasta2tab 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:44,780 Loaded tool: gff2bed1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:44,873 Loaded tool: lav_to_bed1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:45,089 Loaded tool: MAF_To_BED1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:45,297 Loaded tool: MAF_To_Fasta1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:45,328 Loaded tool: tab2fasta 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:45,328 Loading tools in section: Extract Features galaxy.tools DEBUG 2008-03-14 18:57:45,414 Loaded tool: gene2exon1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:45,497 Loaded tool: Extract_features1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:45,497 Loading tools in section: Pattern-Matching galaxy.tools DEBUG 2008-03-14 18:57:45,679 Loaded tool: find_clusters_mysql 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:45,679 Loading tools in section: Fetch Sequences galaxy.tools ERROR 2008-03-14 18:57:45,712 error reading tool from path: extract/extract_genomic_dna.xml Traceback (most recent call last): File "/galaxy_dist/lib/galaxy/tools/__init__.py", line 65, in init_tools tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/galaxy_dist/lib/galaxy/tools/__init__.py", line 91, in load_tool return ToolClass( config_file, root, self.app ) File "/galaxy_dist/lib/galaxy/tools/__init__.py", line 178, in __init__ self.parse( root ) File "/galaxy_dist/lib/galaxy/tools/__init__.py", line 251, in parse self.parse_inputs( root ) File "/galaxy_dist/lib/galaxy/tools/__init__.py", line 325, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/galaxy_dist/lib/galaxy/tools/__init__.py", line 421, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/galaxy_dist/lib/galaxy/tools/__init__.py", line 463, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/galaxy_dist/lib/galaxy/tools/__init__.py", line 473, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/galaxy_dist/lib/galaxy/tools/parameters.py", line 131, in build return parameter_types[param_type]( tool, param ) File "/galaxy_dist/lib/galaxy/tools/parameters.py", line 726, in __init__ ToolParameter.__init__( self, tool, elem ) File "/galaxy_dist/lib/galaxy/tools/parameters.py", line 36, in __init__ self.validators.append( validation.Validator.from_element( elem ) ) File "/galaxy_dist/lib/galaxy/tools/validation.py", line 18, in from_element return validator_types[type].from_element( elem ) File "/galaxy_dist/lib/galaxy/tools/validation.py", line 207, in from_element return cls( filename, metadata_name, metadata_column, message, split, line_startswith ) File "/galaxy_dist/lib/galaxy/tools/validation.py", line 212, in __init__ for line in open( filename ): IOError: [Errno 2] No such file or directory: '/depot/data2/galaxy/alignseq.loc' galaxy.tools DEBUG 2008-03-14 18:57:45,784 Loading tools in section: Fetch Alignments galaxy.tools DEBUG 2008-03-14 18:57:45,829 Loaded tool: Interval2Maf_pairwise1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:45,870 Loaded tool: Interval2Maf1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:45,947 Loaded tool: Interval_Maf_Merged_Fasta2 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:46,005 Loaded tool: GeneBed_Maf_Fasta2 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:46,164 Loaded tool: maf_stats1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:46,191 Loaded tool: MAF_Thread_For_Species1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:46,246 Loaded tool: MAF_Limit_To_Species1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:46,267 Loaded tool: maf_limit_size1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:46,289 Loaded tool: maf_by_block_number1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:46,321 Loaded tool: MAF_Reverse_Complement_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:46,372 Loaded tool: MAF_filter 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:46,372 Loading tools in section: Get Genomic Scores galaxy.tools DEBUG 2008-03-14 18:57:46,459 Loaded tool: wiggle2simple1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:46,705 Loaded tool: aggregate_scores_in_intervals2 1.1.1 galaxy.tools DEBUG 2008-03-14 18:57:46,798 Loaded tool: phastOdds_for_intervals 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:46,798 Loading tools in section: Operate on Genomic Intervals galaxy.tools DEBUG 2008-03-14 18:57:46,896 Loaded tool: gops_intersect_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:46,977 Loaded tool: gops_subtract_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:47,030 Loaded tool: gops_merge_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:47,092 Loaded tool: gops_concat_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:47,132 Loaded tool: gops_basecoverage_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:47,200 Loaded tool: gops_coverage_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:47,266 Loaded tool: gops_complement_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:47,354 Loaded tool: gops_cluster_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:47,474 Loaded tool: gops_join_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:47,563 Loaded tool: get_flanks1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:47,629 Loaded tool: flanking_features1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:47,630 Loading tools in section: Statistics galaxy.tools DEBUG 2008-03-14 18:57:47,807 Loaded tool: Summary_Statistics1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:47,899 Loaded tool: Count1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:48,026 Loaded tool: cor2 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:48,027 Loading tools in section: Graph/Display Data galaxy.tools DEBUG 2008-03-14 18:57:48,140 Loaded tool: histogram_rpy 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:48,225 Loaded tool: scatterplot_rpy 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:48,299 Loaded tool: XY_Plot_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:48,361 Loaded tool: gmaj_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:48,402 Loaded tool: laj_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:48,440 Loaded tool: build_ucsc_custom_track_1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:48,441 Loading tools in section: Regional Variation galaxy.tools DEBUG 2008-03-14 18:57:48,533 Loaded tool: winSplitter 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:48,609 Loaded tool: featureCoverage1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:48,672 Loaded tool: qualityFilter 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:48,747 Loaded tool: cpgFilter 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:48,824 Loaded tool: getIndels_2way 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:48,867 Loaded tool: getIndels_3way 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:48,868 Loading tools in section: Evolution: HyPhy galaxy.tools DEBUG 2008-03-14 18:57:48,923 Loaded tool: hyphy_branch_lengths_wrapper1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:49,005 Loaded tool: hyphy_nj_tree_wrapper1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:49,049 Loaded tool: hyphy_dnds_wrapper1 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:49,050 Loading tools in section: FASTA manipulation galaxy.tools DEBUG 2008-03-14 18:57:49,093 Loaded tool: fasta_compute_length 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:49,117 Loaded tool: fasta_filter_by_length 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:49,117 Loading tools in section: Short Read Analysis galaxy.tools DEBUG 2008-03-14 18:57:49,213 Loaded tool: trim_reads 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:49,271 Loaded tool: blat_wrapper 1.0.0 galaxy.tools DEBUG 2008-03-14 18:57:49,352 Loaded tool: megablast_wrapper 2.0.0 galaxy.datatypes.registry DEBUG 2008-03-14 18:57:49,364 Loading converters from datatype_converters_conf.xml galaxy.datatypes.registry DEBUG 2008-03-14 18:57:49,388 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2008-03-14 18:57:49,406 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2008-03-14 18:57:49,423 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2008-03-14 18:57:49,453 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2008-03-14 18:57:49,471 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2008-03-14 18:57:49,488 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.jobs.schedulingpolicy.roundrobin INFO 2008-03-14 18:57:49,538 RoundRobin policy: initialized galaxy.jobs INFO 2008-03-14 18:57:49,538 job scheduler policy is galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin galaxy.jobs.runners.local INFO 2008-03-14 18:57:49,583 starting workers galaxy.jobs.runners.local DEBUG 2008-03-14 18:57:49,586 5 workers ready galaxy.jobs INFO 2008-03-14 18:57:49,587 job manager started galaxy.web.framework.base DEBUG 2008-03-14 18:57:49,756 Enabling 'admin' controller, class: Admin galaxy.web.framework.base DEBUG 2008-03-14 18:57:49,778 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2008-03-14 18:57:50,099 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2008-03-14 18:57:50,101 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2008-03-14 18:57:50,127 Enabling 'root' controller, class: Universe galaxy.web.framework.base DEBUG 2008-03-14 18:57:50,137 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2008-03-14 18:57:50,146 Enabling 'ucsc_proxy' controller, class: UCSCProxy galaxy.web.framework.base DEBUG 2008-03-14 18:57:50,151 Enabling 'user' controller, class: User galaxy.web.buildapp DEBUG 2008-03-14 18:57:50,191 Enabling 'httpexceptions' middleware galaxy.web.buildapp DEBUG 2008-03-14 18:57:50,208 Enabling 'recursive' middleware galaxy.web.buildapp DEBUG 2008-03-14 18:57:50,303 Enabling 'beaker session' middleware galaxy.web.buildapp DEBUG 2008-03-14 18:57:50,329 Enabling 'print debug' middleware galaxy.web.buildapp DEBUG 2008-03-14 18:57:51,253 Enabling 'eval exceptions' middleware galaxy.web.buildapp DEBUG 2008-03-14 18:57:51,258 Enabling 'trans logger' middleware galaxy.web.buildapp DEBUG 2008-03-14 18:57:51,259 Enabling 'config' middleware galaxy.web.buildapp DEBUG 2008-03-14 18:57:51,291 Enabling 'x-forwarded-host' middleware Starting server in PID 3152. serving on http://127.0.0.1:8080 galaxy.jobs INFO 2008-03-14 19:10:12,438 sending stop signal to worker thread galaxy.jobs INFO 2008-03-14 19:10:12,438 job queue stopped galaxy.jobs.runners.local INFO 2008-03-14 19:10:12,439 sending stop signal to worker threads galaxy.jobs.runners.local INFO 2008-03-14 19:10:12,440 local job runner stopped