Hi Nate, Thanks a lot. It works now. I was too familiar with using the option '--reload' in my daemon ! -_-' For the "--reload" error, perhaps it was a timeout error for the state refresh ? On the qmaster SGE server there were some error logs: 10/23/2013 10:53:18|event_|cluster1|W|acknowledge timeout after 600 seconds for event client (drmaa:6700) on host "pipeline" 10/23/2013 10:53:18|event_|cluster1|E|removing event client (drmaa:6700) on host "pipeline" after acknowledge timeout from event client list I have seen some sleep on drmaa.py code... Regards, Rémy 2013/10/22 Nate Coraor <nate@bx.psu.edu>
Hi Rémy,
What's the behavior you see if you run the server without the --reload argument to run.sh?
--nate
On Oct 17, 2013, at 5:26 AM, Rémy Dernat wrote:
Hi Nate,
I got something like :
Server listening on ....:8080 job id does not exists dataset is in error state Restarting Restarting Restarting -- The job is moving to error state and then, I can get back the access to the Web interface:
Complete log (interesting part is at the end):
galaxy.tools DEBUG 2013-10-17 11:15:57,048 Loaded tool id: cshl_fastq_quality_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,048 Loaded tool id: cshl_fastx_artifacts_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,048 Loaded tool id: cshl_fastx_barcode_splitter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,048 Loaded tool id: cshl_fastx_clipper, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,048 Loaded tool id: cshl_fastx_collapser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,048 Loaded tool id: cshl_fastx_renamer, version: 0.0.11 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,048 Loaded tool id: cshl_fastx_reverse_complement, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,048 Loaded tool id: cshl_fastx_trimmer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,048 Loading section: NGS: Picard (beta) galaxy.tools DEBUG 2013-10-17 11:15:57,049 Loaded label: Conversion galaxy.tools DEBUG 2013-10-17 11:15:57,049 Loaded tool id: picard_FastqToSam, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,049 Loaded tool id: picard_SamToFastq, version: 1.56.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,049 Loaded label: QC/Metrics for sam/bam galaxy.tools DEBUG 2013-10-17 11:15:57,049 Loaded tool id: picard_BamIndexStats, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,049 Loaded tool id: PicardASMetrics, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,049 Loaded tool id: PicardGCBiasMetrics, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,049 Loaded tool id: rgEstLibComp, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,049 Loaded tool id: PicardInsertSize, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,049 Loaded tool id: PicardHsMetrics, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,049 Loaded label: bam/sam Cleaning galaxy.tools DEBUG 2013-10-17 11:15:57,049 Loaded tool id: picard_ARRG, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,049 Loaded tool id: picard_ReorderSam, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,050 Loaded tool id: picard_ReplaceSamHeader, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,050 Loaded tool id: rgPicFixMate, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,050 Loaded tool id: rgPicardMarkDups, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,050 Loading section: NGS: Assembly galaxy.tools DEBUG 2013-10-17 11:15:57,050 Loaded label: Velvet galaxy.tools DEBUG 2013-10-17 11:15:57,050 Loaded tool id: velvetg, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,050 Loaded tool id: velveth, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,050 Loaded tool id: velvetoptimiser_vlsci, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,050 Loaded tool id: abyss, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,050 Loaded tool id: abyss-pe, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,050 Loaded tool id: cap3, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,050 Loaded tool id: runAssembly, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,050 Loaded tool id: runAssembly_cDNA, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,051 Loaded tool id: mira_assembler, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,051 Loaded tool id: soap_denovo, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,051 Loaded tool id: minimus2, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,051 Loaded tool id: phrap, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,051 Loaded tool id: AMOScmp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,051 Loaded tool id: sspace, version: v2.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,051 Loaded tool id: ctg_stats, version: 1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,051 Loading section: NGS: Mapping galaxy.tools DEBUG 2013-10-17 11:15:57,051 Loaded tool id: lastz_wrapper_2, version: 1.2.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,051 Loaded tool id: lastz_paired_reads_wrapper, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,051 Loaded tool id: bowtie_wrapper, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,051 Loaded tool id: bowtie_color_wrapper, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,052 Loaded tool id: bowtie2, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,052 Loaded tool id: bwa_wrapper, version: 1.2.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,052 Loaded tool id: bwa_color_wrapper, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,052 Loaded tool id: bwaMem_wrapper, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,052 Loaded tool id: bfast_wrapper, version: 0.1.3 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,052 Loaded tool id: megablast_wrapper, version: 1.2.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,052 Loaded tool id: megablast_xml_parser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,052 Loaded tool id: PerM, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,052 Loaded tool id: srma_wrapper, version: 0.2.5 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,052 Loaded tool id: mosaik_wrapper, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,052 Loaded tool id: runMapping, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,052 Loaded tool id: runMapping_cDNA, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,052 Loaded tool id: mrFast_wrapper, version: 1.2.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,053 Loaded tool id: gmap, version: 2.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,053 Loaded tool id: gsnap, version: 2.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,053 Loaded tool id: gmap_build, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,053 Loaded tool id: gmap_snpindex, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,053 Loaded tool id: gmap_iit_store, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,053 Loaded tool id: mapsembler, version: 1.3.12 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,053 Loaded tool id: mapsembler_xgmml2fasta, version: 1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,053 Loaded tool id: mapsembler1.3.22, version: 1.3.22 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,053 Loaded tool id: TASR, version: 1.3 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,053 Loading section: NGS: Indel Analysis galaxy.tools DEBUG 2013-10-17 11:15:57,053 Loaded tool id: sam_indel_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,053 Loaded tool id: indel_sam2interval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,053 Loaded tool id: indel_table, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,054 Loaded tool id: indel_analysis, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,054 Loading section: NGS: RNA Analysis galaxy.tools DEBUG 2013-10-17 11:15:57,054 Loaded label: RNA-seq galaxy.tools DEBUG 2013-10-17 11:15:57,054 Loaded tool id: tophat, version: 1.5.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,054 Loaded tool id: tophat_color, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,054 Loaded tool id: cufflinks, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,054 Loaded tool id: cuffcompare, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,054 Loaded tool id: cuffdiff, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,054 Loaded tool id: cuffmerge, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,054 Loaded tool id: express, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,054 Loaded tool id: rgDGE, version: 0.01 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,054 Loaded label: De novo Assembly galaxy.tools DEBUG 2013-10-17 11:15:57,055 Loaded tool id: trinity_all, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,055 Loaded label: Filtering galaxy.tools DEBUG 2013-10-17 11:15:57,055 Loaded tool id: filter_combined_via_tracking, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,055 Loading section: NGS: SAM Tools galaxy.tools DEBUG 2013-10-17 11:15:57,055 Loaded tool id: sam_bw_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,055 Loaded tool id: Filter_sam_insert_size, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,055 Loaded tool id: sam2interval, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,055 Loaded tool id: sam_to_bam, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,055 Loaded tool id: bam_to_sam, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,055 Loaded tool id: bam_to_fastq_pe, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,055 Loaded tool id: bam_to_fastq_se, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,055 Loaded tool id: bam2alr, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,055 Loaded tool id: sam_merge2, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,056 Loaded tool id: Create_VCF_from_bcf, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,056 Loaded tool id: sam_pileup, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,056 Loaded tool id: pileup_parser, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,056 Loaded tool id: pileup_interval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,056 Loaded tool id: samtools_flagstat, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,056 Loaded tool id: samtools_rmdup, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,056 Loaded tool id: samtools_fixmate, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,056 Loaded tool id: Extract_consens, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,056 Loaded tool id: Extract_consens_list_regions, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,056 Loaded tool id: Extract_consens_from_bcf, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,056 Loaded tool id: Extract_lower_depth_positions, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,056 Loaded tool id: Get_coverage_list_regions, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,056 Loaded tool id: Filter_reads_overlapping_regions, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,057 Loaded tool id: Stats_reads_overlapping_regions, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,057 Loaded tool id: Filter_soft_clipped_reads, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,057 Loaded tool id: filter_repeats, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,057 Loaded tool id: filter_edit_distance, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,057 Loaded tool id: Mean_edit_distance, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,057 Loaded tool id: change_mapq, version: 0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,057 Loaded tool id: reads_ident_from_sam, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,057 Loaded tool id: sam_remove_trailing_tabs, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,057 Loading section: NGS: BedTools galaxy.tools DEBUG 2013-10-17 11:15:57,057 Loaded tool id: bedtools_bamtobed, version: 0.1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,057 Loaded tool id: bedtools_coveragebed_counts, version: 0.1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,057 Loaded tool id: bedtools_genomecoveragebed_bedgraph, version: 0.1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,058 Loaded tool id: bedtools_genomecoveragebed_histogram, version: 0.1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,058 Loaded tool id: bedtools_intersect2bed, version: 0.1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,058 Loaded tool id: bedtools_intersectbed_bam, version: 0.1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,058 Loaded tool id: bedtools_multiintersectbed, version: 0.1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,058 Loaded tool id: bedtools_mergebedgraph, version: 0.1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,058 Loading section: NGS: GATK Tools (beta) galaxy.tools DEBUG 2013-10-17 11:15:57,058 Loaded label: Alignment Utilities galaxy.tools DEBUG 2013-10-17 11:15:57,058 Loaded tool id: gatk_depth_of_coverage, version: 0.0.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,058 Loaded tool id: gatk_print_reads, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,058 Loaded label: Realignment galaxy.tools DEBUG 2013-10-17 11:15:57,058 Loaded tool id: gatk_realigner_target_creator, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,058 Loaded tool id: gatk_indel_realigner, version: 0.0.6 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,058 Loaded label: Base Recalibration galaxy.tools DEBUG 2013-10-17 11:15:57,059 Loaded tool id: gatk_count_covariates, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,059 Loaded tool id: gatk_table_recalibration, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,059 Loaded tool id: gatk_analyze_covariates, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,059 Loaded label: Genotyping galaxy.tools DEBUG 2013-10-17 11:15:57,059 Loaded tool id: gatk_unified_genotyper, version: 0.0.6 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,059 Loaded label: Annotation galaxy.tools DEBUG 2013-10-17 11:15:57,059 Loaded tool id: gatk_variant_annotator, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,059 Loaded label: Filtration galaxy.tools DEBUG 2013-10-17 11:15:57,059 Loaded tool id: gatk_variant_filtration, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,059 Loaded tool id: gatk_variant_select, version: 0.0.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,059 Loaded label: Variant Quality Score Recalibration galaxy.tools DEBUG 2013-10-17 11:15:57,059 Loaded tool id: gatk_variant_recalibrator, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,059 Loaded tool id: gatk_variant_apply_recalibration, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,059 Loaded label: Variant Utilities galaxy.tools DEBUG 2013-10-17 11:15:57,060 Loaded tool id: gatk_validate_variants, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,060 Loaded tool id: gatk_variant_eval, version: 0.0.8 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,060 Loaded tool id: gatk_variant_combine, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,060 Loaded label: Format Conversion Utilities galaxy.tools DEBUG 2013-10-17 11:15:57,060 Loaded tool id: gatk_intervals_to_bed, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,060 Loaded tool id: gatk_reducereads, version: 2.3.9 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,060 Loading section: NGS: Peak Calling galaxy.tools DEBUG 2013-10-17 11:15:57,060 Loaded tool id: peakcalling_macs, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,060 Loaded tool id: peakcalling_sicer, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,060 Loaded tool id: peakcalling_ccat, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,060 Loaded tool id: bed2genetrack, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,060 Loaded tool id: predict2genetrack, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,060 Loading section: NGS: Simulation galaxy.tools DEBUG 2013-10-17 11:15:57,061 Loaded tool id: ngs_simulation, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,061 Loaded tool id: dwgsim, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,061 Loaded tool id: dwgsimeval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,061 Loading section: SNP/WGA: Data; Filters galaxy.tools DEBUG 2013-10-17 11:15:57,061 Loaded label: Data: Import and upload galaxy.tools DEBUG 2013-10-17 11:15:57,061 Loaded tool id: upload1, version: 1.1.3 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,061 Loaded tool id: library_access1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,061 Loaded label: Data: Filter and Clean galaxy.tools DEBUG 2013-10-17 11:15:57,061 Loaded tool id: rgClean1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,061 Loaded tool id: rgPedSub1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,061 Loaded tool id: rgLDIndep1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,061 Loaded label: Simulate galaxy.tools DEBUG 2013-10-17 11:15:57,062 Loaded tool id: fakePhe1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,062 Loaded tool id: rgfakePed1, version: 0.02 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,062 Loading section: SNP/WGA: QC; LD; Plots galaxy.tools DEBUG 2013-10-17 11:15:57,062 Loaded label: QC; Eigenstrat galaxy.tools DEBUG 2013-10-17 11:15:57,062 Loaded tool id: rgQC1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,062 Loaded tool id: rgEigPCA1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,062 Loaded label: LD; Manhattan/QQ; GRR galaxy.tools DEBUG 2013-10-17 11:15:57,062 Loaded tool id: rgHaploView1, version: 0.3 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,062 Loaded tool id: rgManQQ1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,062 Loaded tool id: rgGRR1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,062 Loading section: SNP/WGA: Statistical Models galaxy.tools DEBUG 2013-10-17 11:15:57,062 Loaded tool id: rgCaCo1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,062 Loaded tool id: rgTDT1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,063 Loaded tool id: rgGLM1, version: 0.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,063 Loaded tool id: rgManQQ1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,063 Loading section: snpEff galaxy.tools DEBUG 2013-10-17 11:15:57,063 Loaded tool id: snpEff, version: 3.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,063 Loaded tool id: SNP_EFFect, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,063 Loaded tool id: snpEff33, version: 0.9 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,063 Loading section: VCF Tools galaxy.tools DEBUG 2013-10-17 11:15:57,063 Loaded tool id: vcf_intersect, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,063 Loaded tool id: vcf_annotate, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,063 Loaded tool id: vcf_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,063 Loaded tool id: vcf_extract, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,063 Loaded tool id: vcf_stats, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,064 Loading section: MBB_Tools galaxy.tools DEBUG 2013-10-17 11:15:57,064 Loaded label: NGS tools galaxy.tools DEBUG 2013-10-17 11:15:57,064 Loaded tool id: pPassBestHits, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,064 Loaded tool id: soapIndexer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,064 Loaded tool id: soap2sam, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,064 Loaded tool id: abyss, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,064 Loaded tool id: abyss-pe, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,064 Loaded tool id: cap3, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,064 Loaded tool id: assembly_metrics, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,064 Loaded tool id: samtools_idxstats, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,064 Loaded tool id: contigMaster, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,064 Loaded label: Sequence tools galaxy.tools DEBUG 2013-10-17 11:15:57,064 Loaded tool id: Gblocks, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,065 Loaded tool id: fastaToPhylip, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,065 Loaded tool id: muscle, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,065 Loaded tool id: fic_loc, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,065 Loaded tool id: liste_taxa, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,065 Loaded label: Usearch galaxy.tools DEBUG 2013-10-17 11:15:57,065 Loaded tool id: ublast, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,065 Loaded tool id: uc2fastax, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,065 Loaded tool id: uclust_composition, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,065 Loaded tool id: uclust, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,065 Loaded tool id: usearch_sort, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,065 Loaded label: Phylogeny tools galaxy.tools DEBUG 2013-10-17 11:15:57,065 Loaded tool id: SUNDAJOY, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,065 Loaded tool id: phyml_b, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,066 Loaded tool id: Garli, version: 2.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,066 Loaded label: Viewer tools galaxy.tools DEBUG 2013-10-17 11:15:57,066 Loaded tool id: tree_plotter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,066 Loaded label: admin tool galaxy.tools DEBUG 2013-10-17 11:15:57,066 Loaded tool id: display_py, version: 0.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,066 Loaded label: Population genetics galaxy.tools DEBUG 2013-10-17 11:15:57,066 Loaded tool id: msABC, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,066 Loading section: MUMmer tools galaxy.tools DEBUG 2013-10-17 11:15:57,066 Loaded tool id: mummer_tool, version: 0.4.alx into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,066 Loaded tool id: mummer_maxmatch, version: 0.9.alx into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,066 Loaded tool id: mummer_clustering, version: 0.9.alx into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,066 Loaded tool id: mummer_utilities_tool, version: 0.9.alx into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,066 Loaded tool id: mummerplot_tool, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,067 Loaded tool id: MUMmer2ACT_tool, version: 0.1.alx into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,067 Loaded tool id: nucmer_coords2TAB, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,067 Loading section: List construction galaxy.tools DEBUG 2013-10-17 11:15:57,067 Loaded tool id: File_selector, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,067 Loading section: Assembly galaxy.tools DEBUG 2013-10-17 11:15:57,067 Loaded tool id: abyss-multi, version: 1.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,067 Loaded tool id: cap3, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,067 Loaded tool id: pcap, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,067 Loading section: Mapping galaxy.tools DEBUG 2013-10-17 11:15:57,067 Loaded tool id: bwa-multi, version: 1.3 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,067 Loaded tool id: calculmeancov, version: 1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,067 Loaded tool id: sam2alr, version: 2.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,068 Loading section: ORF search and extraction galaxy.tools DEBUG 2013-10-17 11:15:57,068 Loaded tool id: getorf, version: 1.3 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,068 Loaded tool id: trinityorf, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,068 Loaded tool id: ORF_extractor, version: 2.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,068 Loading section: Genotype calling and CDS recovery galaxy.tools DEBUG 2013-10-17 11:15:57,068 Loaded tool id: reads2snp, version: 1.8 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,068 Loading section: Reciprocal Best Blast Hit galaxy.tools DEBUG 2013-10-17 11:15:57,068 Loaded tool id: addoutgroup, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,068 Loaded tool id: popphyl-blast, version: 1.6 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,068 Loaded tool id: reciprocal_best_hits, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,068 Loaded tool id: AlignTwoProfiles, version: 1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,068 Loading section: Population genetics galaxy.tools DEBUG 2013-10-17 11:15:57,068 Loaded tool id: dNdSpiNpiS, version: 3.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,069 Loaded tool id: Site_frequency_spectra, version: 2.5 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,069 Loading section: Other PopPhyl tools galaxy.tools DEBUG 2013-10-17 11:15:57,069 Loaded label: Custom PopPhyl Blast galaxy.tools DEBUG 2013-10-17 11:15:57,069 Loaded tool id: popphyl-blastp, version: 1.6 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,069 Loaded tool id: popphyl-blast, version: 1.6 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,069 Loaded tool id: popphyl-blastx, version: 1.6 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,069 Loaded label: Other programs galaxy.tools DEBUG 2013-10-17 11:15:57,069 Loaded tool id: ExtractIndividuals, version: 1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,069 Loaded tool id: fasta_cleaner, version: 1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,069 Loaded tool id: concatcontig, version: 1.5 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,069 Loaded tool id: PPStatistic, version: 1.2 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,069 Loaded tool id: contigfilter, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,069 Loaded tool id: contigMaster, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,070 Loaded tool id: assembly2database, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,070 Loaded tool id: regenerate_sam_indexes.xml, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,070 Loaded tool id: FakeOutgroupMaker, version: 1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,070 Loaded tool id: ReadsFilter, version: 1.3 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,070 Loaded tool id: Workflow_blocker, version: 1.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,070 Loading section: Popoolation Tools galaxy.tools DEBUG 2013-10-17 11:15:57,070 Loaded tool id: Popoolation_synchronized, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,070 Loaded tool id: Popoolation_snp-frequency-diff, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,070 Loaded tool id: Popoolation_Fst-values, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,070 Loaded tool id: Popool_meanFst-values, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,070 Loaded tool id: Popool_mantel_on_Fst, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,070 Loaded tool id: Popoolation_Fisher_Exact_Test, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,071 Loading section: Varscan Tools galaxy.tools DEBUG 2013-10-17 11:15:57,071 Loaded tool id: varscanSNP, version: 2.3.4 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,071 Loaded tool id: varscanINDEL, version: 2.3.4 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,071 Loaded tool id: varscanCNS, version: 2.3.4 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,071 Loading section: tests galaxy.tools DEBUG 2013-10-17 11:15:57,071 Loaded tool id: generateerror, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,071 Loaded tool id: Splign, version: 1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,071 Loaded tool id: consambig, version: 1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,071 Loaded tool id: consADT, version: 1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,071 Loaded tool id: calcFreqs, version: 1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,071 Loaded tool id: BatchSplign, version: 1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,071 Loaded tool id: BatchconsADT, version: 1.0 into tool panel. galaxy.tools DEBUG 2013-10-17 11:15:57,072 Loaded tool id: BatchcalcFreqs, version: 1.0 into tool panel. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,267 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,269 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,271 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,272 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,273 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,276 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,276 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,279 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,280 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,285 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,290 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,298 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,299 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,301 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,304 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,306 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,307 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,308 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,310 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,311 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,311 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,311 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,311 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,311 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,311 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,312 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,312 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,312 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,312 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,312 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,312 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,313 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,313 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,313 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,313 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,313 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,313 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,313 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,314 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,321 Loaded converter: CONVERTER_Bam_Bai_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,327 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,334 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,344 Loaded converter: CONVERTER_interval_to_coverage_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,356 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,364 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,371 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,378 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,386 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,393 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,400 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,407 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,414 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,421 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,433 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,440 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,447 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,455 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,462 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,469 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,476 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,483 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,490 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,497 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,505 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,512 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,522 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,530 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,537 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,544 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,552 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,559 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,566 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,573 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,580 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,588 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,595 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,606 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,613 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,621 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,628 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,635 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,642 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,650 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,657 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,664 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,671 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,678 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,686 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,697 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,704 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,705 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,712 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,720 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,727 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,734 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,741 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2013-10-17 11:15:57,747 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.imp_exp DEBUG 2013-10-17 11:15:57,754 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2013-10-17 11:15:57,755 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.genome_index DEBUG 2013-10-17 11:15:57,761 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.manager DEBUG 2013-10-17 11:15:57,763 Starting job handler galaxy.jobs.runners DEBUG 2013-10-17 11:15:57,799 Starting 4 DRMAARunner workers galaxy.jobs DEBUG 2013-10-17 11:15:57,800 Loaded job runner 'galaxy.jobs.runners.drmaa:DRMAAJobRunner' as 'drmaa' galaxy.jobs.runners DEBUG 2013-10-17 11:15:57,801 Starting 4 LocalRunner workers galaxy.jobs DEBUG 2013-10-17 11:15:57,802 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs.handler DEBUG 2013-10-17 11:15:57,802 Loaded job runners plugins: drmaa:local galaxy.jobs.handler INFO 2013-10-17 11:15:57,802 job handler stop queue started galaxy.jobs DEBUG 2013-10-17 11:15:57,812 (15637) Working directory for job is: /share/work-galaxy/cur-pipeline/015/15637 galaxy.jobs.handler DEBUG 2013-10-17 11:15:57,812 recovering job 15637 in drmaa runner galaxy.jobs.runners.drmaa DEBUG 2013-10-17 11:15:57,818 (15637/68390) is still in DRM queued state, adding to the DRM queue galaxy.jobs.handler INFO 2013-10-17 11:15:57,819 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2013-10-17 11:15:57,821 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2013-10-17 11:15:57,824 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.web.framework.base DEBUG 2013-10-17 11:15:57,855 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2013-10-17 11:15:57,856 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2013-10-17 11:15:57,856 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2013-10-17 11:15:57,865 Enabling 'data_admin' controller, class: DataAdmin galaxy.web.framework.base DEBUG 2013-10-17 11:15:57,867 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2013-10-17 11:15:57,867 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2013-10-17 11:15:57,869 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,136 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,136 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,136 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,138 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,140 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,155 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,156 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,156 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,157 Enabling 'mobile' controller, class: Mobile galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,157 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,158 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,158 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,159 Enabling 'search' controller, class: SearchController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,160 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,161 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,168 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,168 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,168 Enabling 'ucsc_proxy' controller, class: UCSCProxy galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,168 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,170 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,170 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,191 Enabling 'cloudlaunch' controller, class: CloudController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,192 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,211 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,213 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,214 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,215 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,215 Enabling 'permissions' API controller, class: PermissionsController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,216 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,216 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,216 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,216 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,219 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,219 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,220 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,220 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,221 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,221 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,222 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,222 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,222 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,223 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,238 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,238 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,238 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,244 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,244 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,244 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,249 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,249 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,249 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,250 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,251 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,251 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,251 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,251 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,252 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,257 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2013-10-17 11:15:58,257 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.webapps.galaxy.buildapp DEBUG 2013-10-17 11:15:58,257 app.config.api_folders: False galaxy.webapps.galaxy.buildapp DEBUG 2013-10-17 11:15:58,541 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-10-17 11:15:58,542 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-10-17 11:15:58,545 Enabling 'error' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-10-17 11:15:58,545 Enabling 'trans logger' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-10-17 11:15:58,545 Enabling 'x-forwarded-host' middleware galaxy.webapps.galaxy.buildapp DEBUG 2013-10-17 11:15:58,545 Enabling 'Request ID' middleware Starting server in PID 19972. serving on http://162.38.181.30:8080 galaxy.jobs.runners.drmaa INFO 2013-10-17 11:15:58,853 (15637/68390) job left DRM queue with following message: code 18: The job specified by the 'jobid' does not exist. galaxy.jobs DEBUG 2013-10-17 11:15:59,170 finish(): Moved /share/work-galaxy/cur-pipeline/015/15637/galaxy_dataset_24636.dat to /media/big1T/home/galaxy/galaxy-central.test/database/files/024/dataset_24636.dat galaxy.jobs DEBUG 2013-10-17 11:15:59,193 setting dataset state to ERROR galaxy.jobs DEBUG 2013-10-17 11:15:59,465 job 15637 ended galaxy.datatypes.metadata DEBUG 2013-10-17 11:15:59,465 Cleaning up external metadata files Starting subprocess with file monitor -------------------- Restarting -------------------- -------------------- Restarting -------------------- -------------------- Restarting -------------------- ^C caught in monitor process
2013/10/16 Nate Coraor <nate@bx.psu.edu> Hi Rémy,
Do you have some process that restarts Galaxy if it dies? It should not do this itself. Is there anything being logged right before the server restarts that indicates the problem?
--nate
On Oct 16, 2013, at 4:10 AM, Rémy Dernat wrote:
Hi,
About the last updates on DRMAA: now the job is submitted, it seems to work. However, galaxy is "restarting" constantly... So it became very unusable. I hope you will fix this.
Regards.
2013/10/14 Rémy Dernat <remy.d1@gmail.com> Hi,
After a big upgrade, I have an error when I submit job to SGE through drmaa
Here is the error I get: galaxy.jobs.runners.drmaa WARNING 2013-10-14 11:26:08,075 (15615/68154) job check resulted in InvalidJobException: code 18: The job specified by the 'jobid' does not exist.
The job is launch to sge because I see it with "qstat" SGE command. On the galaxy Web interface, the job is stuck in yellow (running state), although it is finished.
When I submit job by using "local" destination it works fine.
Here is my job_conf.xml file :
<?xml version="1.0"?> <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> <job_conf> <plugins> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="sge_default"> <!--destination id="big_jobs" runner="drmaa"> <param id="nativeSpecification">-P bignodes -R y -pe threads 8</param> </destination--> <destination id="sge_default" runner="drmaa"> <param id="nativeSpecification">-q all.q -V</param> </destination> <destination id="local" runner="local"/> </destinations> </job_conf>
Any help would be usefull.
Regards, Rem
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