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
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
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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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 threads8</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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Hi,
I still get these error when I submit jobs with drmaa to SGE. It seems that the error come from the drmaa new class AsynchronousJobState. When the job is sent to the drm queue, the python paste server is restarting "Running reloading file monitor". Just before that, I have an error in history 'An error occurred while getting updates from the server. Please contact a Galaxy administrator if the problem persists. Details ' (Details
user username remy quota_percent 1 total_disk_usage 275431793 nice_total_disk_usage 262.7 MB email remy.d1@gmail.com model_class User id f2db41e1fa331b3e source HDACollection() xhr readyState 0 responseText responseJSON null status 0 statusText error responseHeaders options data parse true emulateHTTP false emulateJSON false
As you can see the ajax request return a null json value.
After a few restarts, the job left the drm queue and the state became "error" because of it can not find the "jobid" although there is a good external job id (from SGE and in galaxy DB).
So I think this error come from the monitor_queue method which could not retrieve a correct "jobid" (I do not know if it is a job id for galaxy DB or an external job id...).
Hope this help.
Regards.
2013/10/17 Rémy Dernat remy.d1@gmail.com
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 -pethreads 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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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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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 -pethreads 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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-
Nate Coraor -
Rémy Dernat