GDAC_geneListPathwayEnrichmentPipeline Execution Log 4:34 PM Mon Mar 4, '13

Running as user: cgaadm_deadline

GDAC_geneListPathwayEnrichment1 MSigDB_C2 file:/xchip/cga/reference/MSigDB/c2.cp.v3.0-2.symbols.gmt
GDAC_geneListPathwayEnrichment1 refseqGeneInfo file:/xchip/cga/reference/hg18_refseq_download.txt
GDAC_geneListPathwayEnrichment1 geneList_expr file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_ConsensusClusteringPipeline/KIRC-TP/2661813/3.GDAC_selectBestcluster.Finished/KIRC-TP.subclassmarkers.txt
GDAC_geneListPathwayEnrichment1 geneList_gisticAmp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/KIRC-TP/2661799/amp_genes.conf_99.txt
GDAC_geneListPathwayEnrichment1 geneList_gisticDel file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/KIRC-TP/2661799/del_genes.conf_99.txt
GDAC_geneListPathwayEnrichment1 geneList_exprCghCor file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/getCopyNumberExpCor/KIRC-TP/2662480/1.getCNExpCorrelation.Finished/KIRC-TP.CORS.tsv
GDAC_geneListPathwayEnrichment1 geneList_mutation file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/KIRC-TP/2625884/KIRC-TP.sig_genes.txt
GDAC_geneListPathwayEnrichment1 outPrefix pathwayEnrich
Execution Times:
Submitted: 16:34:06 04-03-13
Completed:
Elapsed: 00 hrs 02 mins 19 secs

step 1. GDAC_geneListPathwayEnrichment [id: 334361] Find pathways genes enriched in a gene list

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00268:29
MSigDB_C2 file:/xchip/cga/reference/MSigDB/c2.cp.v3.0-2.symbols.gmt
refseqGeneInfo file:/xchip/cga/reference/hg18_refseq_download.txt
geneList_expr file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_ConsensusClusteringPipeline/KIRC-TP/2661813/3.GDAC_selectBestcluster.Finished/KIRC-TP.subclassmarkers.txt
geneList_gisticAmp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/KIRC-TP/2661799/amp_genes.conf_99.txt
geneList_gisticDel file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/KIRC-TP/2661799/del_genes.conf_99.txt
geneList_exprCghCor file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/getCopyNumberExpCor/KIRC-TP/2662480/1.getCNExpCorrelation.Finished/KIRC-TP.CORS.tsv
geneList_mutation file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/KIRC-TP/2625884/KIRC-TP.sig_genes.txt
outPrefix pathwayEnrich
Output Files:
 genes_withMut.txt
 genes_withCNV_andHighExprCor.txt
 pathwayEnrich_cnvOrMut.txt
 .lsf.out
 pathwayEnrich_subclassMarker.txt
 stdout.txt
Execution Times:
Submitted: 16:34:06 04-03-13
Completed: 16:36:04 04-03-13
Elapsed: 00 hrs 01 mins 58 secs

step 2. GDAC_geneListPathwayEnrichmentReport [id: 334362] GeneListPathwayEnrichment Report

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00290:27
pwEnrich_cnvOrMut pathwayEnrich_cnvOrMut.txt
pwEnrich_subclassMarker pathwayEnrich_subclassMarker.txt
genes_withMut genes_withMut.txt
genes_withCNV genes_withCNV_andHighExprCor.txt
Output Files:
 nozzle.html
 pwEnrich_marker_subtype1.txt
 pwEnrich_marker_subtype2.txt
 pwEnrich_marker_subtype3.txt
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 16:34:06 04-03-13
Completed: 16:36:24 04-03-13
Elapsed: 00 hrs 02 mins 17 secs