writeReducedSegments Execution Log 12:08 PM Thu Jan 10, '13

Running as user: cgaadm_deadline

GetReducedSegments1 seglist file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COAD-TP/2169270/2.GDAC_MergeDataFiles.Finished/COAD-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
GetReducedSegments1 by gene
GetReducedSegments1 featurename Hybridization.REF
GetReducedSegments1 imput FALSE
GetReducedSegments1 XY FALSE
GetReducedSegments1 what median
GetReducedSegments1 outname COAD-TP
GetReducedSegments1 segmentid Sample
GetReducedSegments1 chromosome Chromosome
GetReducedSegments1 start Start
GetReducedSegments1 end End
GetReducedSegments1 segmean Segment_Mean
Execution Times:
Submitted: 12:08:47 10-01-13
Completed:
Elapsed: 00 hrs 01 mins 30 secs

step 1. GetReducedSegments [id: 284156] Taking a copy number level 3 data and then converting it to a gene by sample matrix

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00240:28
seglist file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COAD-TP/2169270/2.GDAC_MergeDataFiles.Finished/COAD-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
by gene
featurename Hybridization.REF
imput FALSE
XY FALSE
what median
outname COAD-TP
segmentid Sample
chromosome Chromosome
start Start
end End
segmean Segment_Mean
Output Files:
 COAD-TP.RS.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:08:54 10-01-13
Completed: 12:10:17 10-01-13
Elapsed: 00 hrs 01 mins 22 secs