writeReducedSegments Execution Log 3:49 PM Thu Jan 10, '13

Running as user: cgaadm_deadline

GetReducedSegments1 seglist file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/SKCM-TM/2172083/2.GDAC_MergeDataFiles.Finished/SKCM-TM.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 SKCM-TM
GetReducedSegments1 segmentid Sample
GetReducedSegments1 chromosome Chromosome
GetReducedSegments1 start Start
GetReducedSegments1 end End
GetReducedSegments1 segmean Segment_Mean
Execution Times:
Submitted: 15:49:11 10-01-13
Completed:
Elapsed: 00 hrs 05 mins 54 secs

step 1. GetReducedSegments [id: 286131] 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/SKCM-TM/2172083/2.GDAC_MergeDataFiles.Finished/SKCM-TM.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 SKCM-TM
segmentid Sample
chromosome Chromosome
start Start
end End
segmean Segment_Mean
Output Files:
 SKCM-TM.RS.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 15:49:11 10-01-13
Completed: 15:55:01 10-01-13
Elapsed: 00 hrs 05 mins 49 secs