GDAC_MergeDataFilesPipeline Execution Log 6:06 PM Fri Jul 13, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.CESC.2012_07_07__00_00_03.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationid snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues7734447314792484072.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues2005097862436171335.tsv
GDAC_MergeDataFiles2 output filename CESC
GDAC_MergeDataFiles2 row_column row
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg.seg
Execution Times:
Submitted: 18:06:03 13-07-12
Completed:
Elapsed: 01 hrs 39 mins 20 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 127783] This module parses a samplestamp based on an input annotation id and creates an SDRF file as output.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00467:9
samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.CESC.2012_07_07__00_00_03.samplestamp.txt
annotationid snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg
sdrffilename
datapathsfile dependentsValues7734447314792484072.tsv
Output Files:
 CESC.merger.sdrf.txt
 dcc_archive.properties
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 18:06:04 13-07-12
Completed: 18:06:34 13-07-12
Elapsed: 00 hrs 00 mins 30 secs

step 2. GDAC_MergeDataFiles [id: 127784] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues2005097862436171335.tsv
output filename CESC
row_column row
num_headers 1
filetype snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg.seg
Output Files:
 CESC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg.seg.txt
 stdout.txt
Execution Times:
Submitted: 18:06:04 13-07-12
Completed: 19:45:18 13-07-12
Elapsed: 01 hrs 39 mins 14 secs