GDAC_MergeDataFilesPipeline Execution Log 12:24 PM Sun May 20, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.PRAD.2012_05_15__00_00_15.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationid snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues7400383757460620162.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues474922475311653316.tsv
GDAC_MergeDataFiles2 output filename PRAD
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_minus_germline_cnv_hg18__seg.seg
Execution Times:
Submitted: 12:24:57 20-05-12
Completed:
Elapsed: 00 hrs 00 mins 30 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 96935] 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.PRAD.2012_05_15__00_00_15.samplestamp.txt
annotationid snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg
sdrffilename
datapathsfile dependentsValues7400383757460620162.tsv
Output Files:
 dcc_archive.properties
 PRAD.merger.sdrf.txt
 dcc_archive_manifest.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:24:57 20-05-12
Completed: 12:25:13 20-05-12
Elapsed: 00 hrs 00 mins 15 secs

step 2. GDAC_MergeDataFiles [id: 96936] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues474922475311653316.tsv
output filename PRAD
row_column row
num_headers 1
filetype snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg.seg
Output Files:
 PRAD.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg.seg.txt
 stdout.txt
Execution Times:
Submitted: 12:24:58 20-05-12
Completed: 12:25:26 20-05-12
Elapsed: 00 hrs 00 mins 28 secs