GDAC_MergeDataFilesPipeline Execution Log 7:06 PM Mon Jul 2, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.OV.2012_06_23__00_00_19.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 dependentsValues5623800379004072414.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues1257717317871329522.tsv
GDAC_MergeDataFiles2 output filename OV
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: 19:06:37 02-07-12
Completed:
Elapsed: 00 hrs 02 mins 40 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 118970] 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.OV.2012_06_23__00_00_19.samplestamp.txt
annotationid snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg
sdrffilename
datapathsfile dependentsValues5623800379004072414.tsv
Output Files:
 dcc_archive.properties
 OV.merger.sdrf.txt
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 19:06:37 02-07-12
Completed: 19:07:15 02-07-12
Elapsed: 00 hrs 00 mins 37 secs

step 2. GDAC_MergeDataFiles [id: 118971] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues1257717317871329522.tsv
output filename OV
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:
 OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg.seg.txt
 stdout.txt
Execution Times:
Submitted: 19:06:37 02-07-12
Completed: 19:09:12 02-07-12
Elapsed: 00 hrs 02 mins 34 secs