GDAC_MergeDataFilesPipeline Execution Log 7:16 PM Mon Jul 2, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.SKCM.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 dependentsValues811613910522209829.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues3049310527646008555.tsv
GDAC_MergeDataFiles2 output filename SKCM
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: 19:16:40 02-07-12
Completed:
Elapsed: 01 hrs 09 mins 32 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 119144] 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.SKCM.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 dependentsValues811613910522209829.tsv
Output Files:
 dcc_archive.properties
 SKCM.merger.sdrf.txt
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 19:16:40 02-07-12
Completed: 19:21:08 02-07-12
Elapsed: 00 hrs 04 mins 27 secs

step 2. GDAC_MergeDataFiles [id: 119145] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues3049310527646008555.tsv
output filename SKCM
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:
 SKCM.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg.seg.txt
 stdout.txt
Execution Times:
Submitted: 19:16:40 02-07-12
Completed: 20:26:11 02-07-12
Elapsed: 01 hrs 09 mins 30 secs