GDAC_MergeDataFilesPipeline Execution Log 11:20 AM Sun May 20, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.UCEC.2012_05_15__00_00_15.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationid snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues8674361584245067696.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues3519698171736253871.tsv
GDAC_MergeDataFiles2 output filename UCEC
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: 11:20:55 20-05-12
Completed:
Elapsed: 00 hrs 00 mins 41 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 96680] 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.UCEC.2012_05_15__00_00_15.samplestamp.txt
annotationid snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg
sdrffilename
datapathsfile dependentsValues8674361584245067696.tsv
Output Files:
 UCEC.merger.sdrf.txt
 dcc_archive.properties
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 11:20:56 20-05-12
Completed: 11:21:11 20-05-12
Elapsed: 00 hrs 00 mins 15 secs

step 2. GDAC_MergeDataFiles [id: 96681] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues3519698171736253871.tsv
output filename UCEC
row_column row
num_headers 1
filetype snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg.seg
Output Files:
 UCEC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg.seg.txt
 .lsf.err
 stdout.txt
Execution Times:
Submitted: 11:20:56 20-05-12
Completed: 11:21:35 20-05-12
Elapsed: 00 hrs 00 mins 39 secs