GDAC_MergeDataFilesPipeline Execution Log 6:26 PM Fri Jul 13, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.KIRP.2012_07_07__00_00_03.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationid rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues5665805667725333592.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues6292572205603654409.tsv
GDAC_MergeDataFiles2 output filename KIRP
GDAC_MergeDataFiles2 row_column column
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data.data
Execution Times:
Submitted: 18:26:35 13-07-12
Completed:
Elapsed: 02 hrs 26 mins 44 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 128070] 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.KIRP.2012_07_07__00_00_03.samplestamp.txt
annotationid rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data
sdrffilename
datapathsfile dependentsValues5665805667725333592.tsv
Output Files:
 KIRP.merger.sdrf.txt
 dcc_archive.properties
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 18:26:36 13-07-12
Completed: 18:27:15 13-07-12
Elapsed: 00 hrs 00 mins 39 secs

step 2. GDAC_MergeDataFiles [id: 128071] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues6292572205603654409.tsv
output filename KIRP
row_column column
num_headers 1
filetype rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data.data
Output Files:
 KIRP.rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data.data.txt
 stdout.txt
Execution Times:
Submitted: 18:26:36 13-07-12
Completed: 20:53:17 13-07-12
Elapsed: 02 hrs 26 mins 41 secs