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 rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues6056867540909312089.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues534546006867062037.tsv
GDAC_MergeDataFiles2 output filename KIRP
GDAC_MergeDataFiles2 row_column column
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.data
Execution Times:
Submitted: 18:26:50 13-07-12
Completed:
Elapsed: 02 hrs 27 mins 47 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 128082] 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 rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data
sdrffilename
datapathsfile dependentsValues6056867540909312089.tsv
Output Files:
 dcc_archive.properties
 KIRP.merger.sdrf.txt
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 18:26:50 13-07-12
Completed: 18:27:32 13-07-12
Elapsed: 00 hrs 00 mins 41 secs

step 2. GDAC_MergeDataFiles [id: 128083] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues534546006867062037.tsv
output filename KIRP
row_column column
num_headers 1
filetype rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.data
Output Files:
 KIRP.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.data.txt
 stdout.txt
Execution Times:
Submitted: 18:26:50 13-07-12
Completed: 20:54:34 13-07-12
Elapsed: 02 hrs 27 mins 44 secs