GDAC_MergeDataFilesPipeline Execution Log 12:24 PM Sun May 20, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.PRAD.2012_05_15__00_00_15.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationid mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues885834808462492597.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues103131029970095036.tsv
GDAC_MergeDataFiles2 output filename PRAD
GDAC_MergeDataFiles2 row_column column
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.data
Execution Times:
Submitted: 12:24:23 20-05-12
Completed:
Elapsed: 00 hrs 00 mins 32 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 96920] 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.PRAD.2012_05_15__00_00_15.samplestamp.txt
annotationid mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data
sdrffilename
datapathsfile dependentsValues885834808462492597.tsv
Output Files:
 PRAD.merger.sdrf.txt
 dcc_archive.properties
 dcc_archive_manifest.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:24:23 20-05-12
Completed: 12:24:42 20-05-12
Elapsed: 00 hrs 00 mins 18 secs

step 2. GDAC_MergeDataFiles [id: 96921] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues103131029970095036.tsv
output filename PRAD
row_column column
num_headers 1
filetype mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.data
Output Files:
 PRAD.mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.data.txt
 stdout.txt
Execution Times:
Submitted: 12:24:23 20-05-12
Completed: 12:24:52 20-05-12
Elapsed: 00 hrs 00 mins 29 secs