GDAC_MergeDataFilesPipeline Execution Log 5:04 PM Mon Jul 2, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.KIRC.2012_06_23__00_00_19.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationid mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues5292970412647252283.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues8403077317144494242.tsv
GDAC_MergeDataFiles2 output filename KIRC
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: 17:04:21 02-07-12
Completed:
Elapsed: 00 hrs 00 mins 44 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 118608] 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.KIRC.2012_06_23__00_00_19.samplestamp.txt
annotationid mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data
sdrffilename
datapathsfile dependentsValues5292970412647252283.tsv
Output Files:
 dcc_archive.properties
 KIRC.merger.sdrf.txt
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 17:04:22 02-07-12
Completed: 17:04:46 02-07-12
Elapsed: 00 hrs 00 mins 24 secs

step 2. GDAC_MergeDataFiles [id: 118609] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues8403077317144494242.tsv
output filename KIRC
row_column column
num_headers 1
filetype mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.data
Output Files:
 KIRC.mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.data.txt
 stdout.txt
Execution Times:
Submitted: 17:04:22 02-07-12
Completed: 17:05:02 02-07-12
Elapsed: 00 hrs 00 mins 40 secs