GDAC_MergeDataFilesPipeline Execution Log 7:18 PM Mon Jul 2, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.SKCM.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 dependentsValues6764149955810747900.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues9155516927768067540.tsv
GDAC_MergeDataFiles2 output filename SKCM
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: 19:18:59 02-07-12
Completed:
Elapsed: 00 hrs 58 mins 44 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 119183] 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.SKCM.2012_06_23__00_00_19.samplestamp.txt
annotationid mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data
sdrffilename
datapathsfile dependentsValues6764149955810747900.tsv
Output Files:
 dcc_archive.properties
 SKCM.merger.sdrf.txt
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 19:19:00 02-07-12
Completed: 19:20:19 02-07-12
Elapsed: 00 hrs 01 mins 19 secs

step 2. GDAC_MergeDataFiles [id: 119184] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues9155516927768067540.tsv
output filename SKCM
row_column column
num_headers 1
filetype mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.data
Output Files:
 SKCM.mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.data.txt
 stdout.txt
Execution Times:
Submitted: 19:19:00 02-07-12
Completed: 20:17:39 02-07-12
Elapsed: 00 hrs 58 mins 39 secs