GDAC_MergeDataFilesPipeline Execution Log 6:33 AM Mon Jun 25, '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 rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues3730446961506581290.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues1633668205849888008.tsv
GDAC_MergeDataFiles2 output filename SKCM
GDAC_MergeDataFiles2 row_column column
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data.data
Execution Times:
Submitted: 06:33:07 25-06-12
Completed:
Elapsed: 00 hrs 00 mins 47 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 115653] 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 rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data
sdrffilename
datapathsfile dependentsValues3730446961506581290.tsv
Output Files:
 dcc_archive.properties
 SKCM.merger.sdrf.txt
 dcc_archive_manifest.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 06:33:08 25-06-12
Completed: 06:33:25 25-06-12
Elapsed: 00 hrs 00 mins 16 secs

step 2. GDAC_MergeDataFiles [id: 115654] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues1633668205849888008.tsv
output filename SKCM
row_column column
num_headers 1
filetype rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data.data
Output Files:
 SKCM.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data.data.txt
 stdout.txt
Execution Times:
Submitted: 06:33:08 25-06-12
Completed: 06:33:53 25-06-12
Elapsed: 00 hrs 00 mins 45 secs