GDAC_MergeDataFilesPipeline Execution Log 6:35 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__RSEM_genes__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues1630626944559195501.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues5668116246034407887.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__RSEM_genes__data.data
Execution Times:
Submitted: 06:35:32 25-06-12
Completed:
Elapsed: 00 hrs 00 mins 42 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 115680] 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__RSEM_genes__data
sdrffilename
datapathsfile dependentsValues1630626944559195501.tsv
Output Files:
 dcc_archive.properties
 SKCM.merger.sdrf.txt
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 06:35:33 25-06-12
Completed: 06:35:50 25-06-12
Elapsed: 00 hrs 00 mins 16 secs

step 2. GDAC_MergeDataFiles [id: 115681] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues5668116246034407887.tsv
output filename SKCM
row_column column
num_headers 1
filetype rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.data
Output Files:
 SKCM.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.data.txt
 stdout.txt
Execution Times:
Submitted: 06:35:33 25-06-12
Completed: 06:36:13 25-06-12
Elapsed: 00 hrs 00 mins 40 secs