GDAC_MergeDataFilesPipeline Execution Log 11:53 AM Mon Apr 8, '13

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.SKCM.2013_04_06__17_54_05.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationids rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/SKCM/2897820/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/SKCM/2897820/GDAC_MergeDataFiles2.inputfilelist.filename.input.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_normalized__data.data
Execution Times:
Submitted: 11:53:50 08-04-13
Completed:
Elapsed: 12 hrs 26 mins 09 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 371546] 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:00467:12
samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.SKCM.2013_04_06__17_54_05.samplestamp.txt
annotationids rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data
sdrfName
doNotCreateManifest
datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/SKCM/2897820/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 dcc_archive.properties
 SKCM.merger.sdrf.txt
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 11:55:44 08-04-13
Completed: 12:37:56 08-04-13
Elapsed: 00 hrs 42 mins 11 secs

step 2. GDAC_MergeDataFiles [id: 371547] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/SKCM/2897820/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename SKCM
row_column column
num_headers 1
filetype rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data
Output Files:
 SKCM.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 11:55:44 08-04-13
Completed: 00:19:58 09-04-13
Elapsed: 12 hrs 24 mins 13 secs