GDAC_MergeDataFilesPipeline Execution Log 7:06 PM Mon Dec 10, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.LUAD.2012_12_06__00_00_32.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/LUAD-NORMALS/2124684/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LUAD-NORMALS/2124684/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
GDAC_MergeDataFiles2 output filename LUAD-NORMALS
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: 19:06:41 10-12-12
Completed:
Elapsed: 02 hrs 06 mins 34 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 247880] 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.LUAD.2012_12_06__00_00_32.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/LUAD-NORMALS/2124684/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 LUAD.merger.sdrf.txt
 dcc_archive.properties
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 19:07:10 10-12-12
Completed: 20:04:18 10-12-12
Elapsed: 00 hrs 57 mins 07 secs

step 2. GDAC_MergeDataFiles [id: 247881] 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/LUAD-NORMALS/2124684/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename LUAD-NORMALS
row_column column
num_headers 1
filetype rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data
Output Files:
 LUAD-NORMALS.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:07:10 10-12-12
Completed: 21:13:14 10-12-12
Elapsed: 02 hrs 06 mins 03 secs