GDAC_DataMergerPipeline Execution Log 12:43 PM Tue Mar 12, '13

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.OV.2013_03_09__11_03_12.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationids protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_DataMergerPipeline/OV/2712131/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_DataMerger2 output OV.protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.data.txt
GDAC_DataMerger2 dataPaths file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_DataMergerPipeline/OV/2712131/GDAC_DataMerger2.dataPaths.input.tsv
Execution Times:
Submitted: 12:43:22 12-03-13
Completed:
Elapsed: 01 hrs 20 mins 32 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 342331] 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.OV.2013_03_09__11_03_12.samplestamp.txt
annotationids protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data
sdrfName
doNotCreateManifest
datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_DataMergerPipeline/OV/2712131/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 dcc_archive.properties
 OV.merger.sdrf.txt
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 12:43:25 12-03-13
Completed: 13:24:13 12-03-13
Elapsed: 00 hrs 40 mins 48 secs

step 2. GDAC_DataMerger [id: 342332] Merge a list of files into a single file. Validate that all the files have the same columns and row names.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00481:4
output OV.protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.data.txt
dataPaths file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_DataMergerPipeline/OV/2712131/GDAC_DataMerger2.dataPaths.input.tsv
Output Files:
 OV.protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.data.txt
 .lsf.out
Execution Times:
Submitted: 12:43:25 12-03-13
Completed: 14:03:54 12-03-13
Elapsed: 01 hrs 20 mins 29 secs