GDAC_DataMergerPipeline Execution Log 6:35 PM Fri Dec 21, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.BLCA.2012_12_21__11_18_10.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/BLCA/2168845/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_DataMerger2 output BLCA.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/BLCA/2168845/GDAC_DataMerger2.dataPaths.input.tsv
Execution Times:
Submitted: 18:35:48 21-12-12
Completed:
Elapsed: 00 hrs 02 mins 14 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 267531] 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.BLCA.2012_12_21__11_18_10.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/BLCA/2168845/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 dcc_archive.properties
 BLCA.merger.sdrf.txt
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 18:35:54 21-12-12
Completed: 18:36:36 21-12-12
Elapsed: 00 hrs 00 mins 42 secs

step 2. GDAC_DataMerger [id: 267532] 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 BLCA.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/BLCA/2168845/GDAC_DataMerger2.dataPaths.input.tsv
Output Files:
 BLCA.protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.data.txt
 .lsf.out
Execution Times:
Submitted: 18:35:54 21-12-12
Completed: 18:38:01 21-12-12
Elapsed: 00 hrs 02 mins 07 secs