ParadigmPreprocessExpression1 broadFile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/856652/1.GDAC_MergeDataFiles.Finished/OV.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt |
ParadigmPreprocessExpression1 exonFile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/856530/1.GDAC_MergeDataFiles.Finished/OV.exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data.txt |
ParadigmPreprocessExpression1 uncFile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/856641/1.GDAC_MergeDataFiles.Finished/OV.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt |
ParadigmPreprocess2 evidence prefix | OV |
ParadigmPreprocess2 copynumber file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/OV/868533/1.GetReducedSegments.Finished/OV.RS.tsv |
ParadigmPrepare3 tolerance | 0.001 |
ParadigmPrepare3 nullBatches | 2 |
ParadigmPrepare3 minSampleFraction | 0.25 |
ParadigmPrepare3 minGeneFraction | 0.25 |
Paradigm4 tolerance | 0.001 |
Execution Times: | |
Submitted: | 11:47:03 25-02-12 |
Completed: | |
Elapsed: | 04 hrs 59 mins 47 secs |
step 1. ParadigmPreprocessExpression [id: 56312] Median center expression data before providing to PARADIGM.
urn:lsid:broadinstitute.org:cancer.genome.analysis:00420:9
broadFile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/856652/1.GDAC_MergeDataFiles.Finished/OV.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt |
exonFile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/856530/1.GDAC_MergeDataFiles.Finished/OV.exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data.txt |
uncFile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/856641/1.GDAC_MergeDataFiles.Finished/OV.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt |
broadNormalsFile | |
exonNormalsFile | |
uncNormalsFile |
Output Files: | |
RunR.sh | |
selectedExpressionFile.txt | |
normalizedExpression.txt | |
paradigmInputs.txt | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 11:47:03 25-02-12 |
Completed: | 11:48:57 25-02-12 |
Elapsed: | 00 hrs 01 mins 54 secs |
step 2. ParadigmPreprocess [id: 56313] Preprocessing module for broad data input to PARADIGM
urn:lsid:broadinstitute.org:cancer.genome.analysis:00366:9
evidence prefix | OV |
expression file | normalizedExpression.txt |
copynumber file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/OV/868533/1.GetReducedSegments.Finished/OV.RS.tsv |
paradigm inputs | paradigmInputs.txt |
Output Files: | |
Evidence_OV.zip | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 11:47:03 25-02-12 |
Completed: | 11:50:20 25-02-12 |
Elapsed: | 00 hrs 03 mins 17 secs |
step 3. ParadigmPrepare [id: 56314] Gathers data files and prepares job lists for the iterative-scatter-gather PARADIGM run.
urn:lsid:broadinstitute.org:cancer.genome.analysis:00401:12
evidence | Evidence_OV.zip |
tolerance | 0.001 |
nullBatches | 2 |
pathwayZip | |
minSampleFraction | 0.25 |
minGeneFraction | 0.25 |
Output Files: | |
config.txt | |
configEM.txt | |
params0.txt | |
jobs.sh | |
templateEM.sh | |
clusterFiles.tar | |
.lsf.out |
Execution Times: | |
Submitted: | 11:47:03 25-02-12 |
Completed: | 12:39:44 25-02-12 |
Elapsed: | 00 hrs 52 mins 40 secs |
step 4. Paradigm [id: 56315] PARADIGM (PAthway Recognition Algorithm using Data Integration on Genomic Models)
urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:19
tolerance | 0.001 |
clusterFilesTar | clusterFiles.tar |
configEM | configEM.txt |
templateEMScript | templateEM.sh |
config | config.txt |
jobsScript | jobs.sh |
paramsFile | params0.txt |
Output Files: | |
.lsf.out | |
stderr.txt | |
finalParams.txt | |
jobName.txt | |
merge_merged.tab | |
mergeFiles.zip | |
finished | |
iterator.out.txt | |
jobSubmissions.txt | |
stdout.txt |
Execution Times: | |
Submitted: | 11:47:03 25-02-12 |
Completed: | 16:42:59 25-02-12 |
Elapsed: | 04 hrs 55 mins 55 secs |
step 5. ParadigmReportPreprocess [id: 56316] PARADIGM Report Preprocess
urn:lsid:broadinstitute.org:cancer.genome.analysis:00365:4
mergeFilesZip | mergeFiles.zip |
Output Files: | |
fontList.cache | |
resultPngs.zip | |
resultSummary.tab | |
resultTables.zip | |
pngToPathwayMap.txt | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 11:47:03 25-02-12 |
Completed: | 16:45:17 25-02-12 |
Elapsed: | 04 hrs 58 mins 13 secs |
step 6. ParadigmReport [id: 56317] PARADIGM Report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00363:19
summaryTableFile | resultSummary.tab |
resultTablesZip | resultTables.zip |
resultPngsZip | resultPngs.zip |
pngToPathwayMapTxt | pngToPathwayMap.txt |
paradigmInputs | paradigmInputs.txt |
Execution Times: | |
Submitted: | 11:47:03 25-02-12 |
Completed: | 16:46:48 25-02-12 |
Elapsed: | 04 hrs 59 mins 44 secs |