ParadigmPreprocessExpression1 uncFile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/KIRP/1551399/2.GDAC_MergeDataFiles.Finished/KIRP.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt |
ParadigmPreprocess2 evidence prefix | KIRP |
ParadigmPrepare3 tolerance | 0.001 |
ParadigmPrepare3 nullBatches | 2 |
ParadigmPrepare3 minSampleFraction | 0.25 |
ParadigmPrepare3 minGeneFraction | 0.25 |
Paradigm4 tolerance | 0.001 |
Execution Times: | |
Submitted: | 17:46:22 01-08-12 |
Completed: | |
Elapsed: | 08 hrs 22 mins 00 secs |
step 1. ParadigmPreprocessExpression [id: 140527] Median center expression data before providing to PARADIGM.
urn:lsid:broadinstitute.org:cancer.genome.analysis:00420:9
broadFile | |
exonFile | |
uncFile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/KIRP/1551399/2.GDAC_MergeDataFiles.Finished/KIRP.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: | 17:46:23 01-08-12 |
Completed: | 17:47:30 01-08-12 |
Elapsed: | 00 hrs 01 mins 07 secs |
step 2. ParadigmPreprocess [id: 140528] Preprocessing module for broad data input to PARADIGM
urn:lsid:broadinstitute.org:cancer.genome.analysis:00366:9
evidence prefix | KIRP |
expression file | normalizedExpression.txt |
copynumber file | |
paradigm inputs | paradigmInputs.txt |
Output Files: | |
Evidence_KIRP.zip | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 17:46:23 01-08-12 |
Completed: | 17:50:14 01-08-12 |
Elapsed: | 00 hrs 03 mins 51 secs |
step 3. ParadigmPrepare [id: 140529] 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_KIRP.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: | 17:46:23 01-08-12 |
Completed: | 17:59:10 01-08-12 |
Elapsed: | 00 hrs 12 mins 47 secs |
step 4. Paradigm [id: 140530] PARADIGM (PAthway Recognition Algorithm using Data Integration on Genomic Models)
urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:21
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 | |
inferredPathwayLevels.tab | |
mergeFiles.zip | |
finished | |
jobSubmissions.txt | |
iterator.out.txt | |
stdout.txt |
Execution Times: | |
Submitted: | 17:46:23 01-08-12 |
Completed: | 02:03:30 02-08-12 |
Elapsed: | 08 hrs 17 mins 07 secs |
step 5. ParadigmReportPreprocess [id: 140531] 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: | 17:46:23 01-08-12 |
Completed: | 02:07:20 02-08-12 |
Elapsed: | 08 hrs 20 mins 57 secs |
step 6. ParadigmReport [id: 140532] 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: | 17:46:23 01-08-12 |
Completed: | 02:08:21 02-08-12 |
Elapsed: | 08 hrs 21 mins 58 secs |