Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 10:12 PM Mon Apr 8, '13

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/PRAD-TP/2901094/0.GDAC_MethylationPreprocess.Finished/PRAD-TP.meth.for_correlation.filtered_data.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/PRAD-TP/2844171/1.GDAC_clinicalDataPicker.Finished/PRAD-TP.clin.merged.picked.txt
ClinicalAnalysisAllGenesReport_nozzle2 cutoff p 1
ClinicalAnalysisAllGenesReport_nozzle2 cutoff fdr 0.05
ClinicalAnalysisAllGenesReport_nozzle2 max table rows 10
ClinicalAnalysisAllGenesReport_nozzle2 nozzle ver Nozzle.R1
ClinicalAnalysisAllGenesReport_nozzle2 options METHYLATION
Execution Times:
Submitted: 22:12:02 08-04-13
Completed:
Elapsed: 02 hrs 21 mins 41 secs

step 1. ClinicalAnalysisAllGenes_new [id: 373474] Associate individual gene expression profiles to clinical parameters by survival test, t-test, correlation test, or ANOVA test

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00333:14
data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/PRAD-TP/2901094/0.GDAC_MethylationPreprocess.Finished/PRAD-TP.meth.for_correlation.filtered_data.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/PRAD-TP/2844171/1.GDAC_clinicalDataPicker.Finished/PRAD-TP.clin.merged.picked.txt
genes filtered by list
genes filtered by variance ALL
samples filtered by list
features used ALL
output name
job description
Output Files:
 PRAD-TP.clin.merged.picked.clindata.txt
 PRAD-TP.meth.for_correlation.filtered_data.exprdata.gct
 .lsf.out
 PRAD-TP.meth.for_correlation.filtered_data.analysis.results.RData
 PRAD-TP.meth.for_correlation.filtered_data.clinical.results.txt
 stdout.txt
Execution Times:
Submitted: 22:12:02 08-04-13
Completed: 00:23:24 09-04-13
Elapsed: 02 hrs 11 mins 21 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 373475] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file PRAD-TP.meth.for_correlation.filtered_data.clinical.results.txt
RData file PRAD-TP.meth.for_correlation.filtered_data.analysis.results.RData
expression file PRAD-TP.meth.for_correlation.filtered_data.exprdata.gct
clinical file PRAD-TP.clin.merged.picked.clindata.txt
cutoff p 1
cutoff fdr 0.05
max table rows 10
nozzle ver Nozzle.R1
options METHYLATION
report title
job description
Output Files:
 supp.table1.txt
 table1.txt
 V2ex.pdf
 table4.txt
 V2ex.png
 nozzle.html
 V3ex.png
 table6.txt
 .lsf.out
 nozzle.RData
 V3ex.pdf
 stdout.txt
Execution Times:
Submitted: 22:12:02 08-04-13
Completed: 00:33:40 09-04-13
Elapsed: 02 hrs 21 mins 38 secs