Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 1:09 PM Mon Mar 4, '13

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/BLCA-TP/2660647/0.GDAC_MethylationPreprocess.Finished/BLCA-TP.meth.for_correlation.filtered_data.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BLCA-TP/2585709/1.GDAC_clinicalDataPicker.Finished/BLCA-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: 13:09:25 04-03-13
Completed:
Elapsed: 00 hrs 15 mins 38 secs

step 1. ClinicalAnalysisAllGenes_new [id: 332521] 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/BLCA-TP/2660647/0.GDAC_MethylationPreprocess.Finished/BLCA-TP.meth.for_correlation.filtered_data.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BLCA-TP/2585709/1.GDAC_clinicalDataPicker.Finished/BLCA-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:
 BLCA-TP.meth.for_correlation.filtered_data.exprdata.gct
 BLCA-TP.clin.merged.picked.clindata.txt
 BLCA-TP.meth.for_correlation.filtered_data.clinical.results.txt
 BLCA-TP.meth.for_correlation.filtered_data.analysis.results.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 13:09:26 04-03-13
Completed: 13:24:48 04-03-13
Elapsed: 00 hrs 15 mins 22 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 332522] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file BLCA-TP.meth.for_correlation.filtered_data.clinical.results.txt
RData file BLCA-TP.meth.for_correlation.filtered_data.analysis.results.RData
expression file BLCA-TP.meth.for_correlation.filtered_data.exprdata.gct
clinical file BLCA-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:
 table11.txt
 V9ex.pdf
 table5.txt
 V3ex.png
 table15.txt
 V8ex.pdf
 table1.txt
 V10ex.png
 V9ex.png
 supp.table1.txt
 V10ex.pdf
 V8ex.png
 V3ex.pdf
 table13.txt
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 13:09:26 04-03-13
Completed: 13:25:03 04-03-13
Elapsed: 00 hrs 15 mins 37 secs