Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 1:06 AM Tue Apr 9, '13

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/LUSC-TP/2904226/0.GDAC_MethylationPreprocess.Finished/LUSC-TP.meth.for_correlation.filtered_data.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUSC-TP/2843850/1.GDAC_clinicalDataPicker.Finished/LUSC-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: 01:06:19 09-04-13
Completed:
Elapsed: 00 hrs 53 mins 17 secs

step 1. ClinicalAnalysisAllGenes_new [id: 374338] 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/LUSC-TP/2904226/0.GDAC_MethylationPreprocess.Finished/LUSC-TP.meth.for_correlation.filtered_data.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUSC-TP/2843850/1.GDAC_clinicalDataPicker.Finished/LUSC-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:
 LUSC-TP.meth.for_correlation.filtered_data.exprdata.gct
 LUSC-TP.clin.merged.picked.clindata.txt
 LUSC-TP.meth.for_correlation.filtered_data.clinical.results.txt
 .lsf.out
 LUSC-TP.meth.for_correlation.filtered_data.analysis.results.RData
 stdout.txt
Execution Times:
Submitted: 01:06:19 09-04-13
Completed: 01:58:58 09-04-13
Elapsed: 00 hrs 52 mins 39 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 374339] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file LUSC-TP.meth.for_correlation.filtered_data.clinical.results.txt
RData file LUSC-TP.meth.for_correlation.filtered_data.analysis.results.RData
expression file LUSC-TP.meth.for_correlation.filtered_data.exprdata.gct
clinical file LUSC-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:
 table1.txt
 supp.table1.txt
 V3ex.png
 V1ex.pdf
 table6.txt
 V5ex.png
 V8ex.pdf
 V10ex.png
 V1ex.png
 table3.txt
 V10ex.pdf
 V5ex.pdf
 V8ex.png
 table9.txt
 table16.txt
 V3ex.pdf
 table13.txt
 V12ex.png
 table19.txt
 table22.txt
 V12ex.pdf
 V14ex.pdf
 nozzle.RData
 V14ex.png
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 01:06:19 09-04-13
Completed: 01:59:34 09-04-13
Elapsed: 00 hrs 53 mins 15 secs