Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 6:52 PM Mon Apr 8, '13

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/COADREAD-TP/2843420/0.GDAC_RPPA_preprocess.Finished/COADREAD-TP.rppa.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COADREAD-TP/2843108/1.GDAC_clinicalDataPicker.Finished/COADREAD-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 RPPA_EXPR
Execution Times:
Submitted: 18:52:25 08-04-13
Completed:
Elapsed: 00 hrs 23 mins 25 secs

step 1. ClinicalAnalysisAllGenes_new [id: 372947] 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:00333:13
data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/COADREAD-TP/2843420/0.GDAC_RPPA_preprocess.Finished/COADREAD-TP.rppa.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COADREAD-TP/2843108/1.GDAC_clinicalDataPicker.Finished/COADREAD-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:
 COADREAD-TP.clin.merged.picked.clindata.txt
 COADREAD-TP.rppa.exprdata.gct
 COADREAD-TP.rppa.analysis.results.RData
 COADREAD-TP.rppa.clinical.results.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 18:52:32 08-04-13
Completed: 19:04:05 08-04-13
Elapsed: 00 hrs 11 mins 32 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 372948] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file COADREAD-TP.rppa.clinical.results.txt
RData file COADREAD-TP.rppa.analysis.results.RData
expression file COADREAD-TP.rppa.exprdata.gct
clinical file COADREAD-TP.clin.merged.picked.clindata.txt
cutoff p 1
cutoff fdr 0.05
max table rows 10
nozzle ver Nozzle.R1
options RPPA_EXPR
report title
job description
Output Files:
 table1.txt
 supp.table1.txt
 table8.txt
 table5.txt
 V3ex.png
 V6ex.png
 V5ex.png
 V5ex.pdf
 V3ex.pdf
 V12ex.png
 table18.txt
 V9ex.pdf
 table15.txt
 V6ex.pdf
 table20.txt
 table10.txt
 V12ex.pdf
 V9ex.png
 V11ex.pdf
 table12.txt
 nozzle.RData
 V11ex.png
 V7ex.pdf
 V7ex.png
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 18:52:32 08-04-13
Completed: 19:15:48 08-04-13
Elapsed: 00 hrs 23 mins 15 secs