Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 3:29 PM Mon Mar 4, '13

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/LUSC-TP/2587685/0.GDAC_RPPA_preprocess.Finished/LUSC-TP.rppa.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUSC-TP/2587688/1.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 RPPA_EXPR
Execution Times:
Submitted: 15:29:32 04-03-13
Completed:
Elapsed: 00 hrs 01 mins 07 secs

step 1. ClinicalAnalysisAllGenes_new [id: 333749] 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/LUSC-TP/2587685/0.GDAC_RPPA_preprocess.Finished/LUSC-TP.rppa.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUSC-TP/2587688/1.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.rppa.exprdata.gct
 LUSC-TP.clin.merged.picked.clindata.txt
 LUSC-TP.rppa.analysis.results.RData
 LUSC-TP.rppa.clinical.results.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 15:29:33 04-03-13
Completed: 15:30:09 04-03-13
Elapsed: 00 hrs 00 mins 36 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 333751] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file LUSC-TP.rppa.clinical.results.txt
RData file LUSC-TP.rppa.analysis.results.RData
expression file LUSC-TP.rppa.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 RPPA_EXPR
report title
job description
Output Files:
 table1.txt
 supp.table1.txt
 table5.txt
 V2ex.pdf
 V1ex.pdf
 V2ex.png
 V1ex.png
 table3.txt
 table11.txt
 V9ex.pdf
 V6ex.png
 V6ex.pdf
 table22.txt
 V5ex.png
 V14ex.pdf
 V9ex.png
 nozzle.RData
 V5ex.pdf
 table9.txt
 table16.txt
 V14ex.png
 V7ex.pdf
 V7ex.png
 table13.txt
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 15:29:33 04-03-13
Completed: 15:30:39 04-03-13
Elapsed: 00 hrs 01 mins 05 secs