Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 10:47 AM Thu Jun 6, '13

Running as user: cgaadm

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/OV-TP/3353209/0.GDAC_RPPA_preprocess.Finished/OV-TP.rppa.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/OV-TP/3351705/OV-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: 10:47:14 06-06-13
Completed:
Elapsed: 00 hrs 06 mins 30 secs

step 1. ClinicalAnalysisAllGenes_new [id: 416082] 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/OV-TP/3353209/0.GDAC_RPPA_preprocess.Finished/OV-TP.rppa.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/OV-TP/3351705/OV-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:
 OV-TP.clin.merged.picked.clindata.txt
 OV-TP.rppa.exprdata.gct
 OV-TP.rppa.analysis.results.RData
 OV-TP.rppa.clinical.results.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:47:37 06-06-13
Completed: 10:50:49 06-06-13
Elapsed: 00 hrs 03 mins 12 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 416083] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file OV-TP.rppa.clinical.results.txt
RData file OV-TP.rppa.analysis.results.RData
expression file OV-TP.rppa.exprdata.gct
clinical file OV-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
 nozzle.html
 V6ex.png
 V6ex.pdf
 table10.txt
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 10:47:37 06-06-13
Completed: 10:53:44 06-06-13
Elapsed: 00 hrs 06 mins 06 secs