Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 6:04 AM Wed Jun 12, '13

Running as user: cgaadm

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/KIRC-TP/3527718/KIRC-TP.meth.by_min_expr_corr.data.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KIRC-TP/3351227/KIRC-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: 06:04:48 12-06-13
Completed:
Elapsed: 01 hrs 56 mins 18 secs

step 1. ClinicalAnalysisAllGenes_new [id: 421107] 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/KIRC-TP/3527718/KIRC-TP.meth.by_min_expr_corr.data.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KIRC-TP/3351227/KIRC-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:
 KIRC-TP.clin.merged.picked.clindata.txt
 KIRC-TP.meth.by_min_expr_corr.data.exprdata.gct
 KIRC-TP.meth.by_min_expr_corr.data.clinical.results.txt
 KIRC-TP.meth.by_min_expr_corr.data.analysis.results.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 06:04:48 12-06-13
Completed: 08:00:32 12-06-13
Elapsed: 01 hrs 55 mins 44 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 421108] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file KIRC-TP.meth.by_min_expr_corr.data.clinical.results.txt
RData file KIRC-TP.meth.by_min_expr_corr.data.analysis.results.RData
expression file KIRC-TP.meth.by_min_expr_corr.data.exprdata.gct
clinical file KIRC-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
 table5.txt
 V3ex.png
 V2ex.pdf
 V1ex.pdf
 table10.txt
 V5ex.png
 table7.txt
 V2ex.png
 V1ex.png
 table3.txt
 V5ex.pdf
 V3ex.pdf
 nozzle.html
 V6ex.png
 table14.txt
 V6ex.pdf
 table12.txt
 nozzle.RData
 V7ex.pdf
 V7ex.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 06:04:48 12-06-13
Completed: 08:01:05 12-06-13
Elapsed: 01 hrs 56 mins 16 secs