Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 1:33 PM Thu May 2, '13

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/COAD-TP/3140316/0.GDAC_mRNA_Preprocess_Median.Finished/COAD-TP.medianexp.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COAD-TP/3132635/1.GDAC_clinicalDataPicker.Finished/COAD-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 MRNA_EXPR
Execution Times:
Submitted: 13:33:12 02-05-13
Completed:
Elapsed: 00 hrs 13 mins 47 secs

step 1. ClinicalAnalysisAllGenes_new [id: 394934] 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_mRNA_Preprocess_Median/COAD-TP/3140316/0.GDAC_mRNA_Preprocess_Median.Finished/COAD-TP.medianexp.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COAD-TP/3132635/1.GDAC_clinicalDataPicker.Finished/COAD-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:
 COAD-TP.clin.merged.picked.clindata.txt
 COAD-TP.medianexp.exprdata.gct
 COAD-TP.medianexp.clinical.results.txt
 COAD-TP.medianexp.analysis.results.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 13:33:13 02-05-13
Completed: 13:46:25 02-05-13
Elapsed: 00 hrs 13 mins 12 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 394935] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file COAD-TP.medianexp.clinical.results.txt
RData file COAD-TP.medianexp.analysis.results.RData
expression file COAD-TP.medianexp.exprdata.gct
clinical file COAD-TP.clin.merged.picked.clindata.txt
cutoff p 1
cutoff fdr 0.05
max table rows 10
nozzle ver Nozzle.R1
options MRNA_EXPR
report title
job description
Output Files:
 table1.txt
 supp.table1.txt
 table8.txt
 V3ex.png
 V2ex.pdf
 V4ex.png
 table6.txt
 table4.txt
 V2ex.png
 V4ex.pdf
 V3ex.pdf
 nozzle.html
 V9ex.pdf
 table15.txt
 V9ex.png
 table12.txt
 nozzle.RData
 V7ex.pdf
 V7ex.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 13:33:13 02-05-13
Completed: 13:46:58 02-05-13
Elapsed: 00 hrs 13 mins 45 secs