Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 10:14 PM Mon Apr 8, '13

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRP-TP/2900732/0.GDAC_mRNA_Preprocess_Median.Finished/KIRP-TP.medianexp.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRP-TP/2843150/1.GDAC_clinicalDataPicker.Finished/KIRP-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: 22:14:21 08-04-13
Completed:
Elapsed: 02 hrs 19 mins 40 secs

step 1. ClinicalAnalysisAllGenes_new [id: 373503] 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/KIRP-TP/2900732/0.GDAC_mRNA_Preprocess_Median.Finished/KIRP-TP.medianexp.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRP-TP/2843150/1.GDAC_clinicalDataPicker.Finished/KIRP-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:
 KIRP-TP.clin.merged.picked.clindata.txt
 KIRP-TP.medianexp.exprdata.gct
 KIRP-TP.medianexp.analysis.results.RData
 KIRP-TP.medianexp.clinical.results.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 22:14:21 08-04-13
Completed: 00:23:20 09-04-13
Elapsed: 02 hrs 08 mins 59 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 373504] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file KIRP-TP.medianexp.clinical.results.txt
RData file KIRP-TP.medianexp.analysis.results.RData
expression file KIRP-TP.medianexp.exprdata.gct
clinical file KIRP-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
 V2ex.pdf
 table4.txt
 V2ex.png
 nozzle.html
 V3ex.png
 table6.txt
 .lsf.out
 nozzle.RData
 V3ex.pdf
 stdout.txt
Execution Times:
Submitted: 22:14:21 08-04-13
Completed: 00:34:00 09-04-13
Elapsed: 02 hrs 19 mins 38 secs