Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 5:57 PM Wed Aug 1, '12

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRP/1590232/0.GDAC_mRNA_Preprocess_Median.Finished/KIRP.medianexp.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRP/1552281/1.GDAC_clinicalDataPicker.Finished/KIRP.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: 17:57:53 01-08-12
Completed:
Elapsed: 00 hrs 13 mins 46 secs

step 1. ClinicalAnalysisAllGenes_new [id: 140695] 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:00333:11
data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRP/1590232/0.GDAC_mRNA_Preprocess_Median.Finished/KIRP.medianexp.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRP/1552281/1.GDAC_clinicalDataPicker.Finished/KIRP.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.clin.merged.picked.clindata.txt
 KIRP.medianexp.exprdata.gct
 KIRP.medianexp.analysis.results.RData
 KIRP.medianexp.clinical.results.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 17:57:53 01-08-12
Completed: 18:10:39 01-08-12
Elapsed: 00 hrs 12 mins 45 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 140696] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:20
all result file KIRP.medianexp.clinical.results.txt
RData file KIRP.medianexp.analysis.results.RData
expression file KIRP.medianexp.exprdata.gct
clinical file KIRP.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.png
 nozzle.html
 V3ex.png
 V2ex.pdf
 table6.txt
 table4.txt
 .lsf.out
 nozzle.RData
 V3ex.pdf
 stdout.txt
Execution Times:
Submitted: 17:57:53 01-08-12
Completed: 18:11:38 01-08-12
Elapsed: 00 hrs 13 mins 45 secs