Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 3:58 PM Mon Mar 4, '13

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/LUSC-TP/2662149/0.GDAC_MethylationPreprocess.Finished/LUSC-TP.meth.for_correlation.filtered_data.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUSC-TP/2587688/1.GDAC_clinicalDataPicker.Finished/LUSC-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: 15:58:57 04-03-13
Completed:
Elapsed: 00 hrs 17 mins 43 secs

step 1. ClinicalAnalysisAllGenes_new [id: 334152] 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/LUSC-TP/2662149/0.GDAC_MethylationPreprocess.Finished/LUSC-TP.meth.for_correlation.filtered_data.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUSC-TP/2587688/1.GDAC_clinicalDataPicker.Finished/LUSC-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:
 LUSC-TP.meth.for_correlation.filtered_data.exprdata.gct
 LUSC-TP.clin.merged.picked.clindata.txt
 LUSC-TP.meth.for_correlation.filtered_data.clinical.results.txt
 .lsf.out
 LUSC-TP.meth.for_correlation.filtered_data.analysis.results.RData
 stdout.txt
Execution Times:
Submitted: 15:58:57 04-03-13
Completed: 16:16:00 04-03-13
Elapsed: 00 hrs 17 mins 02 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 334153] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file LUSC-TP.meth.for_correlation.filtered_data.clinical.results.txt
RData file LUSC-TP.meth.for_correlation.filtered_data.analysis.results.RData
expression file LUSC-TP.meth.for_correlation.filtered_data.exprdata.gct
clinical file LUSC-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
 V3ex.png
 V1ex.pdf
 table6.txt
 V5ex.png
 V8ex.pdf
 V10ex.png
 V1ex.png
 table3.txt
 V10ex.pdf
 V5ex.pdf
 V8ex.png
 table9.txt
 table16.txt
 V3ex.pdf
 table13.txt
 V13ex.png
 table20.txt
 nozzle.RData
 V13ex.pdf
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 15:58:57 04-03-13
Completed: 16:16:39 04-03-13
Elapsed: 00 hrs 17 mins 41 secs