Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 5:22 PM Thu Jan 10, '13

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/THCA-TP/2284229/0.GDAC_MethylationPreprocess.Finished/THCA-TP.meth.for_correlation.filtered_data.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/THCA-TP/2174352/1.GDAC_clinicalDataPicker.Finished/THCA-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: 17:22:09 10-01-13
Completed:
Elapsed: 00 hrs 06 mins 52 secs

step 1. ClinicalAnalysisAllGenes_new [id: 286602] 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/THCA-TP/2284229/0.GDAC_MethylationPreprocess.Finished/THCA-TP.meth.for_correlation.filtered_data.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/THCA-TP/2174352/1.GDAC_clinicalDataPicker.Finished/THCA-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:
 THCA-TP.clin.merged.picked.clindata.txt
 THCA-TP.meth.for_correlation.filtered_data.exprdata.gct
 THCA-TP.meth.for_correlation.filtered_data.analysis.results.RData
 THCA-TP.meth.for_correlation.filtered_data.clinical.results.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 17:22:17 10-01-13
Completed: 17:28:28 10-01-13
Elapsed: 00 hrs 06 mins 11 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 286603] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file THCA-TP.meth.for_correlation.filtered_data.clinical.results.txt
RData file THCA-TP.meth.for_correlation.filtered_data.analysis.results.RData
expression file THCA-TP.meth.for_correlation.filtered_data.exprdata.gct
clinical file THCA-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
 V1ex.pdf
 V1ex.png
 table5.txt
 V3ex.png
 V2ex.pdf
 V4ex.png
 table7.txt
 V2ex.png
 table3.txt
 V3ex.pdf
 nozzle.html
 table11.txt
 V5ex.png
 V4ex.pdf
 nozzle.RData
 V5ex.pdf
 table9.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 17:22:17 10-01-13
Completed: 17:29:00 10-01-13
Elapsed: 00 hrs 06 mins 43 secs