Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 1:37 PM Thu May 2, '13

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_preprocessor/COADREAD-TP/3140370/0.miRseq_preprocessor.Finished/COADREAD-TP.miRseq_RPKM_log2.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COADREAD-TP/3132640/1.GDAC_clinicalDataPicker.Finished/COADREAD-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 MIRNASEQ_EXPR
Execution Times:
Submitted: 13:37:23 02-05-13
Completed:
Elapsed: 00 hrs 02 mins 57 secs

step 1. ClinicalAnalysisAllGenes_new [id: 395000] 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/miRseq_preprocessor/COADREAD-TP/3140370/0.miRseq_preprocessor.Finished/COADREAD-TP.miRseq_RPKM_log2.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COADREAD-TP/3132640/1.GDAC_clinicalDataPicker.Finished/COADREAD-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:
 COADREAD-TP.miRseq_RPKM_log2.exprdata.gct
 COADREAD-TP.clin.merged.picked.clindata.txt
 COADREAD-TP.miRseq_RPKM_log2.analysis.results.RData
 COADREAD-TP.miRseq_RPKM_log2.clinical.results.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 13:37:23 02-05-13
Completed: 13:38:44 02-05-13
Elapsed: 00 hrs 01 mins 20 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 395002] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file COADREAD-TP.miRseq_RPKM_log2.clinical.results.txt
RData file COADREAD-TP.miRseq_RPKM_log2.analysis.results.RData
expression file COADREAD-TP.miRseq_RPKM_log2.exprdata.gct
clinical file COADREAD-TP.clin.merged.picked.clindata.txt
cutoff p 1
cutoff fdr 0.05
max table rows 10
nozzle ver Nozzle.R1
options MIRNASEQ_EXPR
report title
job description
Output Files:
 table1.txt
 supp.table1.txt
 table8.txt
 V3ex.png
 V6ex.png
 V2ex.pdf
 V4ex.png
 table14.txt
 V6ex.pdf
 table6.txt
 table10.txt
 table4.txt
 V5ex.png
 V2ex.png
 V4ex.pdf
 table12.txt
 V5ex.pdf
 V8ex.png
 V7ex.pdf
 V3ex.pdf
 V7ex.png
 V12ex.png
 table18.txt
 table23.txt
 V9ex.pdf
 table21.txt
 V8ex.pdf
 V12ex.pdf
 V9ex.png
 V11ex.pdf
 nozzle.RData
 V11ex.png
 table16.txt
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 13:37:23 02-05-13
Completed: 13:40:18 02-05-13
Elapsed: 00 hrs 02 mins 54 secs