Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 10:51 AM Thu Jun 6, '13

Running as user: cgaadm

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_preprocessor/OV-TP/3471943/0.miRseq_preprocessor.Finished/OV-TP.miRseq_RPKM_log2.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/OV-TP/3351705/OV-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: 10:51:02 06-06-13
Completed:
Elapsed: 00 hrs 06 mins 33 secs

step 1. ClinicalAnalysisAllGenes_new [id: 416637] 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/OV-TP/3471943/0.miRseq_preprocessor.Finished/OV-TP.miRseq_RPKM_log2.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/OV-TP/3351705/OV-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:
 OV-TP.miRseq_RPKM_log2.exprdata.gct
 OV-TP.clin.merged.picked.clindata.txt
 OV-TP.miRseq_RPKM_log2.analysis.results.RData
 OV-TP.miRseq_RPKM_log2.clinical.results.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:51:06 06-06-13
Completed: 10:54:48 06-06-13
Elapsed: 00 hrs 03 mins 42 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 416638] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file OV-TP.miRseq_RPKM_log2.clinical.results.txt
RData file OV-TP.miRseq_RPKM_log2.analysis.results.RData
expression file OV-TP.miRseq_RPKM_log2.exprdata.gct
clinical file OV-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
 V6ex.png
 V2ex.pdf
 V6ex.pdf
 table10.txt
 table4.txt
 V5ex.png
 V2ex.png
 nozzle.RData
 V5ex.pdf
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:51:06 06-06-13
Completed: 10:57:34 06-06-13
Elapsed: 00 hrs 06 mins 28 secs