Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 2:03 PM Thu May 2, '13

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_preprocessor/LUSC-TP/3140846/0.miRseq_preprocessor.Finished/LUSC-TP.miRseq_RPKM_log2.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUSC-TP/3132702/1.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 MIRNASEQ_EXPR
Execution Times:
Submitted: 14:03:36 02-05-13
Completed:
Elapsed: 00 hrs 02 mins 16 secs

step 1. ClinicalAnalysisAllGenes_new [id: 395679] 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/LUSC-TP/3140846/0.miRseq_preprocessor.Finished/LUSC-TP.miRseq_RPKM_log2.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUSC-TP/3132702/1.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.clin.merged.picked.clindata.txt
 LUSC-TP.miRseq_RPKM_log2.exprdata.gct
 LUSC-TP.miRseq_RPKM_log2.clinical.results.txt
 LUSC-TP.miRseq_RPKM_log2.analysis.results.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 14:03:37 02-05-13
Completed: 14:05:13 02-05-13
Elapsed: 00 hrs 01 mins 36 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 395680] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file LUSC-TP.miRseq_RPKM_log2.clinical.results.txt
RData file LUSC-TP.miRseq_RPKM_log2.analysis.results.RData
expression file LUSC-TP.miRseq_RPKM_log2.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 MIRNASEQ_EXPR
report title
job description
Output Files:
 table1.txt
 supp.table1.txt
 table8.txt
 V4ex.png
 table6.txt
 V5ex.png
 V8ex.pdf
 V4ex.pdf
 table12.txt
 V5ex.pdf
 V8ex.png
 nozzle.html
 table18.txt
 V13ex.png
 table20.txt
 V14ex.pdf
 nozzle.RData
 V13ex.pdf
 V14ex.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 14:03:37 02-05-13
Completed: 14:05:48 02-05-13
Elapsed: 00 hrs 02 mins 11 secs