Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 6:52 PM Mon Apr 8, '13

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/HNSC-TP/2843680/HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/HNSC-TP/2843134/1.GDAC_clinicalDataPicker.Finished/HNSC-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 MRNASEQ_EXPR
Execution Times:
Submitted: 18:52:39 08-04-13
Completed:
Elapsed: 00 hrs 30 mins 06 secs

step 1. ClinicalAnalysisAllGenes_new [id: 373015] 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/mRNAseq_preprocessor/HNSC-TP/2843680/HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/HNSC-TP/2843134/1.GDAC_clinicalDataPicker.Finished/HNSC-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:
 HNSC-TP.clin.merged.picked.clindata.txt
 HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.exprdata.gct
 HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.clinical.results.txt
 .lsf.out
 HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.analysis.results.RData
 stdout.txt
Execution Times:
Submitted: 18:52:52 08-04-13
Completed: 19:19:48 08-04-13
Elapsed: 00 hrs 26 mins 56 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 373016] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.clinical.results.txt
RData file HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.analysis.results.RData
expression file HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.exprdata.gct
clinical file HNSC-TP.clin.merged.picked.clindata.txt
cutoff p 1
cutoff fdr 0.05
max table rows 10
nozzle ver Nozzle.R1
options MRNASEQ_EXPR
report title
job description
Output Files:
 supp.table1.txt
 table19.txt
 V9ex.pdf
 table8.txt
 V3ex.png
 V4ex.png
 table14.txt
 V1ex.pdf
 table6.txt
 table10.txt
 V5ex.png
 V8ex.pdf
 table1.txt
 V4ex.pdf
 V9ex.png
 V11ex.pdf
 V1ex.png
 table3.txt
 V5ex.pdf
 V11ex.png
 V8ex.png
 table16.txt
 V3ex.pdf
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 18:52:52 08-04-13
Completed: 19:22:44 08-04-13
Elapsed: 00 hrs 29 mins 51 secs