Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 10:46 AM Thu Jun 6, '13

Running as user: cgaadm

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BLCA-TP/3350935/BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/BLCA-TP/3348537/BLCA-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: 10:46:38 06-06-13
Completed:
Elapsed: 00 hrs 16 mins 40 secs

step 1. ClinicalAnalysisAllGenes_new [id: 415682] 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/BLCA-TP/3350935/BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/BLCA-TP/3348537/BLCA-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:
 BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.exprdata.gct
 BLCA-TP.clin.merged.picked.clindata.txt
 BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.clinical.results.txt
 BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.analysis.results.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:46:42 06-06-13
Completed: 11:02:06 06-06-13
Elapsed: 00 hrs 15 mins 24 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 415686] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.clinical.results.txt
RData file BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.analysis.results.RData
expression file BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.exprdata.gct
clinical file BLCA-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
 table1.txt
 table5.txt
 V3ex.png
 table10.txt
 V8ex.pdf
 table12.txt
 V8ex.png
 V7ex.pdf
 V3ex.pdf
 V7ex.png
 nozzle.html
 V9ex.pdf
 table14.txt
 V9ex.png
 nozzle.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:46:42 06-06-13
Completed: 11:03:11 06-06-13
Elapsed: 00 hrs 16 mins 29 secs