Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 7:19 PM Mon Apr 8, '13

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/THCA-TP/2845121/0.GDAC_RPPA_preprocess.Finished/THCA-TP.rppa.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/THCA-TP/2844384/1.GDAC_clinicalDataPicker.Finished/THCA-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 RPPA_EXPR
Execution Times:
Submitted: 19:19:34 08-04-13
Completed:
Elapsed: 00 hrs 09 mins 47 secs

step 1. ClinicalAnalysisAllGenes_new [id: 373288] 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/GDAC_RPPA_preprocess/THCA-TP/2845121/0.GDAC_RPPA_preprocess.Finished/THCA-TP.rppa.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/THCA-TP/2844384/1.GDAC_clinicalDataPicker.Finished/THCA-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:
 THCA-TP.clin.merged.picked.clindata.txt
 THCA-TP.rppa.exprdata.gct
 THCA-TP.rppa.clinical.results.txt
 THCA-TP.rppa.analysis.results.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:19:40 08-04-13
Completed: 19:23:09 08-04-13
Elapsed: 00 hrs 03 mins 28 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 373290] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file THCA-TP.rppa.clinical.results.txt
RData file THCA-TP.rppa.analysis.results.RData
expression file THCA-TP.rppa.exprdata.gct
clinical file THCA-TP.clin.merged.picked.clindata.txt
cutoff p 1
cutoff fdr 0.05
max table rows 10
nozzle ver Nozzle.R1
options RPPA_EXPR
report title
job description
Output Files:
 table1.txt
 supp.table1.txt
 V3ex.png
 V1ex.pdf
 V1ex.png
 table3.txt
 V3ex.pdf
 table8.txt
 V4ex.png
 table6.txt
 V5ex.png
 V4ex.pdf
 V5ex.pdf
 V6ex.png
 table15.txt
 V6ex.pdf
 table10.txt
 V8ex.pdf
 table12.txt
 V8ex.png
 table18.txt
 table20.txt
 V10ex.png
 V11ex.pdf
 nozzle.RData
 V10ex.pdf
 V11ex.png
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:19:40 08-04-13
Completed: 19:29:20 08-04-13
Elapsed: 00 hrs 09 mins 40 secs