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/GDAC_MergeDataFilesPipeline/GBM-TP/2841398/2.GDAC_MergeDataFiles.Finished/GBM-TP.mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/GBM-TP/2843145/1.GDAC_clinicalDataPicker.Finished/GBM-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 MIR_EXPR
Execution Times:
Submitted: 18:52:33 08-04-13
Completed:
Elapsed: 00 hrs 23 mins 40 secs

step 1. ClinicalAnalysisAllGenes_new [id: 372981] 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:00333:11
data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM-TP/2841398/2.GDAC_MergeDataFiles.Finished/GBM-TP.mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/GBM-TP/2843145/1.GDAC_clinicalDataPicker.Finished/GBM-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:
 GBM-TP.mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.exprdata.gct
 GBM-TP.clin.merged.picked.clindata.txt
 GBM-TP.mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.analysis.results.RData
 GBM-TP.mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.clinical.results.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 18:52:44 08-04-13
Completed: 19:07:09 08-04-13
Elapsed: 00 hrs 14 mins 24 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 372982] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file GBM-TP.mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.clinical.results.txt
RData file GBM-TP.mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.analysis.results.RData
expression file GBM-TP.mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.exprdata.gct
clinical file GBM-TP.clin.merged.picked.clindata.txt
cutoff p 1
cutoff fdr 0.05
max table rows 10
nozzle ver Nozzle.R1
options MIR_EXPR
report title
job description
Output Files:
 table1.txt
 supp.table1.txt
 nozzle.html
 table5.txt
 V2ex.pdf
 V1ex.pdf
 V2ex.png
 V1ex.png
 table3.txt
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 18:52:44 08-04-13
Completed: 19:16:11 08-04-13
Elapsed: 00 hrs 23 mins 26 secs