Correlate_Clinical_AllGenes_Expression_nozzle Execution Log 2:34 PM Thu May 2, '13

Running as user: cgaadm_deadline

ClinicalAnalysisAllGenes_new1 data file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/SKCM-TM/3032890/SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.txt
ClinicalAnalysisAllGenes_new1 clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/SKCM-TM/3132753/1.GDAC_clinicalDataPicker.Finished/SKCM-TM.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: 14:34:13 02-05-13
Completed:
Elapsed: 00 hrs 17 mins 12 secs

step 1. ClinicalAnalysisAllGenes_new [id: 396166] 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/SKCM-TM/3032890/SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.txt
clinical file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/SKCM-TM/3132753/1.GDAC_clinicalDataPicker.Finished/SKCM-TM.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:
 SKCM-TM.clin.merged.picked.clindata.txt
 SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.exprdata.gct
 SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.clinical.results.txt
 SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.analysis.results.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 14:34:18 02-05-13
Completed: 14:50:35 02-05-13
Elapsed: 00 hrs 16 mins 17 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 396167] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.clinical.results.txt
RData file SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.analysis.results.RData
expression file SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.exprdata.gct
clinical file SKCM-TM.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:
 table1.txt
 supp.table1.txt
 table5.txt
 V2ex.pdf
 V1ex.pdf
 V2ex.png
 V1ex.png
 table3.txt
 table11.txt
 V3ex.png
 V6ex.png
 V4ex.png
 table15.txt
 V6ex.pdf
 V5ex.png
 table7.txt
 V4ex.pdf
 nozzle.RData
 V5ex.pdf
 table9.txt
 V7ex.pdf
 V3ex.pdf
 V7ex.png
 table13.txt
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 14:34:18 02-05-13
Completed: 14:51:24 02-05-13
Elapsed: 00 hrs 17 mins 06 secs