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/mRNAseq_preprocessor/THCA-TP/2845244/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.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 MRNASEQ_EXPR
Execution Times:
Submitted: 19:19:35 08-04-13
Completed:
Elapsed: 00 hrs 23 mins 10 secs

step 1. ClinicalAnalysisAllGenes_new [id: 373289] 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/THCA-TP/2845244/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.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.uncv2.mRNAseq_RSEM_normalized_log2.exprdata.gct
 THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.clinical.results.txt
 THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.analysis.results.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:19:40 08-04-13
Completed: 19:41:22 08-04-13
Elapsed: 00 hrs 21 mins 42 secs

step 2. ClinicalAnalysisAllGenesReport_nozzle [id: 373291] Generate a report to summarize the results from ClinicalAnalysisAllGenes module

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00334:29
all result file THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.clinical.results.txt
RData file THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.analysis.results.RData
expression file THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.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 MRNASEQ_EXPR
report title
job description
Output Files:
 table1.txt
 supp.table1.txt
 table11.txt
 table5.txt
 V3ex.png
 V6ex.png
 V2ex.pdf
 V4ex.png
 table15.txt
 V6ex.pdf
 V1ex.pdf
 V5ex.png
 V8ex.pdf
 table7.txt
 V2ex.png
 table17.txt
 V4ex.pdf
 V9ex.png
 V1ex.png
 table3.txt
 V5ex.pdf
 V8ex.png
 table9.txt
 V7ex.pdf
 V3ex.pdf
 V7ex.png
 table13.txt
 V12ex.png
 table19.txt
 table23.txt
 V9ex.pdf
 table21.txt
 V13ex.png
 table25.txt
 table27.txt
 V12ex.pdf
 V10ex.png
 V11ex.pdf
 nozzle.RData
 V10ex.pdf
 V13ex.pdf
 V11ex.png
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:19:40 08-04-13
Completed: 19:42:44 08-04-13
Elapsed: 00 hrs 23 mins 04 secs