CNVarms_ClinicalAnalysis_nozzle Execution Log 4:58 PM Tue Aug 14, '12

Running as user: cgaadm_deadline

cnvarms2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/KIRP/1604671/1.Gistic2_Analysis.Finished/broad_values_by_arm.txt
Correlate_Clinical_Cnvsarms_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRP/1552281/1.GDAC_clinicalDataPicker.Finished/KIRP.clin.merged.picked.txt
Correlate_Clinical_Cnvsarms_onlysig2 filter cluster smaller than 3
Correlate_Clinical_Cnvsarms_onlysig2 output name KIRP
Correlate_Clinical_Cnvsarms_onlysig2 figure height 5
Correlate_Clinical_Cnvsarms_onlysig2 figure width 9
Correlate_Clinical_Cnvsarms_onlysig2 survival legend position OUT
Correlate_Clinical_Cnvsarms_onlysig2 pvalue cutoff 1
Correlate_Clinical_Cnvsarms_onlysig2 qvalue cutoff 0.25
Correlate_Clinical_Cnvsarms_onlysig2 make figure ONLYSIG
Correlate_Clinical_Cnvsarms_onlysig2 nozzle ver Nozzle.R1
Execution Times:
Submitted: 16:58:06 14-08-12
Completed:
Elapsed: 00 hrs 02 mins 05 secs

step 1. cnvarms2cluster [id: 146079] Convert mutsig results to cluster files

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00499:3
sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/KIRP/1604671/1.Gistic2_Analysis.Finished/broad_values_by_arm.txt
maf file
sig gene file
sig gene q cutoff 0.01
output name
Output Files:
 broad_values_by_arm.mutsig.cluster.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 16:58:07 14-08-12
Completed: 16:58:57 14-08-12
Elapsed: 00 hrs 00 mins 50 secs

step 2. Correlate_Clinical_Cnvsarms_onlysig [id: 146080]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00498:11
cluster label file broad_values_by_arm.mutsig.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRP/1552281/1.GDAC_clinicalDataPicker.Finished/KIRP.clin.merged.picked.txt
features used ALL
filter cluster smaller than 3
output name KIRP
figure height 5
figure width 9
survival legend position OUT
pvalue cutoff 1
qvalue cutoff 0.25
make figure ONLYSIG
nozzle ver Nozzle.R1
options MUTSIG
report title
job description
Output Files:
 D1V1.pdf
 D1V1.png
 D11V1.png
 D11V1.pdf
 D22V5.pdf
 D22V5.png
 table.1.txt
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 16:58:07 14-08-12
Completed: 17:00:06 14-08-12
Elapsed: 00 hrs 01 mins 59 secs