CNVarms_cluster_nozzle Execution Log 10:05 AM Tue Apr 9, '13

Running as user: cgaadm_deadline

cnvarms2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/LUSC-TP/2859876/broad_values_by_arm.txt
Correlate_Cluster_cnvarms_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LUSC-TP/2909314/1.GDAC_mergedClustering.Finished/LUSC-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvarms_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvarms_onlysig2 output name LUSC-TP
Correlate_Cluster_cnvarms_onlysig2 figure height 5
Correlate_Cluster_cnvarms_onlysig2 figure width 9
Correlate_Cluster_cnvarms_onlysig2 survival legend position OUT
Correlate_Cluster_cnvarms_onlysig2 pvalue cutoff 1
Correlate_Cluster_cnvarms_onlysig2 qvalue cutoff 0.25
Correlate_Cluster_cnvarms_onlysig2 make figure ONLYSIG
Correlate_Cluster_cnvarms_onlysig2 nozzle ver Nozzle.R1
Execution Times:
Submitted: 10:05:42 09-04-13
Completed:
Elapsed: 00 hrs 13 mins 43 secs

step 1. cnvarms2cluster [id: 376249] 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_Analysis/LUSC-TP/2859876/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: 10:05:55 09-04-13
Completed: 10:06:43 09-04-13
Elapsed: 00 hrs 00 mins 47 secs

step 2. Correlate_Cluster_cnvarms_onlysig [id: 376250]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00508:2
cluster label file broad_values_by_arm.mutsig.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LUSC-TP/2909314/1.GDAC_mergedClustering.Finished/LUSC-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name LUSC-TP
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:
 D2V3.png
 D2V3.pdf
 D3V3.png
 D3V3.pdf
 D3V4.png
 D3V4.pdf
 D3V8.png
 D3V8.pdf
 D4V3.png
 D4V3.pdf
 D4V7.png
 D4V7.pdf
 D9V3.png
 D9V3.pdf
 D12V3.png
 D12V3.pdf
 D13V3.pdf
 D13V3.png
 D14V4.pdf
 D14V4.png
 D14V3.pdf
 D14V3.png
 D17V6.pdf
 D17V6.png
 D23V3.png
 D23V3.pdf
 D24V3.pdf
 D24V3.png
 D29V3.png
 D29V3.pdf
 D31V3.pdf
 D31V3.png
 D32V2.pdf
 D32V2.png
 D32V3.png
 D32V3.pdf
 D34V3.png
 D34V3.pdf
 D36V3.pdf
 D36V3.png
 D37V3.png
 D37V3.pdf
 D39V3.pdf
 D39V3.png
 D41V3.png
 D41V3.pdf
 D41V4.png
 D41V4.pdf
 D45V3.png
 D45V4.png
 D45V3.pdf
 D45V4.pdf
 D47V3.pdf
 D47V4.png
 D47V4.pdf
 D47V3.png
 D48V3.pdf
 D48V4.pdf
 D48V4.png
 D48V3.png
 D50V4.pdf
 D50V3.png
 D50V3.pdf
 D50V4.png
 D51V3.png
 D51V3.pdf
 D55V3.pdf
 D55V3.png
 D57V3.png
 D57V4.png
 D57V3.pdf
 D57V4.pdf
 D58V3.png
 D58V4.png
 D58V3.pdf
 D58V4.pdf
 D58V8.png
 D58V8.pdf
 D59V3.png
 D59V3.pdf
 D59V4.png
 D59V4.pdf
 D59V10.png
 D59V10.pdf
 D60V2.png
 D60V3.png
 D60V2.pdf
 D60V3.pdf
 D60V4.png
 D60V4.pdf
 D61V3.png
 D61V3.pdf
 D62V3.png
 D62V3.pdf
 D65V3.pdf
 D65V3.png
 D65V4.pdf
 D65V4.png
 D66V7.png
 D66V7.pdf
 D66V8.png
 D66V8.pdf
 D68V3.png
 D68V3.pdf
 D70V3.pdf
 D70V3.png
 D70V4.pdf
 D70V4.png
 D74V8.png
 D74V8.pdf
 D78V3.png
 D78V3.pdf
 D78V4.pdf
 D78V4.png
 D80V6.png
 D80V6.pdf
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:05:55 09-04-13
Completed: 10:19:25 09-04-13
Elapsed: 00 hrs 13 mins 30 secs