CNVarms_cluster_nozzle Execution Log 9:50 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/CESC-TP/2859755/broad_values_by_arm.txt
Correlate_Cluster_cnvarms_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/CESC-TP/2907374/1.GDAC_mergedClustering.Finished/CESC-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvarms_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvarms_onlysig2 output name CESC-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: 09:50:34 09-04-13
Completed:
Elapsed: 00 hrs 02 mins 22 secs

step 1. cnvarms2cluster [id: 375828] 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/CESC-TP/2859755/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: 09:50:39 09-04-13
Completed: 09:51:20 09-04-13
Elapsed: 00 hrs 00 mins 41 secs

step 2. Correlate_Cluster_cnvarms_onlysig [id: 375829]

    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/CESC-TP/2907374/1.GDAC_mergedClustering.Finished/CESC-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name CESC-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:
 D6V1.pdf
 D6V1.png
 D34V1.png
 D34V1.pdf
 D41V4.png
 D41V4.pdf
 D43V1.png
 D43V1.pdf
 D64V4.pdf
 D64V4.png
 D68V3.png
 D68V3.pdf
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 09:50:39 09-04-13
Completed: 09:52:55 09-04-13
Elapsed: 00 hrs 02 mins 16 secs