CNVarms_cluster_nozzle Execution Log 9:54 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/DLBC-TP/2859761/broad_values_by_arm.txt
Correlate_Cluster_cnvarms_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/DLBC-TP/2907746/1.GDAC_mergedClustering.Finished/DLBC-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvarms_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvarms_onlysig2 output name DLBC-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: 09:54:43 09-04-13
Completed:
Elapsed: 00 hrs 01 mins 52 secs

step 1. cnvarms2cluster [id: 375950] 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/DLBC-TP/2859761/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: 09:55:21 09-04-13
Completed: 09:55:58 09-04-13
Elapsed: 00 hrs 00 mins 36 secs

step 2. Correlate_Cluster_cnvarms_onlysig [id: 375951]

    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/DLBC-TP/2907746/1.GDAC_mergedClustering.Finished/DLBC-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name DLBC-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:
 nozzle.html
 nozzle.RData
 table.1.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 09:55:21 09-04-13
Completed: 09:56:34 09-04-13
Elapsed: 00 hrs 01 mins 12 secs