CNVarms_cluster_nozzle Execution Log 4:32 PM Mon Mar 4, '13

Running as user: cgaadm_deadline

cnvarms2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/BLCA-TP/2660651/broad_values_by_arm.txt
Correlate_Cluster_cnvarms_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/BLCA-TP/2662494/1.GDAC_mergedClustering.Finished/BLCA-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvarms_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvarms_onlysig2 output name BLCA-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: 16:32:10 04-03-13
Completed:
Elapsed: 00 hrs 01 mins 38 secs

step 1. cnvarms2cluster [id: 334341] 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/BLCA-TP/2660651/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: 16:32:10 04-03-13
Completed: 16:32:46 04-03-13
Elapsed: 00 hrs 00 mins 36 secs

step 2. Correlate_Cluster_cnvarms_onlysig [id: 334343]

    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/BLCA-TP/2662494/1.GDAC_mergedClustering.Finished/BLCA-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name BLCA-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:
 D3V1.png
 D5V1.pdf
 D5V1.png
 D3V1.pdf
 D31V1.png
 D31V1.pdf
 D32V1.pdf
 D32V1.png
 D52V2.png
 D52V1.pdf
 D52V1.png
 D50V1.pdf
 D50V1.png
 D52V2.pdf
 D54V1.png
 D54V1.pdf
 D55V1.png
 D55V1.pdf
 D55V6.png
 D55V6.pdf
 D58V1.pdf
 D58V1.png
 D59V1.png
 D59V1.pdf
 D63V1.png
 D63V1.pdf
 D70V1.png
 D70V1.pdf
 D75V1.pdf
 table.1.txt
 D75V1.png
 nozzle.html
 nozzle.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 16:32:10 04-03-13
Completed: 16:33:46 04-03-13
Elapsed: 00 hrs 01 mins 36 secs