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/THCA-TP/2859958/broad_values_by_arm.txt
Correlate_Cluster_cnvarms_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/THCA-TP/2909296/1.GDAC_mergedClustering.Finished/THCA-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvarms_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvarms_onlysig2 output name THCA-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: 10:05:38 09-04-13
Completed:
Elapsed: 00 hrs 03 mins 19 secs

step 1. cnvarms2cluster [id: 376226] 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/THCA-TP/2859958/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: 10:05:40 09-04-13
Completed: 10:07:25 09-04-13
Elapsed: 00 hrs 01 mins 44 secs

step 2. Correlate_Cluster_cnvarms_onlysig [id: 376227]

    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/THCA-TP/2909296/1.GDAC_mergedClustering.Finished/THCA-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name THCA-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:
 D1V1.pdf
 D1V1.png
 D3V1.png
 D3V1.pdf
 D2V1.pdf
 D2V1.png
 D4V1.pdf
 D4V2.pdf
 D5V1.pdf
 D4V8.pdf
 D5V1.png
 D4V2.png
 D4V8.png
 D4V1.png
 D5V8.pdf
 D5V2.pdf
 D5V8.png
 D5V7.pdf
 D5V5.pdf
 D6V2.png
 D6V1.pdf
 D6V1.png
 D5V6.png
 D5V2.png
 D5V5.png
 D5V7.png
 D5V6.pdf
 D6V6.pdf
 D6V6.png
 D6V5.png
 D6V2.pdf
 D7V1.pdf
 D7V1.png
 D6V8.png
 D7V2.pdf
 D6V8.pdf
 D7V2.png
 D6V5.pdf
 D7V7.pdf
 D7V8.png
 D7V6.png
 D7V5.pdf
 D7V5.png
 D7V6.pdf
 D7V8.pdf
 D7V7.png
 D10V1.pdf
 D10V5.png
 D10V6.png
 D10V2.png
 D10V5.pdf
 D9V1.pdf
 D10V1.png
 D9V1.png
 D10V2.pdf
 D11V2.png
 D10V8.pdf
 D10V7.png
 D10V7.pdf
 D11V6.pdf
 D11V5.png
 D11V7.png
 D11V1.png
 D11V1.pdf
 D10V6.pdf
 D11V6.png
 D11V7.pdf
 D11V8.png
 D11V2.pdf
 D10V8.png
 D11V5.pdf
 D14V1.png
 D13V1.pdf
 D13V2.png
 D13V1.png
 D12V1.pdf
 D11V8.pdf
 D14V1.pdf
 D13V2.pdf
 D12V1.png
 D14V5.png
 D14V8.pdf
 D14V6.pdf
 D15V1.pdf
 D15V7.png
 D14V7.pdf
 D15V1.png
 D14V2.png
 D14V2.pdf
 D15V2.png
 D15V2.pdf
 D14V7.png
 D14V8.png
 D14V6.png
 D14V5.pdf
 D16V6.pdf
 D16V2.pdf
 D16V6.png
 D16V1.png
 D16V5.pdf
 D17V1.pdf
 D16V5.png
 D16V1.pdf
 D17V2.png
 D16V2.png
 D15V8.pdf
 D17V1.png
 D16V8.pdf
 D16V7.pdf
 D16V7.png
 D16V8.png
 D15V8.png
 D15V7.pdf
 D20V1.png
 D17V6.pdf
 D17V5.pdf
 D17V8.pdf
 D17V5.png
 D17V7.pdf
 D17V8.png
 D17V6.png
 D17V7.png
 D20V1.pdf
 D17V2.pdf
 D21V1.png
 D22V1.png
 D21V1.pdf
 D22V1.pdf
 D23V1.png
 D23V2.pdf
 D22V2.pdf
 D22V2.png
 D23V1.pdf
 D23V2.png
 D25V1.pdf
 D25V1.png
 D26V6.pdf
 D26V1.pdf
 D26V1.png
 D26V2.png
 D27V1.pdf
 D26V2.pdf
 D26V8.pdf
 D26V5.pdf
 D26V8.png
 D26V7.pdf
 D26V6.png
 D26V7.png
 D27V1.png
 D26V5.png
 D27V7.png
 D27V8.png
 D27V2.png
 D28V1.pdf
 D27V2.pdf
 D27V8.pdf
 D27V7.pdf
 D28V1.png
 D30V1.png
 D30V1.pdf
 D31V1.png
 D31V1.pdf
 D32V1.pdf
 D33V1.pdf
 D34V1.png
 D34V1.pdf
 D32V1.png
 D33V1.png
 D35V1.png
 D35V1.pdf
 D37V1.pdf
 D37V1.png
 D36V1.png
 D36V1.pdf
 D39V1.pdf
 D39V1.png
 D39V8.png
 D39V7.pdf
 D41V1.pdf
 D41V1.png
 D39V7.png
 D39V8.pdf
 D42V1.pdf
 D42V1.png
 D44V1.pdf
 D45V1.png
 D45V1.pdf
 D44V1.png
 D45V2.png
 D45V6.png
 D45V8.pdf
 D45V6.pdf
 D45V7.png
 D45V7.pdf
 D45V2.pdf
 D45V8.png
 D45V5.pdf
 table.1.txt
 D45V5.png
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:05:40 09-04-13
Completed: 10:08:56 09-04-13
Elapsed: 00 hrs 03 mins 15 secs