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/HNSC-TP/2859794/broad_values_by_arm.txt
Correlate_Cluster_cnvarms_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/HNSC-TP/2907413/1.GDAC_mergedClustering.Finished/HNSC-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvarms_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvarms_onlysig2 output name HNSC-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: 09:50:37 09-04-13
Completed:
Elapsed: 00 hrs 02 mins 59 secs

step 1. cnvarms2cluster [id: 375844] 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/HNSC-TP/2859794/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: 09:50:40 09-04-13
Completed: 09:52:07 09-04-13
Elapsed: 00 hrs 01 mins 26 secs

step 2. Correlate_Cluster_cnvarms_onlysig [id: 375845]

    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/HNSC-TP/2907413/1.GDAC_mergedClustering.Finished/HNSC-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name HNSC-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:
 D2V1.pdf
 D2V1.png
 D3V1.png
 D3V2.png
 D3V2.pdf
 D3V1.pdf
 D5V2.pdf
 D5V7.pdf
 D5V2.png
 D5V7.png
 D6V7.pdf
 D6V2.pdf
 D6V7.png
 D6V2.png
 D9V1.png
 D13V1.png
 D9V1.pdf
 D14V1.png
 D13V1.pdf
 D13V2.png
 D14V2.png
 D14V2.pdf
 D14V1.pdf
 D13V2.pdf
 D16V2.pdf
 D16V1.png
 D17V1.pdf
 D16V1.pdf
 D16V2.png
 D17V1.png
 D21V1.png
 D21V1.pdf
 D23V1.png
 D23V7.pdf
 D23V2.pdf
 D23V1.pdf
 D23V7.png
 D23V2.png
 D26V1.pdf
 D26V1.png
 D28V2.png
 D28V2.pdf
 D30V1.png
 D30V1.pdf
 D32V1.pdf
 D32V1.png
 D33V2.png
 D33V2.pdf
 D36V2.pdf
 D36V2.png
 D36V1.png
 D36V1.pdf
 D37V1.pdf
 D37V1.png
 D37V2.pdf
 D37V2.png
 D39V2.png
 D39V1.pdf
 D39V1.png
 D41V1.png
 D39V2.pdf
 D41V1.pdf
 D41V2.png
 D41V2.pdf
 D44V2.png
 D44V1.pdf
 D44V2.pdf
 D44V1.png
 D46V6.png
 D46V2.pdf
 D46V2.png
 D46V1.png
 D46V1.pdf
 D46V7.pdf
 D46V7.png
 D46V6.pdf
 D47V1.pdf
 D47V2.png
 D47V1.png
 D47V2.pdf
 D49V1.pdf
 D49V2.png
 D49V1.png
 D49V2.pdf
 D49V6.png
 D49V6.pdf
 D54V2.pdf
 D56V1.png
 D54V1.png
 D54V2.png
 D56V1.pdf
 D56V2.pdf
 D54V1.pdf
 D56V2.png
 D59V7.pdf
 D58V1.pdf
 D60V1.pdf
 D59V1.png
 D60V1.png
 D59V7.png
 D59V1.pdf
 D58V1.png
 D61V1.pdf
 D61V2.pdf
 D61V1.png
 D61V2.png
 D64V2.png
 D64V2.pdf
 D64V1.png
 D64V1.pdf
 D64V6.png
 D64V6.pdf
 D68V6.png
 D68V5.png
 D68V2.pdf
 D69V2.pdf
 D68V7.pdf
 D68V5.pdf
 D68V2.png
 D68V7.png
 D68V6.pdf
 D69V2.png
 D72V1.png
 D72V2.png
 D72V1.pdf
 D72V2.pdf
 D77V1.pdf
 D77V1.png
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 09:50:40 09-04-13
Completed: 09:53:35 09-04-13
Elapsed: 00 hrs 02 mins 54 secs