CNVarms_cluster_nozzle Execution Log 10:27 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/GBM-TP/2859814/broad_values_by_arm.txt
Correlate_Cluster_cnvarms_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/GBM-TP/2909397/1.GDAC_mergedClustering.Finished/GBM-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvarms_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvarms_onlysig2 output name GBM-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: 10:27:23 09-04-13
Completed:
Elapsed: 00 hrs 04 mins 36 secs

step 1. cnvarms2cluster [id: 376725] 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/GBM-TP/2859814/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: 10:27:40 09-04-13
Completed: 10:30:34 09-04-13
Elapsed: 00 hrs 02 mins 54 secs

step 2. Correlate_Cluster_cnvarms_onlysig [id: 376726]

    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/GBM-TP/2909397/1.GDAC_mergedClustering.Finished/GBM-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name GBM-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:
 D1V5.pdf
 D1V5.png
 D4V3.pdf
 D2V5.pdf
 D2V5.png
 D4V3.png
 D13V1.pdf
 D13V4.png
 D13V2.png
 D13V5.png
 D13V1.png
 D13V4.pdf
 D13V2.pdf
 D13V5.pdf
 D14V1.png
 D14V5.png
 D14V4.pdf
 D14V2.png
 D14V2.pdf
 D14V1.pdf
 D14V4.png
 D14V5.pdf
 D31V5.png
 D31V5.pdf
 D33V2.png
 D33V1.pdf
 D33V2.pdf
 D32V5.pdf
 D32V5.png
 D33V1.png
 D33V5.png
 D34V1.png
 D33V4.pdf
 D33V4.png
 D34V1.pdf
 D33V8.png
 D33V5.pdf
 D33V8.pdf
 D34V8.pdf
 D34V2.png
 D34V5.pdf
 D34V2.pdf
 D34V8.png
 D34V4.png
 D34V5.png
 D34V4.pdf
 D35V5.pdf
 D35V2.pdf
 D35V1.png
 D35V4.pdf
 D35V1.pdf
 D35V5.png
 D35V4.png
 D35V2.png
 D36V2.pdf
 D36V4.pdf
 D36V5.png
 D36V2.png
 D36V4.png
 D36V1.png
 D36V5.pdf
 D36V1.pdf
 D45V5.pdf
 D45V5.png
 D50V5.png
 D50V5.pdf
 D51V5.pdf
 D51V5.png
 D58V2.pdf
 D58V2.png
 D58V4.pdf
 D58V1.pdf
 D58V4.png
 D58V1.png
 D59V2.png
 D58V5.pdf
 D59V1.png
 D58V5.png
 D59V1.pdf
 D59V2.pdf
 D59V7.pdf
 D59V5.pdf
 D59V4.pdf
 D60V1.pdf
 D60V2.png
 D59V5.png
 D60V2.pdf
 D60V1.png
 D59V7.png
 D59V4.png
 D60V4.pdf
 D60V4.png
 D61V1.pdf
 D61V1.png
 D60V5.png
 D60V5.pdf
 D61V5.pdf
 D61V5.png
 D64V2.png
 D64V5.png
 D64V5.pdf
 D64V2.pdf
 D65V1.png
 D65V1.pdf
 D65V5.pdf
 D65V5.png
 D66V2.png
 D66V6.pdf
 D66V1.pdf
 D66V5.pdf
 D66V1.png
 D66V5.png
 D66V6.png
 D66V2.pdf
 D66V4.png
 D66V4.pdf
 D69V5.pdf
 D69V5.png
 D78V5.png
 D78V5.pdf
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:27:40 09-04-13
Completed: 10:31:58 09-04-13
Elapsed: 00 hrs 04 mins 18 secs