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/COAD-TP/2859771/broad_values_by_arm.txt
Correlate_Cluster_cnvarms_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/COAD-TP/2909319/1.GDAC_mergedClustering.Finished/COAD-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvarms_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvarms_onlysig2 output name COAD-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: 10:05:37 09-04-13
Completed:
Elapsed: 00 hrs 03 mins 22 secs

step 1. cnvarms2cluster [id: 376221] 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/COAD-TP/2859771/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: 10:05:39 09-04-13
Completed: 10:06:58 09-04-13
Elapsed: 00 hrs 01 mins 18 secs

step 2. Correlate_Cluster_cnvarms_onlysig [id: 376222]

    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/COAD-TP/2909319/1.GDAC_mergedClustering.Finished/COAD-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name COAD-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:
 D3V7.pdf
 D3V7.png
 D4V3.pdf
 D4V3.png
 D13V3.pdf
 D13V3.png
 D13V4.png
 D13V4.pdf
 D13V8.png
 D13V7.png
 D14V3.pdf
 D13V7.pdf
 D14V3.png
 D13V8.pdf
 D14V8.pdf
 D15V3.png
 D14V7.pdf
 D15V3.pdf
 D14V7.png
 D14V8.png
 D16V3.pdf
 D16V3.png
 D21V3.pdf
 D21V3.png
 D22V3.png
 D22V3.pdf
 D25V1.pdf
 D25V3.pdf
 D25V3.png
 D25V4.png
 D25V2.png
 D25V1.png
 D25V2.pdf
 D25V7.png
 D25V4.pdf
 D25V7.pdf
 D25V8.png
 D25V8.pdf
 D28V3.pdf
 D28V3.png
 D29V3.png
 D29V3.pdf
 D31V7.png
 D31V7.pdf
 D36V2.pdf
 D36V2.png
 D36V3.pdf
 D36V3.png
 D36V7.pdf
 D37V1.pdf
 D37V1.png
 D36V7.png
 D37V2.pdf
 D37V2.png
 D36V8.pdf
 D36V8.png
 D37V7.pdf
 D37V6.png
 D37V8.png
 D37V4.pdf
 D37V7.png
 D37V4.png
 D37V3.png
 D37V6.pdf
 D37V3.pdf
 D37V8.pdf
 D40V3.pdf
 D40V3.png
 D46V3.pdf
 D46V3.png
 D47V3.pdf
 D47V3.png
 D49V3.pdf
 D49V3.png
 D52V1.pdf
 D52V1.png
 D52V3.pdf
 D52V3.png
 D54V3.pdf
 D54V3.png
 D55V3.pdf
 D55V3.png
 D59V3.pdf
 D58V3.png
 D58V4.pdf
 D59V3.png
 D58V4.png
 D59V4.png
 D58V3.pdf
 D60V3.png
 D59V4.pdf
 D60V3.pdf
 D61V3.png
 D61V3.pdf
 D63V1.png
 D63V1.pdf
 D63V3.png
 D63V3.pdf
 D63V4.png
 D63V7.pdf
 D63V8.pdf
 D63V8.png
 D63V7.png
 D63V4.pdf
 D63V2.png
 D63V2.pdf
 D64V8.png
 D64V7.png
 D64V3.png
 D64V3.pdf
 D64V8.pdf
 D64V7.pdf
 D67V4.png
 D67V1.png
 D67V2.png
 D67V1.pdf
 D67V2.pdf
 D67V3.pdf
 D67V3.png
 D67V4.pdf
 D67V7.png
 D67V7.pdf
 D67V8.pdf
 D67V8.png
 D69V3.pdf
 D69V2.pdf
 D69V3.png
 D69V4.pdf
 D69V4.png
 D69V1.png
 D69V2.png
 D69V1.pdf
 D69V8.png
 D69V7.png
 D70V1.png
 D70V4.pdf
 D70V3.pdf
 D70V2.pdf
 D69V8.pdf
 D70V2.png
 D70V4.png
 D70V1.pdf
 D69V7.pdf
 D69V6.png
 D69V6.pdf
 D70V3.png
 D70V8.pdf
 D70V6.pdf
 D70V8.png
 D70V7.pdf
 D70V6.png
 D70V7.png
 D73V3.png
 D73V3.pdf
 D75V3.pdf
 D74V3.pdf
 D75V3.png
 D74V3.png
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:05:40 09-04-13
Completed: 10:08:58 09-04-13
Elapsed: 00 hrs 03 mins 18 secs