CNVarms_cluster_nozzle Execution Log 8:04 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/KIRC-TP/2661799/broad_values_by_arm.txt
Correlate_Cluster_cnvarms_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/KIRC-TP/2666908/1.GDAC_mergedClustering.Finished/KIRC-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvarms_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvarms_onlysig2 output name KIRC-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: 20:04:20 04-03-13
Completed:
Elapsed: 00 hrs 01 mins 51 secs

step 1. cnvarms2cluster [id: 335360] 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/KIRC-TP/2661799/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: 20:04:21 04-03-13
Completed: 20:05:02 04-03-13
Elapsed: 00 hrs 00 mins 41 secs

step 2. Correlate_Cluster_cnvarms_onlysig [id: 335361]

    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/KIRC-TP/2666908/1.GDAC_mergedClustering.Finished/KIRC-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name KIRC-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:
 D3V3.png
 D2V3.png
 D3V3.pdf
 D2V3.pdf
 D4V3.pdf
 D4V3.png
 D6V7.pdf
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 D6V3.pdf
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 D16V8.pdf
 D16V7.pdf
 D16V7.png
 D16V8.png
 D23V3.pdf
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 D23V9.png
 D23V7.pdf
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 D23V9.pdf
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 D23V5.pdf
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 D30V3.pdf
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 D34V3.pdf
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 D36V7.pdf
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 D36V3.pdf
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 D37V3.pdf
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 D43V2.pdf
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 D43V7.pdf
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 D44V1.pdf
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 D50V3.pdf
 D50V9.pdf
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 D50V10.pdf
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 D53V4.pdf
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 D54V4.pdf
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 D55V3.pdf
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 D59V3.pdf
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 D59V9.pdf
 D60V4.pdf
 D60V7.pdf
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 D60V6.pdf
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 D60V5.pdf
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 D60V3.pdf
 D63V1.png
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 D63V2.pdf
 D63V1.pdf
 D64V6.png
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 D63V8.png
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 D64V3.png
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 D64V3.pdf
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 D64V7.pdf
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 D66V9.pdf
 D65V9.pdf
 D69V3.pdf
 D69V3.png
 D69V8.png
 D69V8.pdf
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 20:04:21 04-03-13
Completed: 20:06:10 04-03-13
Elapsed: 00 hrs 01 mins 49 secs