CNV_cluster_nozzle Execution Log 10:05 AM Tue Apr 9, '13

Running as user: cgaadm_deadline

cnv2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/COAD-TP/2859771/all_lesions.conf_99.txt
Correlate_Cluster_cnvs_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_cnvs_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvs_onlysig2 output name COAD-TP
Correlate_Cluster_cnvs_onlysig2 figure height 5
Correlate_Cluster_cnvs_onlysig2 figure width 9
Correlate_Cluster_cnvs_onlysig2 survival legend position OUT
Correlate_Cluster_cnvs_onlysig2 pvalue cutoff 1
Correlate_Cluster_cnvs_onlysig2 qvalue cutoff 0.25
Correlate_Cluster_cnvs_onlysig2 make figure ONLYSIG
Correlate_Cluster_cnvs_onlysig2 nozzle ver Nozzle.R1
Execution Times:
Submitted: 10:05:34 09-04-13
Completed:
Elapsed: 00 hrs 11 mins 57 secs

step 1. cnv2cluster [id: 376192] Convert mutsig results to cluster files

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00494:12
sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/COAD-TP/2859771/all_lesions.conf_99.txt
maf file
sig gene file
sig gene q cutoff 0.01
output name
Output Files:
 all_lesions.conf_99.cnv.cluster.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:05:34 09-04-13
Completed: 10:06:20 09-04-13
Elapsed: 00 hrs 00 mins 45 secs

step 2. Correlate_Cluster_cnvs_onlysig [id: 376193]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00507:2
cluster label file all_lesions.conf_99.cnv.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:
 D1V3.pdf
 D1V3.png
 D2V3.png
 D2V3.pdf
 D4V3.pdf
 D4V3.png
 D5V3.pdf
 D5V3.png
 D6V3.png
 D6V3.pdf
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 D7V3.pdf
 D8V3.pdf
 D8V3.png
 D9V1.png
 D9V3.png
 D9V3.pdf
 D9V1.pdf
 D9V2.pdf
 D9V2.png
 D11V1.png
 D11V1.pdf
 D11V2.png
 D11V3.png
 D11V3.pdf
 D11V2.pdf
 D11V4.png
 D11V4.pdf
 D11V7.png
 D11V8.pdf
 D11V7.pdf
 D11V8.png
 D12V3.png
 D12V2.png
 D12V3.pdf
 D12V1.pdf
 D12V2.pdf
 D12V1.png
 D13V1.pdf
 D12V7.pdf
 D13V1.png
 D12V8.pdf
 D12V8.png
 D12V7.png
 D13V2.png
 D13V3.pdf
 D13V2.pdf
 D13V3.png
 D14V1.png
 D14V1.pdf
 D13V7.png
 D13V7.pdf
 D14V2.png
 D14V2.pdf
 D14V3.pdf
 D14V3.png
 D15V3.png
 D15V3.pdf
 D15V6.png
 D15V7.png
 D15V6.pdf
 D15V7.pdf
 D16V3.pdf
 D16V3.png
 D16V7.pdf
 D16V7.png
 D17V3.pdf
 D17V3.png
 D19V3.png
 D19V3.pdf
 D20V3.png
 D20V3.pdf
 D21V2.pdf
 D21V3.png
 D21V2.png
 D21V3.pdf
 D21V7.png
 D21V7.pdf
 D21V8.png
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 D22V1.pdf
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 D22V3.pdf
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 D22V6.png
 D22V6.pdf
 D22V7.png
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 D22V7.pdf
 D23V1.png
 D22V8.pdf
 D23V1.pdf
 D23V2.pdf
 D23V2.png
 D23V3.pdf
 D23V3.png
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 D23V4.pdf
 D23V6.png
 D23V6.pdf
 D23V7.png
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 D23V8.pdf
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 D24V2.pdf
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 D24V3.pdf
 D24V4.pdf
 D24V6.pdf
 D24V6.png
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 D24V7.pdf
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 D24V8.png
 D25V1.pdf
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 D25V3.pdf
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 D25V7.pdf
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 D30V3.pdf
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 D35V4.pdf
 D35V7.pdf
 D35V7.png
 D36V3.pdf
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 D53V3.pdf
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 D55V3.png
 D55V3.pdf
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 D56V4.pdf
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 D56V8.pdf
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 D59V2.pdf
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 D59V4.png
 D59V6.pdf
 D59V6.png
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 D59V7.pdf
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 D59V8.pdf
 D61V1.pdf
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 D62V1.pdf
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 D62V2.pdf
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 D62V4.pdf
 D62V4.png
 D62V6.png
 D62V6.pdf
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 D62V7.png
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 D62V8.pdf
 D63V1.png
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 D63V1.pdf
 D63V3.png
 D63V3.pdf
 D63V4.png
 D63V4.pdf
 D63V2.pdf
 D63V6.pdf
 D63V7.pdf
 D63V8.pdf
 D63V8.png
 D63V7.png
 D63V6.png
 D64V2.png
 D64V3.png
 D64V3.pdf
 D64V2.pdf
 D64V1.png
 D64V1.pdf
 D64V6.png
 D64V6.pdf
 D64V4.pdf
 D64V4.png
 D64V8.png
 D64V7.png
 D64V7.pdf
 D64V8.pdf
 D66V3.png
 D66V3.pdf
 D66V7.png
 D66V7.pdf
 D67V3.png
 D67V3.pdf
 D68V1.png
 D68V1.pdf
 D68V3.pdf
 D68V3.png
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:05:34 09-04-13
Completed: 10:17:30 09-04-13
Elapsed: 00 hrs 11 mins 56 secs