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/COADREAD-TP/2859805/all_lesions.conf_99.txt
Correlate_Cluster_cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/COADREAD-TP/2909317/1.GDAC_mergedClustering.Finished/COADREAD-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvs_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvs_onlysig2 output name COADREAD-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: 10:05:35 09-04-13
Completed:
Elapsed: 00 hrs 02 mins 57 secs

step 1. cnv2cluster [id: 376195] 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/COADREAD-TP/2859805/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: 10:05:35 09-04-13
Completed: 10:06:15 09-04-13
Elapsed: 00 hrs 00 mins 40 secs

step 2. Correlate_Cluster_cnvs_onlysig [id: 376196]

    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/COADREAD-TP/2909317/1.GDAC_mergedClustering.Finished/COADREAD-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name COADREAD-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
 D2V8.png
 D2V7.png
 D2V8.pdf
 D2V7.pdf
 D2V3.pdf
 D3V3.png
 D3V3.pdf
 D5V3.pdf
 D5V3.png
 D6V7.pdf
 D6V8.png
 D6V4.pdf
 D6V7.png
 D6V8.pdf
 D6V4.png
 D6V3.png
 D6V3.pdf
 D8V3.pdf
 D7V3.png
 D7V3.pdf
 D8V3.png
 D9V3.png
 D9V3.pdf
 D10V3.pdf
 D10V3.png
 D10V7.png
 D10V7.pdf
 D12V1.pdf
 D12V1.png
 D12V7.pdf
 D12V3.png
 D12V3.pdf
 D12V8.pdf
 D12V8.png
 D12V7.png
 D14V1.png
 D14V4.pdf
 D14V7.pdf
 D14V2.png
 D14V2.pdf
 D14V1.pdf
 D14V7.png
 D14V4.png
 D14V3.pdf
 D14V3.png
 D14V8.pdf
 D15V4.pdf
 D15V1.pdf
 D15V3.png
 D15V1.png
 D15V3.pdf
 D15V4.png
 D15V2.png
 D15V2.pdf
 D14V8.png
 D15V7.png
 D16V1.png
 D15V8.pdf
 D15V8.png
 D15V7.pdf
 D16V2.pdf
 D16V4.png
 D16V1.pdf
 D16V4.pdf
 D16V2.png
 D16V3.pdf
 D16V3.png
 D16V8.pdf
 D16V7.pdf
 D16V7.png
 D16V8.png
 D18V3.png
 D18V3.pdf
 D18V7.png
 D19V3.pdf
 D19V3.png
 D18V7.pdf
 D19V7.png
 D19V7.pdf
 D20V3.png
 D20V4.png
 D20V3.pdf
 D20V7.pdf
 D20V4.pdf
 D20V7.png
 D22V3.png
 D21V3.pdf
 D21V3.png
 D22V3.pdf
 D23V3.pdf
 D23V3.png
 D23V7.pdf
 D23V2.pdf
 D23V7.png
 D23V2.png
 D24V4.png
 D24V8.pdf
 D24V2.png
 D24V7.png
 D23V8.png
 D24V1.png
 D24V2.pdf
 D24V3.pdf
 D24V4.pdf
 D23V8.pdf
 D24V8.png
 D24V3.png
 D24V7.pdf
 D24V1.pdf
 D25V1.pdf
 D25V3.pdf
 D25V3.png
 D25V4.png
 D25V2.png
 D25V4.pdf
 D25V1.png
 D25V2.pdf
 D26V1.pdf
 D26V1.png
 D25V7.png
 D26V2.png
 D26V2.pdf
 D25V7.pdf
 D26V3.png
 D25V8.png
 D25V8.pdf
 D26V4.pdf
 D26V4.png
 D26V8.pdf
 D26V8.png
 D26V7.pdf
 D26V7.png
 D27V1.png
 D26V3.pdf
 D27V7.png
 D27V8.png
 D27V4.png
 D27V2.png
 D27V2.pdf
 D27V1.pdf
 D27V3.pdf
 D27V4.pdf
 D27V8.pdf
 D27V7.pdf
 D27V3.png
 D28V3.pdf
 D28V3.png
 D29V1.png
 D29V4.png
 D29V3.png
 D29V4.pdf
 D29V1.pdf
 D29V3.pdf
 D29V8.pdf
 D29V7.pdf
 D29V7.png
 D29V8.png
 D30V4.png
 D30V4.pdf
 D30V3.png
 D30V3.pdf
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 D38V3.pdf
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 D39V3.pdf
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 D38V7.pdf
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 D38V8.pdf
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 D39V7.pdf
 D40V3.pdf
 D40V7.pdf
 D40V3.png
 D40V7.png
 D39V7.png
 D39V8.pdf
 D41V7.png
 D41V7.pdf
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 D41V3.png
 D41V3.pdf
 D40V8.pdf
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 D46V3.pdf
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 D46V3.png
 D46V7.pdf
 D46V7.png
 D46V4.pdf
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 D47V3.pdf
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 D51V3.png
 D51V3.pdf
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 D53V3.pdf
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 D54V7.pdf
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 D54V8.png
 D56V3.pdf
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 D58V1.pdf
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 D58V1.png
 D58V2.pdf
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 D58V2.png
 D58V4.pdf
 D58V7.pdf
 D58V4.png
 D58V5.pdf
 D58V5.png
 D58V8.png
 D58V8.pdf
 D58V3.pdf
 D59V3.pdf
 D59V7.pdf
 D59V8.png
 D59V3.png
 D59V7.png
 D59V8.pdf
 D60V7.pdf
 D60V7.png
 D60V8.pdf
 D60V3.png
 D60V8.png
 D60V3.pdf
 D61V3.png
 D61V3.pdf
 D61V7.png
 D61V8.pdf
 D61V7.pdf
 D61V8.png
 D64V2.png
 D64V3.png
 D64V3.pdf
 D64V2.pdf
 D64V1.png
 D64V4.pdf
 D64V1.pdf
 D64V4.png
 D66V1.pdf
 D64V8.png
 D66V1.png
 D64V7.png
 D64V8.pdf
 D64V7.pdf
 D66V3.pdf
 D66V7.png
 D66V2.png
 D66V3.png
 D66V8.pdf
 D66V7.pdf
 D66V8.png
 D66V2.pdf
 D66V4.png
 D66V4.pdf
 D67V4.png
 D67V1.png
 D67V2.png
 D67V7.png
 D67V1.pdf
 D67V2.pdf
 D67V7.pdf
 D67V3.pdf
 D67V3.png
 D67V4.pdf
 D67V8.png
 D68V3.pdf
 D68V2.pdf
 D68V4.png
 D67V8.pdf
 D68V1.png
 D68V1.pdf
 D68V2.png
 D68V7.png
 D68V3.png
 D68V4.pdf
 D69V3.pdf
 D69V2.pdf
 D69V3.png
 D68V7.pdf
 D69V4.pdf
 D68V8.png
 D68V8.pdf
 D69V4.png
 D69V1.png
 D69V2.png
 D69V1.pdf
 D69V8.png
 D69V7.png
 D70V3.pdf
 D69V8.pdf
 D69V7.pdf
 D70V3.png
 D71V3.png
 D72V3.png
 D72V3.pdf
 D71V3.pdf
 D72V4.pdf
 D72V4.png
 D73V3.png
 D73V3.pdf
 D73V4.png
 D73V4.pdf
 D74V3.pdf
 D74V3.png
 D75V3.pdf
 D75V3.png
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:05:35 09-04-13
Completed: 10:08:30 09-04-13
Elapsed: 00 hrs 02 mins 55 secs