CNV_cluster_nozzle Execution Log 9:50 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/LAML-TB/2859850/all_lesions.conf_99.txt
Correlate_Cluster_cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LAML-TB/2907506/1.GDAC_mergedClustering.Finished/LAML-TB.transferedmergedcluster.txt
Correlate_Cluster_cnvs_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvs_onlysig2 output name LAML-TB
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: 09:50:48 09-04-13
Completed:
Elapsed: 00 hrs 02 mins 06 secs

step 1. cnv2cluster [id: 375888] 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/LAML-TB/2859850/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: 09:51:07 09-04-13
Completed: 09:52:22 09-04-13
Elapsed: 00 hrs 01 mins 15 secs

step 2. Correlate_Cluster_cnvs_onlysig [id: 375889]

    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/LAML-TB/2907506/1.GDAC_mergedClustering.Finished/LAML-TB.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name LAML-TB
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:
 D1V1.pdf
 D1V1.png
 D2V2.pdf
 D3V1.png
 D2V2.png
 D3V2.png
 D3V2.pdf
 D3V1.pdf
 D6V2.pdf
 D4V1.pdf
 D5V1.pdf
 D6V2.png
 D5V1.png
 D6V1.pdf
 D6V1.png
 D4V1.png
 D7V1.pdf
 D7V1.png
 D7V6.png
 D7V5.pdf
 D7V5.png
 D7V6.pdf
 D9V1.pdf
 D9V2.pdf
 D9V2.png
 D9V1.png
 D9V5.png
 D11V2.png
 D10V1.pdf
 D10V3.pdf
 D11V1.png
 D11V1.pdf
 D10V4.png
 D10V2.png
 D9V6.png
 D10V1.png
 D10V3.png
 D10V2.pdf
 D9V5.pdf
 D10V4.pdf
 D9V6.pdf
 D11V5.png
 D11V2.pdf
 D11V5.pdf
 D12V5.png
 D11V6.pdf
 D12V2.png
 D12V6.pdf
 D12V1.pdf
 D11V6.png
 D12V2.pdf
 D12V5.pdf
 D12V6.png
 D12V1.png
 D14V1.png
 D14V2.png
 D14V2.pdf
 D14V1.pdf
 D16V1.png
 D17V1.pdf
 D16V1.pdf
 D17V1.png
 D17V6.pdf
 D17V6.png
 D17V2.png
 D18V1.png
 D17V2.pdf
 D18V2.pdf
 D18V1.pdf
 D18V2.png
 D20V1.png
 D19V2.png
 D19V2.pdf
 D20V1.pdf
 D19V1.pdf
 D19V1.png
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 09:51:07 09-04-13
Completed: 09:52:53 09-04-13
Elapsed: 00 hrs 01 mins 46 secs