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/ESCA-TP/2859763/all_lesions.conf_99.txt
Correlate_Cluster_cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/ESCA-TP/2907363/1.GDAC_mergedClustering.Finished/ESCA-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvs_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvs_onlysig2 output name ESCA-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: 09:50:34 09-04-13
Completed:
Elapsed: 00 hrs 02 mins 16 secs

step 1. cnv2cluster [id: 375825] 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/ESCA-TP/2859763/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: 09:50:39 09-04-13
Completed: 09:51:27 09-04-13
Elapsed: 00 hrs 00 mins 48 secs

step 2. Correlate_Cluster_cnvs_onlysig [id: 375826]

    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/ESCA-TP/2907363/1.GDAC_mergedClustering.Finished/ESCA-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name ESCA-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:
 D17V1.pdf
 D17V1.png
 table.1.txt
 nozzle.html
 nozzle.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 09:50:39 09-04-13
Completed: 09:52:49 09-04-13
Elapsed: 00 hrs 02 mins 10 secs