CNV_cluster_nozzle Execution Log 1:52 PM Fri May 24, '13

Running as user: cgaadm

cnv2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/HNSC-TP/3140480/all_lesions.conf_99.txt
Correlate_Cluster_cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/HNSC-TP/3144284/1.GDAC_mergedClustering.Finished/HNSC-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvs_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvs_onlysig2 output name HNSC-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: 13:52:44 24-05-13
Completed:
Elapsed: 00 hrs 01 mins 30 secs

step 1. cnv2cluster [id: 411546] 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/HNSC-TP/3140480/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: 13:52:44 24-05-13
Completed: 13:52:59 24-05-13
Elapsed: 00 hrs 00 mins 15 secs

step 2. Correlate_Cluster_cnvs_onlysig [id: 411547]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00507:4
cluster label file all_lesions.conf_99.cnv.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/HNSC-TP/3144284/1.GDAC_mergedClustering.Finished/HNSC-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name HNSC-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:
 D1V1.pdf
 D1V1.png
 D2V2.pdf
 D1V5.pdf
 D2V2.png
 D1V7.pdf
 D1V2.png
 D1V2.pdf
 D1V5.png
 D2V1.pdf
 D1V7.png
 D2V1.png
 D3V1.png
 D4V1.pdf
 D4V2.pdf
 D3V2.png
 D3V2.pdf
 D3V1.pdf
 D4V2.png
 D4V1.png
 D4V6.pdf
 D5V1.pdf
 D4V6.png
 D5V1.png
 D6V1.png
 D7V1.pdf
 D7V1.png
 D8V1.pdf
 D6V1.pdf
 D8V1.png
 D10V1.pdf
 D10V2.png
 D9V1.pdf
 D9V2.pdf
 D10V1.png
 D9V2.png
 D9V1.png
 D10V2.pdf
 D12V1.pdf
 D12V1.png
 D13V1.pdf
 D13V2.png
 D13V5.png
 D13V1.png
 D13V6.pdf
 D13V2.pdf
 D13V5.pdf
 D13V6.png
 D14V1.png
 D15V1.pdf
 D15V1.png
 D13V8.png
 D14V1.pdf
 D13V8.pdf
 D16V1.png
 D16V1.pdf
 D17V1.pdf
 D17V1.png
 D18V1.png
 D18V2.pdf
 D18V1.pdf
 D18V2.png
 D19V1.pdf
 D19V1.png
 D20V1.png
 D21V1.png
 D20V2.png
 D20V2.pdf
 D20V1.pdf
 D23V1.png
 D22V2.pdf
 D22V1.png
 D22V2.png
 D21V1.pdf
 D22V1.pdf
 D25V1.pdf
 D25V1.png
 D23V1.pdf
 D26V1.pdf
 D26V1.png
 D26V2.png
 D26V2.pdf
 D26V5.pdf
 D26V5.png
 D27V2.png
 D27V2.pdf
 D27V1.pdf
 D26V7.pdf
 D26V7.png
 D27V1.png
 D27V7.png
 D27V7.pdf
 D29V7.pdf
 D29V7.png
 D32V1.pdf
 D31V2.pdf
 D31V1.png
 D32V1.png
 D31V2.png
 D31V1.pdf
 D33V2.png
 D33V1.pdf
 D32V2.pdf
 D32V2.png
 D33V2.pdf
 D33V1.png
 D34V1.png
 D34V2.png
 D34V2.pdf
 D34V1.pdf
 D36V2.pdf
 D36V2.png
 D35V2.pdf
 D35V1.png
 D36V1.png
 D35V1.pdf
 D36V1.pdf
 D35V2.png
 D37V1.pdf
 D37V1.png
 D37V2.pdf
 D37V2.png
 D38V1.png
 D38V1.pdf
 D38V2.pdf
 D38V2.png
 D39V2.png
 D39V2.pdf
 D39V1.pdf
 D39V1.png
 D40V2.pdf
 D40V6.png
 D41V2.png
 D40V1.pdf
 D40V6.pdf
 D41V2.pdf
 D40V1.png
 D40V2.png
 D43V1.png
 D43V1.pdf
 D44V2.png
 D44V1.pdf
 D44V2.pdf
 D44V1.png
 D45V2.png
 D46V2.pdf
 D47V1.png
 D46V2.png
 D46V1.png
 D46V1.pdf
 D45V1.png
 D45V2.pdf
 D45V1.pdf
 D48V1.pdf
 D49V1.pdf
 D47V1.pdf
 D48V1.png
 D49V1.png
 D50V1.pdf
 D50V1.png
 D51V1.pdf
 D51V1.png
 D52V2.png
 D52V7.png
 D52V1.pdf
 D52V1.png
 D52V7.pdf
 D52V2.pdf
 D54V2.pdf
 D54V1.png
 D54V2.png
 D53V1.pdf
 D54V1.pdf
 D53V1.png
 D56V1.png
 D56V1.pdf
 D54V6.png
 D56V2.pdf
 D54V6.pdf
 D56V2.png
 D57V1.pdf
 D57V6.png
 D57V6.pdf
 D57V5.pdf
 D57V5.png
 D57V1.png
 D57V2.png
 D57V2.pdf
 D59V2.png
 D59V2.pdf
 D59V5.pdf
 D59V6.pdf
 D59V6.png
 D59V5.png
 D61V7.png
 D61V7.pdf
 D61V2.pdf
 D61V2.png
 D61V5.pdf
 D61V5.png
 D61V6.pdf
 D61V6.png
 D62V6.pdf
 D62V6.png
 D65V1.png
 D64V2.png
 D65V1.pdf
 D64V2.pdf
 D64V1.png
 D64V1.pdf
 D65V2.pdf
 D66V1.pdf
 D66V1.png
 D65V2.png
 D67V1.png
 D67V2.png
 D67V1.pdf
 D68V1.png
 D67V2.pdf
 D68V1.pdf
 D69V2.pdf
 D69V1.png
 D69V2.png
 D69V1.pdf
 D70V7.pdf
 D70V7.png
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 13:52:44 24-05-13
Completed: 13:54:13 24-05-13
Elapsed: 00 hrs 01 mins 29 secs