CNV_ClinicalAnalysis_nozzle Execution Log 6:52 PM Mon Apr 8, '13

Running as user: cgaadm_deadline

cnv2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/GBM-TP/2859814/all_lesions.conf_99.txt
Correlate_Clinical_Cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/GBM-TP/2843145/1.GDAC_clinicalDataPicker.Finished/GBM-TP.clin.merged.picked.txt
Correlate_Clinical_Cnvs_onlysig2 filter cluster smaller than 3
Correlate_Clinical_Cnvs_onlysig2 output name GBM-TP
Correlate_Clinical_Cnvs_onlysig2 figure height 5
Correlate_Clinical_Cnvs_onlysig2 figure width 9
Correlate_Clinical_Cnvs_onlysig2 survival legend position OUT
Correlate_Clinical_Cnvs_onlysig2 pvalue cutoff 1
Correlate_Clinical_Cnvs_onlysig2 qvalue cutoff 0.25
Correlate_Clinical_Cnvs_onlysig2 make figure ONLYSIG
Correlate_Clinical_Cnvs_onlysig2 nozzle ver Nozzle.R1
Execution Times:
Submitted: 18:52:38 08-04-13
Completed:
Elapsed: 00 hrs 13 mins 23 secs

step 1. cnv2cluster [id: 372998] 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/GBM-TP/2859814/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: 18:52:48 08-04-13
Completed: 18:54:15 08-04-13
Elapsed: 00 hrs 01 mins 27 secs

step 2. Correlate_Clinical_Cnvs_onlysig [id: 372999]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00495:48
cluster label file all_lesions.conf_99.cnv.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/GBM-TP/2843145/1.GDAC_clinicalDataPicker.Finished/GBM-TP.clin.merged.picked.txt
features used ALL
filter cluster smaller than 3
output name GBM-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:
 D8V2.pdf
 D8V1.pdf
 D8V1.png
 D8V2.png
 D9V1.pdf
 D9V2.pdf
 D9V2.png
 D9V1.png
 D10V2.png
 D10V2.pdf
 D43V2.png
 D43V2.pdf
 D45V2.png
 D45V1.png
 D45V2.pdf
 D45V1.pdf
 D46V2.pdf
 D46V2.png
 D46V1.png
 D46V1.pdf
 D47V1.pdf
 D47V2.png
 D47V1.png
 D47V2.pdf
 D48V1.pdf
 D48V1.png
 D49V2.png
 D48V2.png
 D49V2.pdf
 D48V2.pdf
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 18:52:48 08-04-13
Completed: 19:06:00 08-04-13
Elapsed: 00 hrs 13 mins 12 secs