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/KIRP-TP/2859841/all_lesions.conf_99.txt
Correlate_Clinical_Cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRP-TP/2843150/1.GDAC_clinicalDataPicker.Finished/KIRP-TP.clin.merged.picked.txt
Correlate_Clinical_Cnvs_onlysig2 filter cluster smaller than 3
Correlate_Clinical_Cnvs_onlysig2 output name KIRP-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: 18:52:54 08-04-13
Completed:
Elapsed: 00 hrs 22 mins 19 secs

step 1. cnv2cluster [id: 373057] 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/KIRP-TP/2859841/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: 18:53:14 08-04-13
Completed: 19:01:00 08-04-13
Elapsed: 00 hrs 07 mins 46 secs

step 2. Correlate_Clinical_Cnvs_onlysig [id: 373058]

    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/KIRP-TP/2843150/1.GDAC_clinicalDataPicker.Finished/KIRP-TP.clin.merged.picked.txt
features used ALL
filter cluster smaller than 3
output name KIRP-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:
 D6V8.png
 D6V8.pdf
 D15V1.pdf
 D15V1.png
 D32V1.pdf
 D32V1.png
 test_dim_tbl.txt
 D33V1.pdf
 D33V1.png
 table.1.txt
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 18:53:14 08-04-13
Completed: 19:15:12 08-04-13
Elapsed: 00 hrs 21 mins 58 secs