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/COADREAD-TP/2859805/all_lesions.conf_99.txt
Correlate_Clinical_Cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COADREAD-TP/2843108/1.GDAC_clinicalDataPicker.Finished/COADREAD-TP.clin.merged.picked.txt
Correlate_Clinical_Cnvs_onlysig2 filter cluster smaller than 3
Correlate_Clinical_Cnvs_onlysig2 output name COADREAD-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: 18:52:29 08-04-13
Completed:
Elapsed: 00 hrs 14 mins 23 secs

step 1. cnv2cluster [id: 372959] 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/COADREAD-TP/2859805/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: 18:52:33 08-04-13
Completed: 18:54:18 08-04-13
Elapsed: 00 hrs 01 mins 44 secs

step 2. Correlate_Clinical_Cnvs_onlysig [id: 372960]

    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/COADREAD-TP/2843108/1.GDAC_clinicalDataPicker.Finished/COADREAD-TP.clin.merged.picked.txt
features used ALL
filter cluster smaller than 3
output name COADREAD-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:
 D5V7.pdf
 D5V7.png
 D6V7.pdf
 D6V5.png
 D6V9.pdf
 D6V9.png
 D6V7.png
 D6V5.pdf
 D14V5.png
 D14V5.pdf
 D15V5.pdf
 D15V7.png
 D14V9.pdf
 D14V7.pdf
 D14V9.png
 D15V5.png
 D14V7.png
 D16V5.pdf
 D16V5.png
 D15V9.pdf
 D15V9.png
 D16V7.png
 D15V7.pdf
 D16V7.pdf
 D18V9.png
 D18V9.pdf
 D18V7.pdf
 D18V7.png
 D24V5.png
 D24V5.pdf
 D25V5.png
 D25V3.pdf
 D25V3.png
 D25V5.pdf
 D25V9.pdf
 D26V3.png
 D26V3.pdf
 D25V9.png
 D26V5.png
 D27V3.pdf
 D26V5.pdf
 D26V9.png
 D27V5.png
 D27V5.pdf
 D27V3.png
 D26V9.pdf
 D27V9.png
 D27V9.pdf
 D38V10.pdf
 D38V10.png
 D46V3.pdf
 D46V9.pdf
 D46V5.png
 D46V3.png
 D46V9.png
 D46V7.pdf
 D46V7.png
 D46V5.pdf
 D47V7.png
 D47V5.pdf
 D47V9.pdf
 D47V5.png
 D47V9.png
 D47V7.pdf
 D47V12.png
 D47V12.pdf
 D58V5.pdf
 D58V5.png
 D62V1.pdf
 D62V1.png
 D64V5.png
 D64V5.pdf
 D64V9.png
 D64V9.pdf
 D64V7.png
 D64V7.pdf
 D66V3.pdf
 D66V3.png
 D66V5.pdf
 D66V5.png
 D67V9.pdf
 D67V7.png
 D67V5.pdf
 D67V7.pdf
 D67V3.pdf
 D67V3.png
 D67V9.png
 D67V5.png
 D68V3.pdf
 D68V5.png
 D68V9.png
 D68V7.pdf
 D68V5.pdf
 D68V7.png
 D68V9.pdf
 D68V3.png
 D69V3.pdf
 D69V7.png
 D69V3.png
 D69V5.pdf
 D69V9.png
 D69V5.png
 D69V7.pdf
 D69V9.pdf
 D70V7.pdf
 D70V7.png
 test_dim_tbl.txt
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 18:52:33 08-04-13
Completed: 19:06:50 08-04-13
Elapsed: 00 hrs 14 mins 17 secs