CNV_ClinicalAnalysis_nozzle Execution Log 6:54 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/LAML-TB/2859850/all_lesions.conf_99.txt
Correlate_Clinical_Cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LAML-TB/2843136/1.GDAC_clinicalDataPicker.Finished/LAML-TB.clin.merged.picked.txt
Correlate_Clinical_Cnvs_onlysig2 filter cluster smaller than 3
Correlate_Clinical_Cnvs_onlysig2 output name LAML-TB
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: 18:54:55 08-04-13
Completed:
Elapsed: 00 hrs 23 mins 37 secs

step 1. cnv2cluster [id: 373068] 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/LAML-TB/2859850/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: 18:54:55 08-04-13
Completed: 19:11:06 08-04-13
Elapsed: 00 hrs 16 mins 11 secs

step 2. Correlate_Clinical_Cnvs_onlysig [id: 373069]

    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/LAML-TB/2843136/1.GDAC_clinicalDataPicker.Finished/LAML-TB.clin.merged.picked.txt
features used ALL
filter cluster smaller than 3
output name LAML-TB
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:
 D6V1.pdf
 D6V1.png
 D8V2.pdf
 D7V1.pdf
 D7V1.png
 D9V1.png
 D8V2.png
 D9V1.pdf
 D14V1.png
 D15V2.png
 D14V1.pdf
 D15V2.pdf
 table.1.txt
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 18:54:55 08-04-13
Completed: 19:18:30 08-04-13
Elapsed: 00 hrs 23 mins 35 secs