CNV_ClinicalAnalysis_nozzle Execution Log 12:37 PM Thu Jun 6, '13

Running as user: cgaadm

cnv2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/OV-TP/3471936/all_lesions.conf_99.txt
Correlate_Clinical_Cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/OV-TP/3351705/OV-TP.clin.merged.picked.txt
Correlate_Clinical_Cnvs_onlysig2 filter cluster smaller than 3
Correlate_Clinical_Cnvs_onlysig2 output name OV-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: 12:37:11 06-06-13
Completed:
Elapsed: 00 hrs 01 mins 39 secs

step 1. cnv2cluster [id: 417457] 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/OV-TP/3471936/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: 12:37:13 06-06-13
Completed: 12:37:32 06-06-13
Elapsed: 00 hrs 00 mins 19 secs

step 2. Correlate_Clinical_Cnvs_onlysig [id: 417458]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00495:49
cluster label file all_lesions.conf_99.cnv.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/OV-TP/3351705/OV-TP.clin.merged.picked.txt
features used ALL
filter cluster smaller than 3
output name OV-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:
 D2V2.pdf
 D2V2.png
 D12V2.png
 D12V2.pdf
 D14V2.png
 D14V2.pdf
 D17V2.png
 D17V2.pdf
 D18V2.pdf
 D18V2.png
 D25V2.png
 D25V2.pdf
 D26V2.png
 D26V2.pdf
 D28V2.png
 D28V2.pdf
 D29V2.png
 D29V2.pdf
 D60V2.png
 D60V2.pdf
 test_dim_tbl.txt
 table.1.txt
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 12:37:13 06-06-13
Completed: 12:38:49 06-06-13
Elapsed: 00 hrs 01 mins 36 secs