REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:

Dear Sir/Madam,

I'm using MutSigCV(v1.35) on GenePattern to discover driver mutations in some cohorts. The input files were generated by function 'prepareMutSig' in R package 'maftools' and their formats were consistent with example file.

However, some errors occured in the job, only 5 output files including 'categs.txt', 'coverage.txt',  'mutations.txt', 'stdout.txt' and 'stderr.txt''. The file 'sig_genes.txt' which should record driver genes with their p-values was not obtained successfully. 

The error messages was:

silent and nonsilent rates are too different Error in gp_MutSigCV (line 194)'

I checked the 'stdout.txt' and found that MutSigCV: PREPROCESS was finished, while the code ended in MutSigCV: RUN and the last line was 'Building n and N tables...'

I have consulted with staff of GenePattern Help Forum. And Their suggestion was to seek help at GATK forum since they were not familiar with the algorithm. I would appreciate it if there is a solution to my problem or any substitute methods to discover driver mutation in a cohort.

Regards,

Liu.