I am trying to generate a set of null sequences with the package gkmSVM. It works perfectly for human but for mouse it does not. I am wondering if any of you have never used this package for mice and had the same problem.

I use the function genNullseqs function as follow:  

library(gkmSVM) library(BSgenome.Mmusculus.UCSC.mm10)
library(BSgenome.Mmusculus.UCSC.mm10.masked)
library(IRanges)

genome=BSgenome.Mmusculus.UCSC.mm10.masked

fileBedBreaks="Rep1.intersec.Rep2.cov.major2.sort.uniq.bed"
fileFastaPos="Rep1.intersec.Rep2.cov.major2.all.sort.uniq.bed.pos.fa"
fileBedNeg="Rep1.intersec.Rep2.cov.major2.all.sort.uniq.Random.gkmSVM.bed"
fileFastaNeg="Rep1.intersec.Rep2.cov.major2.all.sort.uniq.Random.gkmSVM.fa"
genNullSeqs(inputBedFN=fileBedBreaks,nMaxTrials=5,xfold=2,genome=genome,
            outputPosFastaFN=fileFastaPos,outputBedFN=fileBedNeg,outputNegFastaFN=fileFastaNeg)

This is the error:  

Error in normalizeDoubleBracketSubscript(i, x, exact = exact) : subscript "TRF" matches no name

​​Any idea of what is going on?