Hey,

I'm trying to preform a bisulfite alignment using gmapR package. This is my code:

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library("gmapR")

ggd<-GmapGenomeDirectory(file.path(getwd(),"indices"), create=T)

gg<-GmapGenome(file.path(getwd(),"test.fa"), directory=ggd, name="seq", create=T)

cmet_index <- cmetindex(gg)

gsnapPar <- GsnapParam(genome=gg, unique_only=FALSE, suboptimal_levels=2L, npaths=1000L, novelsplicing=FALSE,clip_overlap=FALSE, mode="cmet-stranded")

gsnapOutput<- gsnap(input_a="/primers/Fprimers.fasta",input_b="/primers/Rprimers.fasta", params=gsnapPar, output = "primer.out")

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Everything is going well until starting the alignment using gsnap function so I am getting the follwoing error:

Error in .system_gsnap(commandLine("gsnap")) : Execution of gsnap failed, command-line: /lib/R/library/gmapR/usr/bin/gsnap --db=seq --dir=/indices --suboptimal-levels=2 --mode=cmet-stranded --npaths=1000 --format=sam --split-output=primer.out /primers/Fprimers.fasta primers/Rprimers.fasta 2> /tmp/RtmpmHpuzf/gsnap-stderr2e90db57601log'; last output line: 'Cannot find genomic index files in either current or old format'

Any advice?

Thanks in advance!

Best,

Amer