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6.6 years ago
bioinforesearchquestions
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Hi,
I am trying to call copy number from mouse data using HMMcopy.
Created the wig files for my BAM samples. Also created mm10_gc.wig using gcCounter (HMMcopy). I am facing issues while creating the big wig file.
generateMap.pl -w 40 -i mm10 mm10.fa > mm10.bigwig
Getting the following error
HMMcopy_0.1.1/util/mappability/internal/fastaToRead missing, try recompiling...
It looks like your
HMMcopy
install is incomplete. Did you compile it yourself? If the said executable (fastaToRead
) is there then try adding that directory you$PATH
.Hi Genomax, I reinstalled the tool it worked.
I get the same error, I reinstalled and recompiling but still have the same error how should I fix it ?!
the error is
? how should I fix it
I was running the generatemap.pl CMd : util/mappability/generateMap.pl -w 35 -i /Users/mac/Desktop/NGS-/TriTrypDB-47_LmajorLV39c5_Genome.fasta > /Users/mac/Desktop/NGS-/TriTrypDB-47_LmajorLV39c5_Genome-map.bigwig but I get un error : Can't exec "bowtie": Not a directory at util/mappability/generateMap.pl line 105. bowtie not found, obtain from http://bowtie-bio.sourceforge.net/index.shtml and/or add to $PATH how should I fix it. N.B: i was getting bowtie from source , then I get the Path on HMMcopy and I fix on bash_profile. !!