RepeatMasker sequence identifier error
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3 months ago
sumin.jo • 0

Hello,

Could anyone help me to use RepeatMasker?

I was trying to install RepeatMasker following instructions in RepeatMasker.org webpage. However, I keep facing errors related with search engines.

Thus, I wiped everything and installed RepeatMasker using conda.

conda install -c bioconda repeatmasker.

Then everything installed well, and I ran my fasta file.

GenomeFasta="/fasta file path"
OutDir="output directory"
RepeatMasker -species human -nolow -dir ${OutDir} -gff -u ${GenomeFasta}

And I got this error:

FastaDB::_cleanIndexAndCompact(): Fasta file contains a sequence identifier which is too long ( max id length = 50 )
 at /home/sumin/anaconda3/share/RepeatMasker/RepeatMasker line 718.

What should I do? Any feedback would be appreciated!

RepeatMasker • 227 views
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Fasta file contains a sequence identifier which is too long ( max id length = 50 )

Error is clear. You have a fasta file with ID's that are long. You will want to truncate them (after first space in the fasta header may be one option but make sure remaining part of ID is unique). Here is an example answer: Fasta header trimming

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the error states that you need to trim the fasta header.

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