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RepeatMasker version 4.1.5 speciess not known error

Hi,

I am getting below error in RepeatMasker (version 4.1.5). Tried running it locally with just default parameters and running it in Usegalaxy but still getting the same error. Tried different values for species (such as human, mamal, no value ) but still getting the same error.

Species "homo sapiens" is not known to RepeatMasker. There may not be any TE families defined in the libraries for this species/clade or there may be an error in the spelling. Please check your entry against the NCBI Taxonomy database and/or try using a broader clade or related species instead. The full list of species/clades defined in the library may be obtained using the famdb.py script.

Thanks for reading the question.

Cheers, Ambi.

repeatmasker repeatmasker4.1.5
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updated by biofalconch biofalconch • written by ambi1999 • ambi1999

Repeatmasked human genome is already available at Ensembl:

https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_rm.toplevel.fa.gz
https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.toplevel.fa.gz

* 'dna_rm' - masked genomic DNA.  Interspersed repeats and low
     complexity regions are detected with the RepeatMasker tool and masked
     by replacing repeats with 'N's.  
* 'dna_sm' - soft-masked genomic DNA. All repeats and low complexity regions
    have been replaced with lowercased versions of their nucleic base
• 0 views • link
written by GenoMax GenoMax

1 answer

Just in case you want to continue trying RepeatMasker yourself, I checked the code and here is what it says:

=item -species  <query species>   

Specify the species or clade of the input sequence.  The species
name must be a valid NCBI Taxonomy Database species name and be
contained in the RepeatMasker repeat database.  Some examples are:

  -species human
  -species mouse
  -species rattus
  -species "ciona savignyi"
  -species arabidopsis

So basically you just need -species human :)

• 0 views • link
written by biofalconch biofalconch

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