I am trying to run RepeatMasker with the following command:
RepeatMasker --species mammals seq1.fasta
But I get the following error:
RepeatMasker version 4.1.1 Search Engine: HMMER [ 3.3.2 (Nov 2020) ]
Using Master RepeatMasker Database: /Volumes/Seagate/Vasudha/Tools/RepeatMasker/Libraries/RepeatMaskerLib.h5
Species "mammals" 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.
Please help me resolve this.
I face a similar error when I write 'homo sapiens'.
try with species
humaninstead of homo sapiens
Did you install the repeatmasker according to the instructions on https://www.repeatmasker.org/RepeatMasker/ ?
Did you run the configure script?
Check if the file Libraries/Dfam.h5 exists.
Install RepeatMasker Libraries
check out this biostars question: it solved this issue of my repeat marker: RepeatMasker database error