RepeatMasker species error
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2.7 years ago
vasudha • 0

Hi,

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

Title :
Version :
Date :
Families :

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.

species repeatmasker • 2.8k views
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2.7 years ago
Michael 54k

The error message already contains the cause: RM doesn't have repeat libraries for mammals, provide the exact species name, e.g. ´homo sapiens´, ´mus musculus´, (´human´, ´mouse´ may also work) or whatever is your case and try again.

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I face a similar error when I write 'homo sapiens'.

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  • try with species human instead 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

RepeatMasker comes with a copy of the curated portion of Dfam ( Libraries/Dfam.h5 ) and will work out-of-the box with this library. This is a small library ( at this time ). There are two options for supplementing the main RepeatMasker library: The complete Dfam ( curated and uncurated families ) library may be downloaded from www.dfam.org in famdb HDF5 format and used to replace the distributed "Libraries/dfam.h5" file. For example: wget https://www.dfam.org/releases/Dfam_3.2/families/Dfam.h5.gz gunzip Dfam.h5.gz mv Dfam.h5 /usr/local/RepeatMasker/Libraries NOTE: This will overwrite the distributed Dfam.h5 file. and/or: The RepBase RepeatMasker Edition ( final version 10/26/2018 ) may be downloaded from www.girinst.org and unpaked in the RepeatMasker directory. For example: cp RepBaseRepeatMaskerEdition-20181026.tar.gz /usr/local/RepeatMasker/ cd /usr/local/RepeatMasker gunzip RepBaseRepeatMaskerEdition-20181026.tar.gz tar xvf RepBaseRepeatMaskerEdition-20181026.tar rm RepBaseRepeatMaskerEdition-20181026.tar Run Configure Script The program requires some initial configuration. This should also be re-run after updates to the library files. cd /usr/local/RepeatMasker perl ./configure

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  • Same thing happens with human.
  • Yes.
  • Yes.
  • Yes, it exists.
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check out this biostars question: it solved this issue of my repeat marker: RepeatMasker database error

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14 months ago

I faced the same issue, but it turned out to be something related to permission. I ran the command as sudo perl RepeatMasker ..... and then the problem got resolved.

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