Run RepeatMasker problems

Question

[xhfeng0307]

Hello, When I run RepeatMasker, it has error shows below:

    RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $
Search Engine: NCBI/RMBLAST [ 2.2.27+ ]
Rebuilding RepeatMaskerLib.embl library
  - Read in 312 sequences from /home/feng/anaconda3/share/RepeatMasker/Libraries/DfamConsensus.embl
RepeatMaskerLib.embl: 312 total sequences.
Taxononmy::new() Could not locate the taxonomy data file!
 at /home/feng/anaconda3/share/RepeatMasker/RepeatMasker line 638.

Can anyone help to see the problem? Thanks so much.

[Sishuo Wang]

This might be helpful. solution

[xhfeng0307]

Thanks, Sishuo, I will take a look on the post. Not sure could fix it.

[lieven.sterck]

Looks like you are missing the taxonomic data file.

Can you have a look in this folder: /home/feng/anaconda3/share/RepeatMasker/RepeatMasker and see if there is such a file available (or post the listing of that folder).

[xhfeng0307]

It seems like I do not have this folder, ~/anaconda3/share/RepeatMasker$ cd RepeatMasker bash: cd: RepeatMasker: Not a directory I used conda install -c bioconda repeatmasker to installed this software, and not sure the problem in it. Thanks.

[lieven.sterck]

Yes, that will likley be so, as that points the the repeatmasker binary (== the program itself) (my bad btw for pointing you there)

You will need to look for a directory called Libraries in that location and so on. On top of that do indeed follow the steps Sishuo Wang pointed you to (setting the LIB path for repeatmasker)

[xhfeng0307]

Thanks, I can check and follow the solution.