Question: Run RepeatMasker problems
0
gravatar for xhfeng0307
4 weeks ago by
xhfeng03070
xhfeng03070 wrote:

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.

genome • 112 views
ADD COMMENTlink modified 4 weeks ago by h.mon24k • written 4 weeks ago by xhfeng03070

This might be helpful. solution

ADD REPLYlink written 4 weeks ago by Sishuo Wang170

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

ADD REPLYlink written 4 weeks ago by xhfeng03070

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).

ADD REPLYlink written 4 weeks ago by lieven.sterck4.5k

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.

ADD REPLYlink written 4 weeks ago by xhfeng03070

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)

ADD REPLYlink written 4 weeks ago by lieven.sterck4.5k

Thanks, I can check and follow the solution.

ADD REPLYlink written 29 days ago by xhfeng03070
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