Run RepeatMasker problems
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.
• 4,176 views
•
link
updated
by
h.mon
•
written
by
xhfeng0307 •
•
written
by
xhfeng0307 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
error invoking makeblastdb
written by SeaStar •
-
Install RepeatMasker "Enter path" problems
written by xhfeng0307 •
-
Repeat Masker libraries
written by wambuimbichi •
-
RepeatMasker Library Help
written by chris.bonner •
-
Specify output dir when downloading snpEff database?
written by abe •
This might be helpful. solution
Thanks, Sishuo, I will take a look on the post. Not sure could fix it.
Looks like you are missing the taxonomic data file.
Can you have a look in this folder:
/home/feng/anaconda3/share/RepeatMasker/RepeatMaskerand see if there is such a file available (or post the listing of that folder).It seems like I do not have this folder,
~/anaconda3/share/RepeatMasker$ cd RepeatMasker bash: cd: RepeatMasker: Not a directoryI usedconda install -c bioconda repeatmaskerto installed this software, and not sure the problem in it. Thanks.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
Librariesin 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)Thanks, I can check and follow the solution.