RepeatMasker errors and missing output files
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9.0 years ago
pdm37 ▴ 10

I am using RepeatMasker to identify retrotransposons in my non-model organism's assembled transcriptome.

When I tried the following: RepeatMasker xxx.fa -species vertebrates -engine RMBlast

it produced a .masked file and a .cat file but no .tbl and lots and lots of .err files (trfResultsxxxx.err) and lots of empty .out files. When I ran ProcessRepeats on the .cat file it made a .tbl and a .out file and a new .masked file which is of a different size than the .masked file I got at first. Is there a way to figure out what was causing the errors and why those output files weren't written? The IDs in the library file are in the suggested format (and RepeatMasker created the library anyway from RepBase for "vertebrates").

Is it possible that the problem is due to using such a general "species". When I went down a few clades it didn't generate these errors but I want to compare several distantly related species and 'vertebrates' is their common ancestor so I thought it would be a good library to use for all.

Thanks!

software error • 3.5k views
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Entering edit mode
9.0 years ago
Buttonwood ▴ 40
I used to run RepeatMasker by this:
RepeatMasker -nolow -no_is -norna -parallel 1 -lib /data/tanhao/lib/RepeatMasker/Libraries/RepeatMasker.lib genome.fa >repeatmask.log 2>repeatmask.log.2 &;

Hope it will help you.

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