Problem with Dfam-Database and the RepeatClassifier function of repeat modeler

Question

[WaspInSpace]

Hello everyone!

I'm trying to do a repeat modelling for my de novo genome because a lot of the repeats masked with repeatmasker are marked as unclassified. For this I use the RepeatClassifier included in repeat modeler. I got the version 2.0.7 via bioconda. This has an included version of repeatmasker (4.1.9).

When I run my genome against the database delivered with bioconda everything runs fine but a lot of reads are still not classified after the run, so the repeat modeler is not very helpfull/necessary. Furthermore, I get the warning:

#   - 237 consensus sequences
# !!!! WARNING !!!! -- The curated TE consensus library does not appear to be complete.
#                      This may result in poor clasification performance.  Please
#                      ensure that you have the latest version of RepeatMasker
#                      installed and that you have installed the complete set of Dfam
#                      partitions.

So I tried to use the latest Dfam-library that I also used for better results in repeat masker before (drawn from that source: https://www.dfam.org/releases/current/families/Dfam-RepeatMasker.lib.gz.

After that, the warning disappeared but the program fails with

    #   - 26292 consensus sequences
  - Looking for simple/tandem and low complexity sequences..
  - Looking for similarity to known repeat proteins..
  - Looking for similarity to known repeat consensi..

and

RepeatClassifier: ERROR from search engine (255) 

The lib and all of it's subfiles were copied into the right directory in the conda-environment, a backup of the included db is in another folder elsewhere. The database was named RepeatMasker.lib, so it can be used by the RepeatModeler. The program runs for at least 15 minutes before it stops. Nothing has been changed about the Pep-lib.

The headers of the old and the new database look exactly the same.

Has anybody else encountered the same problem and how did you solve it? If your RepeatClassifier works, guys, what library do you use for your comparisons?

I would be very gratefull for any supporting hint! If you have sucessfully used RepeatClassifier or know the background of this error, please just take your time for a quick answer to tell me what you did.

Best wishes!

[GenoMax]

In case you don't get an answer consider posting an issue here: https://github.com/Dfam-consortium/RepeatModeler/issues

There should also be a repeatmodeler.log file that you can check.