Maker (Gene annotation) RepeatMasker error

Question

[ricardoguerreiro2121]

Hey,

I'm very new in genome annotation and am following the tutorial for maker with my own plant genome and transcriptome assemblies. I filled my maker_opts file like this:

 genome=my_genassembly.fasta    
 est=my_RNAassembly.fasta    
 protein=  # kept this one empty    
 est2genome=1

I get immediate problems with the repeat masking. This is the error message:

At this time the hmmer search engine can only be used with the Dfam
database.  Please rerun your search without the -lib option or switch to
a different search engine.

ERROR: RepeatMasker failed    
--> rank=NA, hostname=hilbert115    
ERROR: Failed while doing repeat masking    
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:104

How do I change the default search engine? I don't see that in the config files. I also don't understand how to rerun the search without the -lib option.

This nice workflow appears to use a repeatmodeller to construct a custom repeat library. But I don't have it installed and the wiki section made me understand this is optional.

Its' just overwhelming.. No forum or FAQs to look into. Can someone help me please?

Thank you,
Ricardo

[Juke34]

It’s something related to the installation of repeatmasker. The dB seems to be missing. You can probably find more information into the MAKER-devel google group (archive of the MAKER mailing list) or by posting your question on the MAKER mailing list.

Do not annotate without repeat mask otherwise the result will be really bad.