I have a similar question.
I already masked my repeats using RepeatMasker, so I wanted to include these in Maker instead of having Maker re-do the masking.
Would my file opts look like this?
-----Repeat Masking (leave values blank to skip repeat masking)
model_org= #select a model organism for RepBase masking in RepeatMasker
rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker
repeat_protein=/home/apps/maker/2.31.9/data/te_proteins.fasta #provide a fasta file of transposable element proteins for RepeatRunner
rm_gff=/work/Geomicrobiology/msobol/IODP_329_SPG/1371E14H2/repeatmasker/1371E_14H2_contigs.fasta.out.gff3 #pre-identified repeat elements from an external GFF3 file
prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no
softmask=0 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
It says to leave everything blank if you want to skip repeat masking, so I wonder how that worked if you include a file in rm_gff?