Encountered the following issue:

RepeatModeler Round # 1

Searching for Repeats -- Sampling from the database...

Gathering up to 40000000 bp Final Sample Size = 40000844 bp ( 39718874 non ambiguous ) Num Contigs Represented = 14077 -- Running RepeatScout on the sequences... RepeatScout: Running build_lmer_table ( l = 14 ).. RepeatScout: Running RepeatScout.. Program duration is 565.0 sec = 9.4 min = 0.2 hr Collecting repeat instances... -- Refining Family R=728 / 0 ( RS Elements: 664, Using 100 ): MultAln::buildConsensusFromArray: Matrix alphabet doesn't include the letters: A, B at /users/PAS0615/osu8353/RepeatModeler/Refiner line 395. RepeatModeler: Could not open refined model /users/PAS0615/osu8353/RepeatModeler /RM_31461.MonMay220946262017/round-1/family-0.fa.refiner_cons!

Has anyone experienced this and found a workaround?