[maker-devel] Maker Repeat Masking model_org option with D

[Macguigan, Daniel]

Hello,

I have a straightforward question, but I can't seem to find the answer anywhere. Is it possible to specify a species/clade for Dfam masking using the model_org option in the *maker_opts.ctl file? The comment on this option says "select a model organism for RepBase masking in RepeatMasker."

As an example, I currently have RepeatMasker configured to use Dfam. It works fine when I run RepeatMasker on its own with a command like this.

RepeatMasker -gff -species Arthropoda -dir ./RMask_dir

However, when I specify "model_org=Arthropoda" in the maker_opts.ctl file, I get a message "ERROR: Could not determine if RepBase is installed" 

I am using RepeatMasker v.4.1.1 and Maker v.3.01.03.

Thanks,

Dan

--

Dan MacGuigan, PhD

he-him-his

Postdoctoral Fellow

Department of Biological Sciences

University at Buffalo

@DMacGuig