Is there a way to run this for a custom MT genome?

[sheinasim]

I have several complete MT genome sequences for an insect species along with annotations. Would it be possible to run this with a custom MT genome?

When I try to read in my bam it says, "Error in getMT("all_mt_aligned.coverage.mapped.bam") : Currently unsupported mitochondrial reference detected; exiting."

Thanks!