Inconsistent naming convention warning

[fa8sanger]

I am getting this warning despite the naming convention has no problem. I did some tests and figured out it's just because the "-b" bed file contains entries from GL000008.2 at the beginning while "-a" starts with chr1. If I remove the non-primary chromosome entries from "-b" then the warning disappears. I may be wrong but I think this warning shouldn't be appearing.
Thank you for this awesome tool!!