Hi

I am trying to align 190 full Mycobacterium tuberculosis genomes (~ 4mil base pairs each) with Mugsy.

It seems to run OK, but the maf output file is really small, and only contains:

##maf version=1 scoring=mugsy
##eof

As far as I can tell from other posts there should be scores here. It also ran really quickly (less than a minute) whereas all the other aligners I've been trying haven't worked at all. So I'm not sure that it's run properly.

There are no other error messages.

Any advice would be greatly appreciated.

Thanks
Tasha