jalwillcox

I ran into this same problem. I don't know why it happens, but I switched to using psi-cd-hit.pl, e.g. something like psi-cd-hit.pl -i input.fa -o output -c 0.75 -prog blastn...

Did you ever get this figured out? I'm running into the same (or a similar) problem. It looks like it may be related to where GSNAP is called in MToolBox-master/MToolBox/mapExome.py....

It's been a while since I used this, but at some point I had determined that the problem in my case was b/c I had a "." in the file...