fixes some issues with miseq projects

A project I can't name generated an error, and this should fix it
Catching an AssertionError? That's weird. Because assertions are supposed to model a code contract, statements that are supposed to be true in any conceivable circumstance, else the code is incorrect.

If one catches an AssertionError, it's the same as saying: I know there's a bug in the code, but I don't care.

Maybe the problem is lower in the code? The AssertionError maybe ought to be a ValueError, TypeError or such, which would be a better description of what is going on.