Perhaps it's just naivete on my part (I'm not at all familiar with "try/catch/throw exception" style error handling), but I find it odd that your error-report stack trace ends with this:

STACK: tagfinder.pl:257
[download]

which would suggest to me that the your script that uses those Bio modules and throws that stack trace (i.e. the code that you wrote yourself) should have at least 257 lines in it. The thing that's odd about it is that the code you posted here isn't that long -- it's only 172 lines.

So I don't think it makes a lot of sense to look for the error in the code you posted.

Apart from that, I wonder if maybe you are getting your files confused -- like maybe you are passing your file full of numbers to a function that is expecting a file full of nucleotide letters, or something like that.

Anyway, ask yourself whether you can break things up into smaller components, identify the particular piece that is causing trouble, and present just a small snippet of code and data to demonstrate the problem -- something that can be run by anyone who has the necessary modules installed (which wouldn't include me, I'm afraid). Good luck with that...