genbank:

You're sure that all sequences are fasta format, and it's sure that at least one isn't. You need to *prove* it one way or the other. I'd suggest printing out the line number or something as you process through the file so you can find out where in your file it's having trouble. Then double and/or triple check the input.

Also, take the error message with a grain of salt: Sometimes an error isn't exactly what's claimed. For example, if a descriptor line requires four vertical bars, the record might not be recognized as a descriptor line and generate such a message.

NOTE: I've never used the Bio::SeqIO module (nor any of the other bio modules), so take my advice with a grain of salt. I'm just speaking from experience with other things.

...roboticus

When your only tool is a hammer, all problems look like your thumb.