mswiatek - 2009-03-23

I have run into the same problem but I think I can offer a workaround (and some speculation regarding the root cause). Again, the symptoms are the same: I run nucmer pipeline on two multi-fasta files. postnuc fails, saying that stdin can't be parsed. Now, this stdin is evidently an intermediary file, with .mgaps extension.
I have checked out that file and I found out that FASTA-style header lines had no text in them, only the '>' character.

Turns out, this happens when the query file has header lines formatted with space:
I have changed headers in my FASTA files to
----- no space!

This time everything worked just fine! Obviously, the problem is not with postnuc, but with whatever precedes it in the pipeline.