#11 nucmer will not finihs

[Benjamin Jackson]

using the simplest options

nucmer <file> <query_file>

nucmer will not finish:

4: FINISHING DATA
ERROR: Could not parse input from 'stdin'.
Please check the filename and format, or file a bug report
ERROR: postnuc returned non-zero, please file a bug report

promer finishes fine using the same files.

[mswiatek]

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:
--------
> SEQUENCE_ID
--------
I have changed headers in my FASTA files to
-----
>SEQUENCE_ID
----- no space!

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