#11 nucmer will not finihs

v3.xx
open
nobody
nucmer (5)
5
2014-08-21
2009-01-03
Benjamin Jackson
No

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.

Discussion

  • mswiatek
    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:
    --------
    > 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.