Re: [MUMmer-help] Error message with PROMER and NUCMER

[Adam P. <aph...@gm...>]

Hi Andy,
That error is usually caused by something trivial. If you can send me
your input files I'd be happy to take a look--they don't look very
large.

-Adam

On Tue, Jan 29, 2013 at 2:16 PM, Andy King <and...@yo...> wrote:
> Hi
>
> I am trying to run both nucmer and promer commands on two files.  The
> reference file contains a single contig.  The query file contains multiple
> contigs.
>
> I keep getting the following error message;
>
> 1: PREPARING DATA
> 2,3: RUNNING mummer AND CREATING CLUSTERS
> # reading input file "promer.aaref" of length 1389932
> # construct suffix tree for sequence of length 1389932
> # (maximum reference length is 536870908)
> # (maximum query length is 4294967295)
> # process 13899 characters per dot
> #....................................................................................................
> # CONSTRUCTIONTIME /biol/cnap/people/ak533/MUMmer/MUMmer3_23/mummer
> promer.aaref 0.56
> # reading input file "promer.aaqry" of length 840869
> # matching query-file "promer.aaqry"
> # against subject-file "promer.aaref"
> # COMPLETETIME /biol/cnap/people/ak533/MUMmer/MUMmer3_23/mummer promer.aaref
> 1.01
> # SPACE /biol/cnap/people/ak533/MUMmer/MUMmer3_23/mummer promer.aaref 2.16
> 4: FINISHING DATA
> Jcr4S000
> ERROR: Could not parse input from 'Query File'.
> Please check the filename and format, or file a bug report
> ERROR: postpro returned non-zero
>
>
> the mummer command works fine.
>
> Thanks
>
> Andy
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