Re: [MUMmer-help] Nucmer and Ubuntu 13.10 problems

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

Hi Richard,
Are there multiple records in the fasta file? This kind of failure is often
caused by non-unique fasta headers. The header is defined by the characters
up to the first space, so in your two examples ">test" and
">test_something" would be considered the headers. If those names are
repeated in another record in the same file, it will cause an error.

-Adam



On Mon, Feb 17, 2014 at 6:57 AM, Richard Stabler <
ric...@ls...> wrote:

> Hi
>
> I have been using nucmer through RATT but since a recent upgrade of
> Ubuntu from 13.04 to 13.10 I have started to encounter problems.
>
> However I have traced it to the header of the test sample.
> Ok, to run
> $nucmer ref.fasta test.fasta
>
> if the header in the test.fasta is
> >test
> -- doesn't work
>
> 1: PREPARING DATA
> 2,3: RUNNING mummer AND CREATING CLUSTERS
> # reading input file "out.ntref" of length 4290253
> # construct suffix tree for sequence of length 4290253
> # (maximum reference length is 536870908)
> # (maximum query length is 4294967295)
> # process 42902 characters per dot
>
> #....................................................................................................
> # CONSTRUCTIONTIME /usr/bin/mummer out.ntref 1.25
> # reading input file "/home/richard/work/gnb/temp/630.tst" of length
> 4290252
> # matching query-file "/home/richard/work/gnb/temp/630.tst"
> # against subject-file "out.ntref"
> # COMPLETETIME /usr/bin/mummer out.ntref 3.64
> # SPACE /usr/bin/mummer out.ntref 8.39
> 4: FINISHING DATA
> *ERROR: Could not parse input from 'Query File'. **
> *Please check the filename and format, or file a bug report
> ERROR: postnuc returned non-zero
>
> However if the header has a second work separeted by a space it works!
> >test something
> -- this works
> >test_something
> -- this doesn't work
>
> Can this be fixed as I don't want to have to edit all my fasta files?
>
> Many thanks
>
> Richard
>
>
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