Re: [MUMmer-help] error message

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

Hi Astrid,
It is most likely a memory issue. How much RAM does your machine have? As a
rule of thumb, MUMmer requires approximately 17 bytes per base-pair of
reference sequence. For a reference of your size, that would be over 8GB.

If it is possible to partition your reference into multiple files, you can
run mummer separately on each, which will save memory.

No, MUMmer does not currently support multithreading.

Best,
-Adam



On Tue, Jul 22, 2014 at 9:00 AM, astrid boehne <ast...@un...>
wrote:

> Hi
> I am trying to run mummer to compare very similar genome assemblies (two
> individuals of the same species)
> and get back the following error.
> I reduced the query and reference sequence size I used to match the
> character limitations.
> 1: PREPARING DATA
> 2,3: RUNNING mummer AND CREATING CLUSTERS
> # reading input file "ref_qry.ntref" of length 497187885
> # construct suffix tree for sequence of length 497187885
> # (maximum reference length is 536870908)
> # (maximum query length is 4294967295)
> # process 4971878 characters per dot
>
> #............................................................................ERROR:
> mummer and/or mgaps returned non-zero
>
> Any suggestions on what is happening?
> My guess is that this is a memory issue.
> Is it possible to run Mummer multi-threaded?
> Thank you very much in advance
> All the best
> Astrid Böhne
>
> --
> Astrid Böhne
> Universität Basel
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> Evolutionsbiologie
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>
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