Re: [MUMmer-help] mummer: suffix tree construction failed

[Nagarjun V <arj...@gm...>]

Hi grid bird,

You could try to compile the 64 bit version as described in
http://seqanswers.com/wiki/Talk:MUMmer

This should be able to handle much bigger datasets.

Cheers,

Nagarjun

On Wed, May 25, 2011 at 11:12 PM, grid bird <gri...@gm...> wrote:

> Hi Collegues,
>
> I tried use mummer for bacterial genomes alignment.
> The command line is : ./mummer -maxmatch -b ref.fa query.fa > xaa.out
> Their are 200 reference sequences and the total length is : 752255529
> There was error information reported by mummer: "  ./mummer: suffix tree
> construction failed: textlen=752255529 larger than maximal textlen=536870908
> "
> I want to know if there is limit for reference file size and sequences
> number and also, I find mummer occupied huge memory (about 6GB) when I gave
> one about 300MB reference file.
> How should I do like this case? Do I have to split reference file to one
> sequence one file to do alignment?
> Any ideas?
>
> thank you,
>
>
>
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