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

[grid b. <gri...@gm...>]

---------- Forwarded message ----------
From: grid bird <gri...@gm...>
Date: Wed, May 25, 2011 at 2:58 PM
Subject: Re: [MUMmer-help] mummer: suffix tree construction failed
To: Nagarjun V <arj...@gm...>

I tried the 64 bit version and it finished successfully.
But, Mummer occupied 14GB memory under 718MB reference file.
Is it reasonable?  do you have other ways to use less memory except
splitting reference file.

thanks,


On Wed, May 25, 2011 at 2:20 PM, Nagarjun V <arj...@gm...> wrote:

> 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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>
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