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

[Dan B. <dan...@gm...>]

When I tried this myself (following that note) I found that the
resulting binary runs and runs without ever apparently finishing.

Please let us know if this solution works for you.


Cheers,
Dan.

On 25 May 2011 23:04, grid bird <gri...@gm...> wrote:
>
>
> ---------- 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,
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> vRanger cuts backup time in half-while increasing security.
>>> With the market-leading solution for virtual backup and recovery,
>>> you get blazing-fast, flexible, and affordable data protection.
>>> Download your free trial now.
>>> http://p.sf.net/sfu/quest-d2dcopy1
>>> _______________________________________________
>>> MUMmer-help mailing list
>>> MUM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>>
>>
>>
>>
>> --
>> coopsearch.blogspot.com
>> mysorechronicles.blogspot.com
>
>
>
> ------------------------------------------------------------------------------
> vRanger cuts backup time in half-while increasing security.
> With the market-leading solution for virtual backup and recovery,
> you get blazing-fast, flexible, and affordable data protection.
> Download your free trial now.
> http://p.sf.net/sfu/quest-d2dcopy1
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>