Re: [MUMmer-help] Whole genome length exceeding the max limit for mummer

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

Hi Vishnu,
In the MUMmer base directory, type:

> make clean
> make CPPFLAGS="-O3 -DSIXTYFOURBITS"

That should recompile MUMmer in 64-bit mode so it will be able to construct
very large trees.

Best,
-Adam


On Tue, Jun 22, 2010 at 5:22 AM, Makkapati, Vishnu <
vis...@ph...> wrote:

>  Hi,
>
>
>
> I reported the following error when I tried to compare whole genomes of
> hg19 and Chinese using mummer. Is there a way by which I can increase the
> maximum limit of textlen?
>
>
>
> ./mummer -mum -b -c /Users/ Hg19/WholeGenome_Hg19.fa
> /Users/Chinese/chinese_whole_genome.fa > hg19_chinese_whole.mums
>
> # reading input file " /Users/ Hg19/WholeGenome_Hg19.fa" of length
> 3095694007
>
> # construct suffix tree for sequence of length 3095694007
>
> # (maximum reference length is 536870908)
>
> # (maximum query length is 4294967295)
>
> # process 30956940 characters per dot
>
> ./mummer: suffix tree construction failed: textlen=3095694007 larger than
> maximal textlen=536870908
>
>
>
> Regards,
>
> Vishnu
>
>
>
> Vishnu Vardhan Makkapati
> Senior Scientist, Philips Research Asia - Bangalore
>
> Philips Innovation Campus, Philips Electronics India Limited
>
> Manyata Tech Park, Nagavara
>
> Bangalore - 560 045, Karnataka, India
> Phone: +91-80-41892241, Fax: +91-80-41892265
>
> E-mail: vis...@ph...
>
> Intranet: pww.research.philips.com
>
> Internet: www.research.philips.com
>
>
>
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