[Genome] blat out of memory

[Brooke Rhead]

Hello Eric,

Please see these answers to very similar previously answered questions:

http://www.cse.ucsc.edu/pipermail/genome/2004-December/006284.html

http://www.cse.ucsc.edu/pipermail/genome/2005-June/007900.html

If you still have questions after reviewing these answers, please feel 
free to contact us again.

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--
Brooke Rhead
UCSC Genome Bioinformatics Group


ericho at eden.rutgers.edu wrote:
> Hi,
> 
> my blat is standalone v.33 on linux.
> 
> I want to blat EST sequences against the whole human genomes which is
> ~3GB. I did it by putting a list of nib files into a file and fed it to
> blat.
> 
> ~/blat/blat hs_all_nibs.lis my.seq.fa my.seq.psl -ooc=hs.ooc ...
> 
> But I encountered out of memory. Therefore I added an additonal swap file.
> Here is the output of free command:
> 
>              total       used       free     shared    buffers     cached
> Mem:       1026372     200428     825944          0        888     166924
> -/+ buffers/cache:      32616     993756
> Swap:      9212108      21144    9190964
> 
> Total I have 1GB memory + 1GB swap file (default) + 8GB add-on swap file.
> But I still encountered error when total memory reached ~3GB. Here's the
> error message:
> 
> Out of memory needLargeMem - request size 158821425 bytes
> 
> I don't understand why 3GB genomes needs 158+GB! Is there any way to
> reduce the memory requirement?
> 
> Thanks,
> -- Eric
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