[Biojava-l] BLAST parsing explodes in size

[VERHOEF Frans]

Hi,

 

I am having a problem parsing huge blast results. Basically I am parsing
the blast results pretty much the same way as in "Biojava in Anger",
with as only difference that I use the setModeLazy() of the
BlastLikeSAXParser, since I am using NCBI Blast version 2.2.4 and that
version is not recognised by the parser yet.

Besides that the only difference lays in the things I do with the data.

 

The problem is that when I parse a blast result that is a few hundred
MB, for example 300MB, the java application is ballooning up to around
1.6GB of memory. Sometimes the application even crashes because I only
have got 2GB to play with.

 

Does anyone know what's causing this? Is it because I set the lazy mode?
Is there any way to work around it?

 

Kind regards,

 

Frans Verhoef

Bioinformatics Specialist

Genome Institute of Singapore

Genome, #02-01, 60 Biopolis Street, Singapore 138672

Tel: +65 6478 8000

DID: +65 6478 8060

HP: +65 9848 4325

Email: verhoeff2 at gis.a-star.edu.sg