[Biojava-l] Any memory-optimised blast parser available ?

[Benoit VARVENNE]

Great ! Thanks a lot to all for your answers.
I hadn't thought to that way of solving the problem.
That runs well with -Xmx option.

Thanks again,
Regards,

Benoit


Le 13/11/06 12:28, « Andy Yates » <ayates at ebi.ac.uk> a écrit :

> Hi,
> 
> Have you tried increasing the amount of memory the Java virtual machine
> has available? The problem with Java is that it starts with a default
> memory limit of approx. 128MB which if you've got a memory intensive
> process will not be enough.
> 
> When running your program try adding the option
> 
> -Xmx256M
> 
> So if my class was called Main.class my command line would be:
> 
> java -Xmx256M -cp .:biojava.jar Main
> 
> Or if you're running this from ant then there is an attribute maxmemory
> which can be specified in the <java/> task.
> 
> Hope that helps
> 
> Andy
> 
> Benoit VARVENNE wrote:
>> Hello,
>> 
>> I'm trying to parse blast result files from a remote blast on NCBI
>> databases.
>> In order to do so, i'm using biojava XML parser like this :
>> 
>> -----------
>>       InputStream is = new FileInputStream(blastFile);
>>       BlastXMLParserFacade parser = new BlastXMLParserFacade();
>>       SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
>> 
>>       parser.setContentHandler(adapter);
>> 
>>       List results = new ArrayList();
>> 
>>       SearchContentHandler builder = new BlastLikeSearchBuilder(results,
>>           new DummySequenceDB("queries"), new
>> DummySequenceDBInstallation());
>> 
>>       adapter.setSearchContentHandler(builder);
>> 
>> // Here is the method that throws 'OutOfMemoryException'
>>       parser.parse(new InputSource(is));
>> -----------
>> 
>> While blasting a genomic sequence (i've tried with 50Kb long sequences max),
>> I've got an OutOfMemory exception.
>> 
>> Does anyone know a way to resolve this ? (this aim is not to dividde my
>> genomic locus in too many parts, 50Kb is a quarter of my genomic...)
>> 
>> Thanks,
>> Regards,
>> 
>> Benoit
>> 
>> 
>