[Biojava-dev] SequenceDB way too big!!!

[Schreiber, Mark]

Hi -

Have you tried using the -XMx option to assign more memory to the VM?

- Mark


> -----Original Message-----
> From: Murat Tasan [mailto:tasan at eecs.cwru.edu] 
> Sent: Friday, 31 January 2003 10:13 a.m.
> To: biojava-dev at biojava.org
> Subject: [Biojava-dev] SequenceDB way too big!!!
> 
> 
> I've just started using biojava to help in my development of 
> sequence analysis and searching projects, but I have run into 
> a huge (no pun
> intended) problem.  I make a call to 
> SeqIOTools.readFasta(...), to read a FASTA file of 
> approximately 14MB in size.  Because the file is only 14MB or 
> so, I figure getting a SequenceDB object from it will AT 
> WORST take up twice that in memory (~30MB) (with all of the 
> extra information associated with sequences... although my 
> FASTA file has just sequence data). Instead, my virtual 
> machine eventually crashes out as I run out of memory. I 
> watched the execution using 'top' and witnessed over 75MB 
> being allocated to the running process.
> 
> Is there a more efficient implementation of this?  Better 
> yet, can anyone tell me why so much space is being taken up 
> for only 14MB of sequence data?
> 
> Thanks for any help!!!!
> 
> Murat
> 
> -- 
> Murat Tasan
> mxt6 at po.cwru.edu
> tasan at eecs.cwru.edu
> http://genomics.cwru.edu
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at biojava.org 
> http://biojava.org/mailman/listinfo/biojava-dev
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================