[Bioperl-l] Memory not sufficient when storing human chromosom 1 in BioSQL

Chris Fields cjfields at uiuc.edu
Fri Jul 4 02:14:37 EDT 2008


Have you tried just loading the sequence into memory using  
Bio::SeqIO?  The problem may be the size of the file itself.

chris

On Jul 3, 2008, at 6:48 AM, Andreas Dräger wrote:

> Hi all,
>
> Recently I have successfully installed the latest version of BioPerl  
> and BioSQL on my computer, which has 2 GB RAM. Both works fine, but  
> when trying to insert the genbank file of the human chromosome 1,  
> which I have downloaded from the NCBI website (ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_chr1.gbk.gz 
> ) I receive the error message 'Out of memory'. This takes about one  
> hour. My question is, how I can insert large genbank files in my  
> BioSQL database using BioPerl. I do not know, what to do. Thank you  
> for your help!!!
>
> Cheers,
> Andreas
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign







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