[Bioperl-l] Out of memory errors running Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file

[Mingyi Liu]

Hi, Susan,

Mauricio is right. When there's a problem with Bio::ASN1::EntrezGene, it's better to directly contact me.  I actually deleted a few messages of this discussion before one caught my eye. Nowadays I'm working in some other areas and not tracking bioperl mailing list closely, a direct email to me would usually work out better.

As for the problem you mentioned, there could be two reasons: 1. It 
seems that you converted the file to XML file instead of ASN file. My 
parser is designed for ASN file, so please use gene2xml to convert the 
downloaded file to ASN file instead of XML file.  It is likely the wrong 
syntax of the file caused my parser to attempt to read the entire file 
as a string (because it couldn't find the start/end).  However, there's 
another minor possibility (which you might have taken care of already): 
2. Perl 5.8 added 64 bit support, but I don't know if you have perl 5.8 
64 bit installed on your system to support the 256 GB system memory you 
have?  If not, your >5 GB file is over the 4 GB 32 bit Perl limit.

Let me know if my suggestions work out for you.

Best,

Mingyi

Susan Wilson wrote:
> Hi,
>
> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
> memory.  I get a simple "Out of memory" output even with the  
> following code:
>
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }
>
>
>
> Thanks.
> Susan
>
>
>
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