[Bioperl-l] bus error when indexing large file

[Attila Gulyas-Kovacs]

Dear all,

I can index the SwissProt database without problem but I get bus error 
when I try to index the much larger TrEMBL database. Indexing failed 
with both the swissprot and fasta format (using Bio::Index::Swissprot or 
Bio::Index::Fasta, respectively). I broke up TrEMBL into multiple files 
('chunks'), about the size of the SwissProt database. Then I could could 
create separate indeces for  each chunk. But I got bus error when I 
passed all chunks simultaneously to my script (below) to create a single 
index.
Perl v5.10.0; Bioperl 1.6.0; Mac OS X 10.5.8; MacPro 10 GB RAM.

What do you suggest?

Attila


#! /usr/bin/perl
use warnings;
use strict;
use Bio::Index::Swissprot;
my $index_file_name = shift;
my $inx = Bio::Index::Swissprot->new(
    -filename   =>  $index_file_name,
    -write_flag =>  1);
$inx->make_index(@ARGV);

-- 
Attila Gulyas-Kovacs
Postdoctoral Associate

Rockefeller University
Gadsby Lab (Cardiac/Membrane Physiology)
D.W. Bronk Building, Room 307 
1230 York Avenue
New York, NY, 10065
Tel: (212)327-8617
Fax: (212)327-7589