[Bioperl-l] bus error when indexing large file

[Chris Fields]

I can attempt to reproduce this (I have very similar specs).  I'm  
wondering if it has something to do with large file support.

Have you tried the perl packaged with Mac OS X?  I think it's perl  
5.8.8.

chris

On Aug 13, 2009, at 7:40 PM, Attila Gulyas-Kovacs wrote:

> 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
>
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