[BioRuby] error with big fasta files

[Naohisa GOTO]

On Wed, 7 Jan 2009 14:32:52 +0100 (CET)
"K. Patil" <kpatil at science.uva.nl> wrote:

> Hi,
> 
> I am trying to process some big fasta files. I get the following error;
> 
> /XXX/rubygems/bioruby-1.2.1/lib/bio/db/fasta.rb:156:in `initialize':
> private method `sub' called for nil:NilClass (NoMethodError)
> 
> The corresponding file contains only one sequence with 3200227952
> characters (there are no new lines in the file except the one after the
> header).
> 
> Any clues?
> 
> Cheers,
> Kaustubh

The FastaFormat parser first reads all data into memory.
So, it seems memory exhaust.

In addition, in normal 32-bit OS, maximum memory size given
to an application is about 3GB, and it is possible that the
error might also be caused by a limitation of 32-bit.

Please try again by using 64-bit OS with abundant memory and
running 64-bit compiled Ruby (the newest version is strongly
recommended).

Naohisa Goto
ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp