[Bioperl-l] Trouble with Bio::DB::Fasta and large files

[Lincoln Stein]

I believe you are hitting the 2 GB file limit on some Unix systems.  In 
general, you will have to do three things:

	1) make sure that your kernel supports large files > 2 Gb
	Recompile the kernel if not.

	2) make sure that you have a recent version of the C library,
	libc, that supports large files.  Install a new one if not (good luck!)

	3) make sure that you have a version of Perl that was compiled
	with large file support.  Recompile with large file support turned
	on if not.

It's a big pain.  We just had to do this for one of our servers when we 
experienced a similar problem.

Lincoln

On Tuesday 05 November 2002 07:32 pm, Tyler wrote:
> I have been using Bio::DB::Fasta to extract sequences from fasta BLAST
> databases for zebrafish and fugu with no problems. I've used both the
> tied hash and object oriented implementations and they work great with
> these databases. Thanks Lincoln.
>
> However, when trying to use Bio::DB::Fasta on local mouse or human
> genome databases (ensembl raw data) they throw the "Invalid file or
> dirname" exception. The mouse fasta file is 2.7GB and the human one is
> 3.2GB, as opposed to 1.2GB for zebrafish and 340MB for fugu. All
> scripts are the same except for the name of the database file. All
> databases work fine with standalone blast (both the web interface and
> the bioperl interface).
>
> Is there a work around for dealing with these extremely large files?
>
> -Tyler
>
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