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Help - database size limitation with toblast!

Mathew Woodwark mathew.woodwark at bbsrc.ac.uk
Fri May 17 06:19:16 EST 1996


P A Keller wrote:
> 
> Hi all,
> 
> We use GCG version 8.0 under IRIX 5.3, and I recently got the following
> error message from gcg_pressdb when converting a database to BLAST format:
> 
>    database too big; raise ENTRY_MAX
> 
> I have had a good look through the sources, but I cannot find any
> reference to this (presumably) preprocessor macro. I split the database
> into two parts, which has solved the problem for now.
> 
> Does anyone know how to at least find out what its value is, and if it is
> possible to increase it?
> 
> Many thanks for any help,
> Peter.
> 
> ========================================================================> Peter Keller.            \------------------------------\-----------------------------------------
Hi Peter,

We ran into this problem last year with Genbank (how have you avoided it 
so long?). After consulting with GCG we worked out what the problem was. 
In GCG8.0, they didn't release any source code, so we could up the 
required parameter (ENTRY_MAX) which would seem the obvious solution. In 
GCG8.1, this parameter has been removed from the gcg_pressdb program, 
there is now effectively no limit any more, so the solution was to 
upgrade to GCG8.1. As you presumeably haven't done that, a word of 
warning: the sazfest route is to save all your site specific stuff 
elsewher and install from scratch, replacing your site specific files 
afterwards. We had problems with the upgrade option, and some of the 
parameters in the genetics script caused problems with BLAST processing 
as the file hadn't been upgraded from GCG8. 

Good luck!

Cheers

Mathew Woodwark 
Computational Molecular Biology Support
BBSRC Computing Centre



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