[Bioperl-l] Added 'Installing bioperl-db in Windows' to wiki, problems with bioperl-db

Hilmar Lapp hlapp at gmx.net
Thu Feb 16 01:31:54 EST 2006


On Feb 15, 2006, at 7:56 PM, Chris Fields wrote:

> [...]
> I looked in the mailing list archives and Barry mentions something 
> here:
>
> http://bioperl.org/pipermail/bioperl-l/2005-January/018093.html
>
> He rebuilt the database from scratch and got it working; no reason
> was given.  I wouldn't be surprised if it is something Mysql-related
> that pops up.

Note though that he was using PostgreSQL. With Pg you definitely need 
to 'vacuum,' which is their name for analyzing/optimizing the table(s).

>   The strange thing is that only a few months ago
> everything ran well with this version of MySQL (v.5); this was with
> the first test database I installed on it.  Another strange thing (I
> think I mentioned it) is that NOT loading the taxonomy with
> load_ncbi_taxonomy.pl worked (everything was entered).

That's not really strange, it is in fact consistent with the query you 
report as taking a long time. If you don't pre-load the taxonomy then 
the taxon and taxon_name tables are empty or almost empty and look-ups 
and joins of empty tables are amazingly fast :-J

[...]
> I wanted to also mention that we shouldn't check in the modifications
> to Bio::Root:Root until I confirm something (I'm at home and
> currently can't).

OK we'll hold off.

	-hilmar
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: Hilmar Lapp -:- San Diego, CA -:- hlapp at gmx dot net :
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