[BioSQL-l] trouble cramming genbank

[Hilmar Lapp]

Be aware that if you want to use the HEAD revision of the 
biosql-schema, you also need to use  the head revision of 
bioperl-db, which in turn will not run with a less recent bioperl 
version than 1.1.1 (released on Sunday).

Also, remote and fuzzy locations will not be recoverable from biosql 
using those versions (they should not crash the script though).

Of course, this doesn't apply if you just took the branch-revision 
and added INNODB as the table handler.

	-hilmar

On Monday, October 14, 2002, at 02:38 PM, Josiah Altschuler wrote:

> Ok thanks for the replies.  I increased the size from 4 GB to some huge
> number.  But when I ran load_seqdatabase.pl again, it got stuck 
> after adding
> one entry.  I noticed the newer biosqldb-mysql.sql uses INNODB 
> tables, so I
> am now creating another genbank db from scratch using type=INNODB 
> for all my
> tables.  Hopefully this will work out better.  I guess I'll find 
> out in two
> days.
>
> Josiah
>
>
>
> -----Original Message-----
> From: Tim Henderson [mailto:tjh@alodar.com]
> Sent: Monday, October 14, 2002 2:44 PM
> To: Josiah Altschuler
> Cc: Biosql
> Subject: Re: [BioSQL-l] trouble cramming genbank
>
>
> Josiah,
>
> According to the MySQL docs at
>
> http://www.mysql.com/documentation/mysql/bychapter/
>
> (See "1.2.4 How big can MySQL tables be?")
>
> MySQL tables by default have a maximum size of "about 4 GB". You can
> check this using the "SHOW TABLE STATUS" command.
>
> If you're trying to load all of GenBank, or even all of the EST
> division, it wouldn't surprise me if you exceeded 4 GB in one or more
> tables.
>
>
> -- Tim
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l@open-bio.org
> http://open-bio.org/mailman/listinfo/biosql-l
>
--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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