[Open-bio-l] eyeballs needed -- my biosql install diary

[chris dagdigian]

Hello,

Just in case you have not solved this yet it seems that you may need to 
alter the MySQL configuration value "max_allowed_packet" to be a fairly 
large number in order to handle very large sequence objects.

Keith Allen reported this on bioperl-l; the specific message is online 
at http://bioperl.org/pipermail/bioperl-l/2002-May/007987.html

Hope this helps!

I've incorporated several people's comments into my BioSQL diary and 
will be putting an updated version online shortly.

Regards,
Chris


KATAYAMA Toshiaki wrote:
> Hi,
> 
> Is there any size limitation on biosequence?
> 
> I tried to load recent RefSeq into BioSQL, I've got following errors:
> 
> 
> -----X8-----X8-----
> Reading ../refseq/rscu.gbff
> (..snip..)
> DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/SQL/PrimarySeqAdaptor.pm line 130, <GEN0> line 1662456.
> DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/SQL/PrimarySeqAdaptor.pm line 130, <GEN0> line 1662456.
> -----X8-----X8-----
> 
> The line 1662456 of my RefSeq file was the entry NC_000918, which was
> A. aeolicus genome with length 1551335 bp.  I have already loaded
> part of GenBank (gbvrl*) and Swissprot (thanks to Chris's doc :-) on
> my BioSQL server, however, the maximum length in biosql at that time
> was around 368k bp.
> 
> 
> I also want to know how BioSQL stores over the 16MB sequence entry
> (i.e. Arabidopsis chromosome in RefSeq) into biosequence table
> with MySQL's mediumtext (L < 2^24).
> 
> My silly approach other than BioSQL to store GenBank/RefSeq on MySQL was
>   http://bioruby.org/cgi-bin/cvs/reviz/bioruby/sample/
> gb2tab.rb and gbtab2mysql.rb (used for http://gb.bioruby.org/),
> in this case, I have splitted long sequence into pieces with numbers.
> 
> Furthermore, MySQL's longtext seems long enough, however it didn't
> work well when I tried. (I forgot details but, packet size limitation
> error or something was occured, my configuration problem?)
> 
> 
> At Wed, 15 May 2002 19:11:08 -0400,
> Chris Dagdigian wrote:
> 
>>http://bioteam.net/dag/BioTeam-HOWTO-1-BIOSQL.html
> 
> 
> Your document seems very useful.  From this doc:
> 
> 
>>>Step 10 - What next?
>>>
>>>Figure out how to export/dump the database and see how quickly we
>>>can recreate the database with these raw files instead of
>>>laboriously using BioPerl to parse and load objects one at a
>>>time. Loading the database is slow and it may be cool to package up
>>>tab-delimited biosql exports so that others can load their own
>>>databases much faster.
>>
> 
> Cool. If there were a repository of this format.
> 
> 
> Regards,
> Toshiaki Katayama
> --
> Kanehisa laboratory (Bioinformatics Center)
> Institute for Chemical Research, Kyoto Univ.
> Gokasho, Uji, Kyoto 611-0011, Japan
> TEL +81 774 38 3272, FAX +81 774 38 3269
> http://web.kuicr.kyoto-u.ac.jp/~katayama/
> http://bioruby.org/ (k@bioruby.org)
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l@open-bio.org
> http://open-bio.org/mailman/listinfo/open-bio-l


-- 
Chris Dagdigian, <dag@sonsorol.org>
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