[BioSQL-l] Query regarding loading database with bioperl-db

[Soumyadeep nandi]

Hi everybody,

I am working with bioperl-db-1.1 and biosql-schema-1.1
with bioperl-1.2 in linux environment and the database
is mysql-3.23.53a-max.
I am trying to populate my database(biosql) with a
GenBank sequence file. So I downloaded the genbank
file having lots of annotated
sequences and tried to populate the database with
load_seqdatabase.pl.
While doing so I ended up with an error as follows:-

DBD::mysql::st execute failed: MySQL server has gone
away at
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/PrimarySeqAdaptor.pm
line 130, <GEN0
> line 207245.
DBD::mysql::st execute failed: MySQL server has gone
away at
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/PrimarySeqAdaptor.pm
line 130, <GEN0
> line 207245.

Then I've ommited all the larger sequences from the
genbank file and ran the above program, it worked
fine.

To find a solution of this I checked the mails in the
archives.

I was delighted to see a mail from Keith Allen in the
archive depicting the same problem with a solution.
>From his mail I learnt that he has fixed it up by
setting up the mysql install by increasing the
max_allowed_packet, the sort_buffer, and the
record_buffer to 3M with Chris Dagdigian's advice.

I've also increased the parameter values to 3M in
/etc/my.cnf file which is my configuration file for
MySQL according to your document.
But still I am facing the same problem while storing
the huge sequences (4653728bp). I tried increasing the
parameter values rather more upto 50M.
But still the program ended up with the same error.

I request you to please tell me whether I am heading
towards the right solution.
If so, please tell me what should I do to fix up this
error.

Soumyadeep


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