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

[Soumyadeep nandi]

Hi everybody,

As I've depicted that my work was ending 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.

I've sorted out that solution, it is as follows:-
In my first effort I simply changed the
max_allowed_packet to 40M in [mysqld] section and left
unchanged in section [mysqldump]. So, my work ended
with the same error.
Now i've made the changes in both and I am successful
in dumping data into my database.

Now my [mysqld] and [mysqldump] section looks like.

[mysqld]
port=3306
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
skip-locking
set-variable= key_buffer=256M
set-variable= max_allowed_packet=40M
set-variable= table_cache=256
set-variable= sort_buffer=1M
set-variable= record_buffer=1M
set-variable= myisam_sort_buffer_size=64M
set-variable= thread_cache=8
set-variable= thread_concurrency=4
server-id= 1
tmpdir= /tmp/

[mysqldump]
quick
set-variable= max_allowed_packet=140M

Thanks to Keith Allen for posting the initial answer
to this problem on the  mailing list and Chris
Dagdigian for his advice.

Soumyadeep

__________________________________________________
Do you Yahoo!?
Yahoo! Mail Plus - Powerful. Affordable. Sign up now.
http://mailplus.yahoo.com