[ensembl-dev] problem on interacting with mysql

Zhang Di aureliano.jz at gmail.com
Sun Nov 20 06:23:39 GMT 2011


Hi,
   Strange things here.
   I have run ensembl-compara pipeline for whole genome alignment
successfully a week before.
   When I try to run it again on yesterday, It stoped at StoreSequence
step, compaining that:

  DBI::mysql::do do failed: 'job_file' was not locked with LOCK TABLES at:
/mydir/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line 769.
  DBI::mysql::do do failed: 'job_file' was not locked with LOCK TABLES at:
/mydir/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line 769.

After some debug work, I found that it could not execute the sql statement
'DELETE from job_file WHERE job_id=xxx AND worker_id=xx';
I tried to work around it by modify the DBConnection.pm, replaced line 769:

                     my $result = $self->db_handle->do($string);

                     TO:
                     my $result;
                     system "mysql -ppassword $self>{_dbname} -e '$string'";
                     $result=1;

It worked! But the pipeline still stoped complaining that:
DBD::mysql::st execute failed: Table 'job_file' was not locked with LOCK
TABLES at
/mydir/ensembl-hive/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
line 466.
DBD::mysql::st execute failed: Table 'job_file' was not locked with LOCK
TABLES at
/mydir/ensembl-hive/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
line 466.

Seems another place failed to execute some sql statement related to
'job_file'.

---------------------------------------------------------------------------------------------

When I terminate (Ctrl-C) the pipeline.  The same statement ran without any
problem in a test perl script:

#!/usr/bin/perl -w
use DBI;
my $dbh = DBI->connect("DBI:mysql:mydb:localhost","user","pass");
my $string = "DELETE FROM job_file WHERE job_id=xxx AND worker_id=xx";
$dbh->do($string);

---------------------------------------------------------------------------------------------
Any suggestions?


Best Reguards.




-- 
Zhang Di
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