[ensembl-dev] problem on interacting with mysql

[Zhang Di]

Never Mind! my fault.

I have added some debug lines that ruined the whole pipeline.

On Sun, Nov 20, 2011 at 2:46 PM, Zhang Di <aureliano.jz at gmail.com> wrote:

> more info:
>
> Seems that the pipeline LOCKed  TABLE 'sequence' just before the DELETE
> statement.
>
> But no sequence really inserted into the TABLE 'sequence', and no 'UNLOCK
> TABLES' executed.
>
> still working...
>
> On Sun, Nov 20, 2011 at 2:23 PM, Zhang Di <aureliano.jz at gmail.com> wrote:
>
>> 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
>>
>
>
>
> --
> Zhang Di
>



-- 
Zhang Di
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