[ensembl-dev] skip lock tables for ensembl-compara
Brandon Walts
bwalts at ebi.ac.uk
Thu Nov 9 16:25:12 GMT 2017
Hi Francesco
We have just pushed a fix to the MySQLTransfer.pm runnable, so that it
no longer locks tables by default. If you go to your eHive checkout and
perform a git pull, you should get this fix.
Users who wish to retain the table locking behavior can switch it on by
passing a parameter 'lock_tables=1' to MySQLTransfer.pm
Best
-Brandon
On 09/11/2017 16:20, Mateus Patricio wrote:
> Hi Francesco,
>
> So what’s happening here is that you are trying to lock a table in one
> of our servers.
>
> That can be fixed by telling mysqldump to avoid locking the table.
> (Like you initially suspected)
>
> You could do that directly on the eHive runnable
> "ehive/master/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm”
>
> The dump command is constructed at:
> https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L117
>
> I would suggest you to create a new entry to “mode_options”:
> https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L112
>
> So that you could access directly from your pipeline config file, by
> setting something like:
>
>> { -logic_name => 'copy_ncbi_table',
>> -module => 'Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer',
>> -parameters => {
>> 'src_db_conn' => '#ncbi_db#',
>> 'mode' => ’*SKIP_LOCK*',
>> 'filter_cmd' => 'sed "s/ENGINE=MyISAM/ENGINE=InnoDB/"',
>> },
>> },
>
> Please let me know if that doesn’t work.
>
> Cheers,
>
> Mateus.
>
>
>
>
>> On 9 Nov 2017, at 15:44, Francesco Lamanna
>> <francesco.lamanna at gmail.com <mailto:francesco.lamanna at gmail.com>> wrote:
>>
>> Hi Mateus,
>>
>> thank you for your answer.
>>
>> I am using 'ncbi_db' =>
>> 'mysql://anonymous@ensembldb.ensembl.org/ensembl_compara_90
>> <http://anonymous@ensembldb.ensembl.org/ensembl_compara_90>' to
>> conncect to ncbi_db (I used the same value as in the
>> NoMasterProteinTrees_conf.pm example).
>>
>> The failing analysis is copy_ncbi_table(9).
>>
>> Cheers,
>> Francesco.
>>
>> 2017-11-09 16:29 GMT+01:00 Mateus Patricio <mateus at ebi.ac.uk
>> <mailto:mateus at ebi.ac.uk>>:
>>
>> Hi Francesco,
>>
>> Looks like your pipeline is using the user anonymous to connect
>> to the database.
>>
>> I would suggest that you add the skip option within your runnable.
>>
>> Which analysis is actually failing?
>>
>> Cheers,
>>
>> Mateus.
>>
>>
>>> On 8 Nov 2017, at 17:36, Francesco Lamanna
>>> <francesco.lamanna at gmail.com
>>> <mailto:francesco.lamanna at gmail.com>> wrote:
>>>
>>> Hello,
>>>
>>> I am trying to apply the ProteinTrees pipeline to a set of
>>> Ensembl and non-Ensembl genomes.
>>>
>>> When running the pipeline without a master database (via
>>> beekeeper.pl <http://beekeeper.pl/>) I get the following error:
>>>
>>> ensembl_compara_90 ncbi_taxa_node | sed
>>> "s/ENGINE=MyISAM/ENGINE=InnoDB/" | mysql -h127.0.0.1 -P3306
>>> -uroot -p$EHIVE_TMP_PASSWORD_0
>>> hd_cc141_test_protein_trees_no_master_90' resulted in an error
>>> code=2
>>> stderr is: mysql: [Warning] Using a password on the command line
>>> interface can be insecure.
>>> mysqldump: Got error: 1044: Access denied for user
>>> 'anonymous'@'%' to database 'ensembl_compara_90' when doing LOCK
>>> TABLES
>>>
>>>
>>> Is there a way to pass --skip-lock-tables to the pipeline (e.g.
>>> in the conf file) in order to be able to dump the database?
>>>
>>> Thanks,
>>> Francesco.
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> <http://lists.ensembl.org/mailman/listinfo/dev>
>>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> <http://lists.ensembl.org/mailman/listinfo/dev>
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20171109/3c4659ab/attachment.html>
More information about the Dev
mailing list