[ensembl-dev] skip lock tables for ensembl-compara
Francesco Lamanna
francesco.lamanna at gmail.com
Wed Nov 15 10:23:18 GMT 2017
Hi Mateus,
I am using release/90 of the Compara pipeline.
Cheers,
Francesco.
2017-11-15 11:07 GMT+01:00 Mateus Patricio <mateus at ebi.ac.uk>:
> Hi Francesco,
>
> Could you please confirm which checkout version of the compara code you
> have?
>
> Cheers,
>
> Mateus.
>
> On 13 Nov 2017, at 10:50, Francesco Lamanna <francesco.lamanna at gmail.com>
> wrote:
>
> Hi Mateus and Brandon,
>
> many thanks for your patch, it solved the issue.
>
> Unfortunately, I got stuck at the successive step with the following error
> message:
>
> mysql> SELECT * FROM msg;
> +-------------+----------------------------+----------------
> +--------+---------+-----------+---------------------+------
> -+--------------+-------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> -------+----------+
> | analysis_id | logic_name | log_message_id | job_id |
> role_id | worker_id | when_logged | retry | status |
> msg
>
> | is_error |
> +-------------+----------------------------+----------------
> +--------+---------+-----------+---------------------+------
> -+--------------+-------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> -------+----------+
> | 9 | copy_ncbi_table | 1 | 5
> | 3 | 3 | 2017-11-13 11:16:31 | 0 | WRITE_OUTPUT |
> Successfully copied 1609518 'ncbi_taxa_node' rows
>
> | 0 |
> | 9 | copy_ncbi_table | 2 | 6
> | 4 | 4 | 2017-11-13 11:20:15 | 0 | WRITE_OUTPUT |
> Successfully copied 2438889 'ncbi_taxa_name' rows
>
> | 0 |
> | 18 | make_treebest_species_tree | 3 | 10
> | 9 | 9 | 2017-11-13 11:25:29 | 0 | FETCH_INPUT | Can't
> call method "get_all_subnodes" on an undefined value at
> /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/
> modules/Bio/EnsEMBL/Compara/Utils/SpeciesTree.pm line 150. | 1 |
> | 18 | make_treebest_species_tree | 4 | 10
> | 11 | 11 | 2017-11-13 11:26:29 | 1 | FETCH_INPUT | Can't
> call method "get_all_subnodes" on an undefined value at
> /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/
> modules/Bio/EnsEMBL/Compara/Utils/SpeciesTree.pm line 150. | 1 |
> | 18 | make_treebest_species_tree | 5 | 10
> | 13 | 13 | 2017-11-13 11:27:31 | 2 | FETCH_INPUT | Can't
> call method "get_all_subnodes" on an undefined value at
> /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/
> modules/Bio/EnsEMBL/Compara/Utils/SpeciesTree.pm line 150. | 1 |
> | 18 | make_treebest_species_tree | 6 | 10
> | 16 | 16 | 2017-11-13 11:28:32 | 3 | FETCH_INPUT | Can't
> call method "get_all_subnodes" on an undefined value at
> /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/
> modules/Bio/EnsEMBL/Compara/Utils/SpeciesTree.pm line 150. | 1 |
> +-------------+----------------------------+----------------
> +--------+---------+-----------+---------------------+------
> -+--------------+-------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> -------+----------+
> 6 rows in set (0.00 sec)
>
> Do you have any suggestion?
>
> Thanks,
> Francesco
>
> 2017-11-09 17:25 GMT+01:00 Brandon Walts <bwalts at ebi.ac.uk>:
>
>> 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/6c4877d4eda1bf0
>> 469c29bdbe58932671848cc20/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/6c4877d4eda1bf0
>> 469c29bdbe58932671848cc20/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::RunnableD
>> B::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>
>> wrote:
>>
>> Hi Mateus,
>>
>> thank you for your answer.
>>
>> I am using 'ncbi_db' => 'mysql://anonymous@ensembldb.e
>> nsembl.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>:
>>
>>> 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>
>>> 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)
>>> 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.
>>>
>>>
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