[ensembl-dev] skip lock tables for ensembl-compara
Francesco Lamanna
francesco.lamanna at gmail.com
Mon Nov 13 10:50:17 GMT 2017
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/
> 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>
> wrote:
>
> Hi Mateus,
>
> thank you for your answer.
>
> I am using 'ncbi_db' => 'mysql://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>:
>
>> 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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