[ensembl-dev] skip lock tables for ensembl-compara

[Francesco Lamanna]

Hi Mateus,

thank you for your answer.

I am using 'ncbi_db'   => 'mysql://
anonymous at 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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