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

Mateus Patricio mateus at ebi.ac.uk
Thu Nov 9 15:29:36 GMT 2017

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?



> 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 <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.
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