<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hi Francesco,</div><div class=""><br class=""></div><div class="">So what’s happening here is that you are trying to lock a table in one of our servers.</div><div class=""><br class=""></div><div class="">That can be fixed by telling mysqldump to avoid locking the table. (Like you initially suspected)</div><div class=""><br class=""></div><div class="">You could do that directly on the eHive runnable "ehive/master/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm”</div><div class=""><br class=""></div><div class="">The dump command is constructed at:</div><div class=""><a href="https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L117" class="">https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L117</a></div><div class=""><br class=""></div><div class="">I would suggest you to create a new entry to “mode_options”:</div><div class=""><a href="https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L112" class="">https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L112</a></div><div class=""><br class=""></div><div class="">So that you could access directly from your pipeline config file, by setting something like:</div><div class=""><div class=""><br class=""></div><div class=""></div></div><blockquote type="cite" class=""><div class=""><div class=""><font face="Courier New" class="">        {   -logic_name    => 'copy_ncbi_table',</font></div><div class=""><font face="Courier New" class="">            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer',</font></div><div class=""><font face="Courier New" class="">            -parameters    => {</font></div><div class=""><font face="Courier New" class="">                'src_db_conn'   => '#ncbi_db#',</font></div><div class=""><font face="Courier New" class="">                'mode'          => ’<b class="">SKIP_LOCK</b>',</font></div><div class=""><font face="Courier New" class="">                'filter_cmd'    => 'sed "s/ENGINE=MyISAM/ENGINE=InnoDB/"',</font></div><div class=""><font face="Courier New" class="">            },</font></div><div class=""><font face="Courier New" class="">        },</font></div></div></blockquote><div class=""><br class=""></div><div class="">Please let me know if that doesn’t work.</div><div class=""><br class=""></div><div class="">Cheers,</div><div class=""><br class=""></div><div class="">Mateus.</div><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""></div><br class=""><div><blockquote type="cite" class=""><div class="">On 9 Nov 2017, at 15:44, Francesco Lamanna <<a href="mailto:francesco.lamanna@gmail.com" class="">francesco.lamanna@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class=""><div class="">Hi Mateus,<br class=""><br class=""></div>thank you for your answer.<br class=""><br class=""></div>I am using 'ncbi_db'   => 'mysql://<a href="http://anonymous@ensembldb.ensembl.org/ensembl_compara_90" class="">anonymous@ensembldb.ensembl.org/ensembl_compara_90</a>' to conncect to ncbi_db (I used the same value as in the NoMasterProteinTrees_conf.pm example).<br class=""><br class=""></div>The failing analysis is copy_ncbi_table(9).<br class=""><br class=""></div>Cheers,<br class=""></div>Francesco.<br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2017-11-09 16:29 GMT+01:00 Mateus Patricio <span dir="ltr" class=""><<a href="mailto:mateus@ebi.ac.uk" target="_blank" class="">mateus@ebi.ac.uk</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Hi Francesco,<div class=""><br class=""></div><div class="">Looks like your pipeline is using the user anonymous to connect to the database.</div><div class=""><br class=""></div><div class="">I would suggest that you add the skip option within your runnable.</div><div class=""><br class=""></div><div class="">Which analysis is actually failing?</div><div class=""><br class=""></div><div class="">Cheers,</div><div class=""><br class=""></div><div class="">Mateus.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div class=""><blockquote type="cite" class=""><div class=""><div class="h5"><div class="">On 8 Nov 2017, at 17:36, Francesco Lamanna <<a href="mailto:francesco.lamanna@gmail.com" target="_blank" class="">francesco.lamanna@gmail.com</a>> wrote:</div><br class="m_-3216016505973850452Apple-interchange-newline"></div></div><div class=""><div class=""><div class="h5"><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class="">Hello,<br class=""><br class=""></div>I am trying to apply the ProteinTrees pipeline to a set of Ensembl and non-Ensembl genomes. <br class=""><br class="">When running the pipeline without a master database (via <a href="http://beekeeper.pl/" target="_blank" class="">beekeeper.pl</a>) I get the following error:<br class=""><br class="">ensembl_compara_90 ncbi_taxa_node  | sed "s/ENGINE=MyISAM/ENGINE=<wbr class="">InnoDB/" |  mysql -h127.0.0.1 -P3306 -uroot -p$EHIVE_TMP_PASSWORD_0 hd_cc141_test_protein_trees_<wbr class="">no_master_90' resulted in an error code=2<br class="">stderr is: mysql: [Warning] Using a password on the command line interface can be insecure.<br class="">mysqldump: Got error: 1044: Access denied for user 'anonymous'@'%' to database 'ensembl_compara_90' when doing LOCK TABLES <br class=""><br class=""><br class=""></div>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?<br class=""><br class=""></div>Thanks,<br class=""></div>Francesco.<br class=""><div class=""><div class=""><div class=""><br class=""><br class=""></div></div></div></div></div></div>
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