<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="">Hi Francesco,<div class=""><br class=""></div><div class="">Could you please confirm which checkout version of the compara code you have?</div><div class=""><br class=""></div><div class="">Cheers,</div><div class=""><br class=""></div><div class="">Mateus.</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 13 Nov 2017, at 10:50, 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 and Brandon,<br class=""><br class=""></div>many thanks for your patch, it solved the issue.<br class=""><br class=""></div>Unfortunately, I got stuck at the successive step with the following error message:<br class=""><br class="">mysql> SELECT * FROM msg;<br class="">+-------------+----------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br class="">| analysis_id | logic_name | log_message_id | job_id | role_id | worker_id | when_logged | retry | status | msg | is_error |<br class="">+-------------+----------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br class="">| 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 |<br class="">| 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 |<br class="">| 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 |<br class="">| 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 |<br class="">| 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 |<br class="">| 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 |<br class="">+-------------+----------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br class="">6 rows in set (0.00 sec)<br class=""><br class=""></div>Do you have any suggestion?<br class=""><br class=""></div>Thanks,<br class=""></div>Francesco<br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2017-11-09 17:25 GMT+01:00 Brandon Walts <span dir="ltr" class=""><<a href="mailto:bwalts@ebi.ac.uk" target="_blank" class="">bwalts@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 text="#000000" bgcolor="#FFFFFF" class=""><p class="">Hi Francesco</p><p class="">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. <br class="">
</p><p class="">Users who wish to retain the table locking behavior can switch it
on by passing a parameter 'lock_tables=1' to MySQLTransfer.pm</p><p class="">Best<span class="HOEnZb"><font color="#888888" class=""><br class="">
-Brandon<br class="">
</font></span></p><div class=""><div class="h5">
<br class="">
<div class="m_936139081383433000moz-cite-prefix">On 09/11/2017 16:20, Mateus Patricio
wrote:<br class="">
</div>
<blockquote type="cite" 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/<wbr class="">EnsEMBL/Hive/RunnableDB/<wbr class="">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" target="_blank" class="">https://github.com/Ensembl/<wbr class="">ensembl-hive/blob/<wbr class="">6c4877d4eda1bf0469c29bdbe58932<wbr class="">671848cc20/modules/Bio/<wbr class="">EnsEMBL/Hive/RunnableDB/<wbr class="">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" target="_blank" class="">https://github.com/Ensembl/<wbr class="">ensembl-hive/blob/<wbr class="">6c4877d4eda1bf0469c29bdbe58932<wbr class="">671848cc20/modules/Bio/<wbr class="">EnsEMBL/Hive/RunnableDB/<wbr class="">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>
<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::<wbr class="">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=<wbr class="">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 class="">
<blockquote type="cite" class="">
<div class="">On 9 Nov 2017, at 15:44, Francesco Lamanna
<<a href="mailto:francesco.lamanna@gmail.com" target="_blank" class="">francesco.lamanna@gmail.com</a>>
wrote:</div>
<br class="m_936139081383433000Apple-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" target="_blank" class="">anonymous@ensembldb.<wbr class="">ensembl.org/ensembl_compara_90</a><wbr class="">'
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="m_936139081383433000h5">
<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_936139081383433000m_-3216016505973850452Apple-interchange-newline">
</div>
</div>
<div class="">
<div class="">
<div class="m_936139081383433000h5">
<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=InnoDB<wbr class="">/" | mysql
-h127.0.0.1 -P3306 -uroot
-p$EHIVE_TMP_PASSWORD_0
hd_cc141_test_protein_trees_no<wbr class="">_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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