<div dir="ltr"><div><div><div><div><div>Hi Mateus and Brandon,<br><br></div>many thanks for your patch, it solved the issue.<br><br></div>Unfortunately, I got stuck at the successive step with the following error message:<br><br>mysql> SELECT * FROM msg;<br>+-------------+----------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br>| analysis_id | logic_name | log_message_id | job_id | role_id | worker_id | when_logged | retry | status | msg | is_error |<br>+-------------+----------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br>| 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>| 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>| 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>| 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>| 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>| 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>+-------------+----------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br>6 rows in set (0.00 sec)<br><br></div>Do you have any suggestion?<br><br></div>Thanks,<br></div>Francesco<br></div><div class="gmail_extra"><br><div class="gmail_quote">2017-11-09 17:25 GMT+01:00 Brandon Walts <span dir="ltr"><<a href="mailto:bwalts@ebi.ac.uk" target="_blank">bwalts@ebi.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<p>Hi Francesco</p>
<p>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>
</p>
<p>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>Best<span class="HOEnZb"><font color="#888888"><br>
-Brandon<br>
</font></span></p><div><div class="h5">
<br>
<div class="m_936139081383433000moz-cite-prefix">On 09/11/2017 16:20, Mateus Patricio
wrote:<br>
</div>
<blockquote type="cite">
<div>Hi Francesco,</div>
<div><br>
</div>
<div>So what’s happening here is that you are trying to
lock a table in one of our servers.</div>
<div><br>
</div>
<div>That can be fixed by telling mysqldump to avoid
locking the table. (Like you initially suspected)</div>
<div><br>
</div>
<div>You could do that directly on the eHive runnable
"ehive/master/modules/Bio/<wbr>EnsEMBL/Hive/RunnableDB/<wbr>MySQLTransfer.pm”</div>
<div><br>
</div>
<div>The dump command is constructed at:</div>
<div><a href="https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L117" target="_blank">https://github.com/Ensembl/<wbr>ensembl-hive/blob/<wbr>6c4877d4eda1bf0469c29bdbe58932<wbr>671848cc20/modules/Bio/<wbr>EnsEMBL/Hive/RunnableDB/<wbr>MySQLTransfer.pm#L117</a></div>
<div><br>
</div>
<div>I would suggest you to create a new entry to
“mode_options”:</div>
<div><a href="https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L112" target="_blank">https://github.com/Ensembl/<wbr>ensembl-hive/blob/<wbr>6c4877d4eda1bf0469c29bdbe58932<wbr>671848cc20/modules/Bio/<wbr>EnsEMBL/Hive/RunnableDB/<wbr>MySQLTransfer.pm#L112</a></div>
<div><br>
</div>
<div>So that you could access directly from your pipeline
config file, by setting something like:</div>
<div>
<div><br>
</div>
</div>
<blockquote type="cite">
<div>
<div><font face="Courier New"> {
-logic_name => 'copy_ncbi_table',</font></div>
<div><font face="Courier New">
-module =>
'Bio::EnsEMBL::Hive::<wbr>RunnableDB::MySQLTransfer',</font></div>
<div><font face="Courier New">
-parameters => {</font></div>
<div><font face="Courier New">
'src_db_conn' => '#ncbi_db#',</font></div>
<div><font face="Courier New">
'mode' => ’<b>SKIP_LOCK</b>',</font></div>
<div><font face="Courier New">
'filter_cmd' => 'sed
"s/ENGINE=MyISAM/ENGINE=<wbr>InnoDB/"',</font></div>
<div><font face="Courier New"> },</font></div>
<div><font face="Courier New"> },</font></div>
</div>
</blockquote>
<div><br>
</div>
<div>Please let me know if that doesn’t work.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Mateus.</div>
<div><br>
</div>
<div><br>
<div><br>
</div>
<br>
<div>
<blockquote type="cite">
<div>On 9 Nov 2017, at 15:44, Francesco Lamanna
<<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a>>
wrote:</div>
<br class="m_936139081383433000Apple-interchange-newline">
<div>
<div dir="ltr">
<div>
<div>
<div>
<div>
<div>Hi Mateus,<br>
<br>
</div>
thank you for your answer.<br>
<br>
</div>
I am using 'ncbi_db' => 'mysql://<a href="http://anonymous@ensembldb.ensembl.org/ensembl_compara_90" target="_blank">anonymous@ensembldb.<wbr>ensembl.org/ensembl_compara_90</a><wbr>'
to conncect to ncbi_db (I used the same value as
in the NoMasterProteinTrees_conf.pm example).<br>
<br>
</div>
The failing analysis is copy_ncbi_table(9).<br>
<br>
</div>
Cheers,<br>
</div>
Francesco.<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2017-11-09 16:29 GMT+01:00
Mateus Patricio <span dir="ltr"><<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@ebi.ac.uk</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi
Francesco,
<div><br>
</div>
<div>Looks like your pipeline is using
the user anonymous to connect to the database.</div>
<div><br>
</div>
<div>I would suggest that you add the
skip option within your runnable.</div>
<div><br>
</div>
<div>Which analysis is actually failing?</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Mateus.</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>
<blockquote type="cite">
<div>
<div class="m_936139081383433000h5">
<div>On 8 Nov 2017, at 17:36,
Francesco Lamanna <<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a>>
wrote:</div>
<br class="m_936139081383433000m_-3216016505973850452Apple-interchange-newline">
</div>
</div>
<div>
<div>
<div class="m_936139081383433000h5">
<div dir="ltr">
<div>
<div>
<div>
<div>Hello,<br>
<br>
</div>
I am trying to apply the
ProteinTrees pipeline to a set
of Ensembl and non-Ensembl
genomes. <br>
<br>
When running the pipeline
without a master database (via
<a href="http://beekeeper.pl/" target="_blank">beekeeper.pl</a>)
I get the following error:<br>
<br>
ensembl_compara_90
ncbi_taxa_node | sed
"s/ENGINE=MyISAM/ENGINE=InnoDB<wbr>/" | mysql
-h127.0.0.1 -P3306 -uroot
-p$EHIVE_TMP_PASSWORD_0
hd_cc141_test_protein_trees_no<wbr>_master_90'
resulted in an error code=2<br>
stderr is: mysql: [Warning]
Using a password on the
command line interface can be
insecure.<br>
mysqldump: Got error: 1044:
Access denied for user
'anonymous'@'%' to database
'ensembl_compara_90' when
doing LOCK TABLES <br>
<br>
<br>
</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>
<br>
</div>
Thanks,<br>
</div>
Francesco.<br>
<div>
<div>
<div><br>
<br>
</div>
</div>
</div>
</div>
</div>
</div>
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