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<div class="moz-cite-prefix">Hello Will,<br>
<br>
I've reinstalled the whole API and I'm still getting the same
errors.<br>
I'm testing it with remote ensembl installation to discard there's
a problem with my own DB. In fact I still get the same error. I'm
using example.vcf file provided with vep as input.<br>
<br>
I attach a log in this e-mail with the vep command (same I posted
in my previous e-mail) and the whole output.<br>
<br>
Thank you !<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<br>
On 10/07/2013 05:02 PM, Guillermo Marco Puche wrote:<br>
</div>
<blockquote cite="mid:5252CD03.80702@sistemasgenomicos.com"
type="cite">
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<div class="moz-cite-prefix">Hello Will,<br>
<br>
I'm testing it with example.vcf included in vep73 package.<br>
<br>
This is the command i'm using:<br>
<br>
<b>./variant_effect_predictor.pl -i example.vcf -o example.vep
-dir_plugins
/home/likewise-open/SGNET/gmarco/vep_config/Plugins -plugin
Conservation --database --force_overwrite</b><br>
<br>
<br>
I've installed bioperl, ensembl core, compara, variation,
functgenomics & ontology api (downloaded this morning).<br>
<br>
It's strange because indeed output file has conservation score
in output. I don't know what all those errors come from.<br>
<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 10/07/2013 04:29 PM, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX01DUDCtMqBXeZ6po1b4gzoAuYDhUmwYsxCTJkDukpjeQ@mail.gmail.com"
type="cite">
<div dir="ltr">Hello,
<div><br>
</div>
<div>I don't see any similar issues testing with a small input
file.<br>
<div><br>
</div>
<div>The Conservation plugin depends on the ensembl-compara
API module - check that you have updated it to the latest
version (73). Note that this is not done by the VEP
installer since the ensembl-compara module is not required
by the core VEP.</div>
<div><br>
</div>
<div>If you're using CVS, just do:</div>
<br>
cd /home/likewise-open/SGNET/gmarco/src/ensembl-compara/<br>
cvs up -dPr branch-ensembl-73
<div><br>
</div>
<div>If you still see the issue, can you please provide a
sample of input and the command line flags you were using
that recreates the error.</div>
<div><br>
<div>Thanks<br>
<br>
Will McLaren</div>
<div>Ensembl Variation<br>
<div><br>
</div>
</div>
</div>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 7 October 2013 11:54, Guillermo
Marco Puche <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000066"> Hello,<br>
<br>
I recently updated to ensembl73 database. I've found the
following problem with Conservation plugin:<br>
<br>
<pre>Cannot find the core database of 'takifugu_rubripes' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.</pre>
<pre>Cannot find the core database of 'ciona_savignyi' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.</pre>
<pre>Cannot find the core database of 'macaca_mulatta' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.</pre>
<pre>Cannot find the core database of 'echinops_telfairi' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.</pre>
<pre>Cannot find the core database of 'gasterosteus_aculeatus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.</pre>
(...)<br>
<pre>-------------------- WARNING ----------------------</pre>
<pre>MSG: Unable to find method_link_species_set with method_link_type of Conservation_score and species_set_tag value of mammals</pre>
<pre>FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 567</pre>
<pre>CALLED BY: vep_config/Plugins/Conservation.pm LINE: 82</pre>
<pre>Date (localtime) = Mon Oct 7 12:36:33 2013</pre>
<pre>Ensembl API version = 73</pre>
<pre>---------------------------------------------------</pre>
<pre>2013-10-07 12:36:33 - Failed to instantiate plugin Conservation: Failed to fetch MLSS for Conservation_score and mammals</pre>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
</div>
<br>
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