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<div class="moz-cite-prefix">Hello Matthieu,<br>
<br>
I've been using VEP overnight with a more extense dataset. I've
annotated more than 40k variants and conservation score is being
always reported as empty ("-")<br>
<br>
Currently the "script" I'm using is Conservation.pm plugin
provided in VEP repository:<br>
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
<a
href="https://github.com/ensembl-variation/VEP_plugins/blob/master/Conservation.pm">https://github.com/ensembl-variation/VEP_plugins/blob/master/Conservation.pm</a><br>
<br>
Only problem I see is use of MethodLinkSpeciesSet which is
deprecated in current version.<big><big><big><span style="color:
rgb(85, 85, 85); font-size: 13px; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: 16px; text-align: left; text-indent:
0px; text-transform: none; white-space: normal;
word-spacing: 0px; background-color: rgb(255, 255, 255);
display: inline ! important; float: none;"><big></big></span><big><big><span
style="color: rgb(85, 85, 85); font-size: 13px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: 16px;
text-align: left; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
background-color: rgb(255, 255, 255); display: inline
! important; float: none;"></span></big></big></big></big><br>
<span style="color: rgb(85, 85, 85); font-family: 'Luxi Sans',
Helvetica, Arial, Geneva, sans-serif; font-size: 13px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: 16px; orphans: auto;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255,
255, 255); display: inline !important; float: none;"></span></big><br>
<br>
<br>
<br>
On 10/10/2013 12:04 PM, Guillermo Marco Puche wrote:<br>
</div>
<blockquote cite="mid:52567BC4.2010506@sistemasgenomicos.com"
type="cite">
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http-equiv="Content-Type">
<div class="moz-cite-prefix">Hello Matthieu,<br>
<br>
Indeed conservation score is appearing in output annotated file.<br>
Thank you for the information, I was just wanted to be sure this
wasn't an error and just a warning.<br>
<br>
Again thanks !<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<br>
On 10/10/2013 11:25 AM, Matthieu Muffato wrote:<br>
</div>
<blockquote cite="mid:52567293.7010102@ebi.ac.uk" type="cite">Hi
Guillermo, <br>
<br>
The message "Cannot find the core database of '...' in the
Registry. Be aware that getting Core objects from Compara is not
possible for this species" is not an error, but just a warning
issued by the Compara API. <br>
<br>
I think it is still fine in your case (getting conservation
scores). There could only be a problem if you have a script that
tries to get a Slice, Gene, Transcript object from a Compara
alignment, gene tree, etc <br>
<br>
The code in e73 is systematically showing those warnings, whilst
the previous versions did not at all. It will be less verbose
again in e74. <br>
<br>
Best, <br>
Matthieu <br>
<br>
On 10/10/13 09:19, Guillermo Marco Puche wrote: <br>
<blockquote type="cite">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 <br>
problem with my own DB. In fact I still get the same error.
I'm using <br>
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 <br>
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>
<blockquote type="cite">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>
*./variant_effect_predictor.pl -i example.vcf -o example.vep
<br>
-dir_plugins
/home/likewise-open/SGNET/gmarco/vep_config/Plugins <br>
-plugin Conservation --database --force_overwrite* <br>
<br>
<br>
I've installed bioperl, ensembl core, compara, variation, <br>
functgenomics & ontology api (downloaded this morning).
<br>
<br>
It's strange because indeed output file has conservation
score in <br>
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>
<blockquote type="cite">Hello, <br>
<br>
I don't see any similar issues testing with a small input
file. <br>
<br>
The Conservation plugin depends on the ensembl-compara API
module - <br>
check that you have updated it to the latest version (73).
Note that <br>
this is not done by the VEP installer since the
ensembl-compara <br>
module is not required by the core VEP. <br>
<br>
If you're using CVS, just do: <br>
<br>
cd /home/likewise-open/SGNET/gmarco/src/ensembl-compara/ <br>
cvs up -dPr branch-ensembl-73 <br>
<br>
If you still see the issue, can you please provide a
sample of input <br>
and the command line flags you were using that recreates
the error. <br>
<br>
Thanks <br>
<br>
Will McLaren <br>
Ensembl Variation <br>
<br>
<br>
<br>
On 7 October 2013 11:54, Guillermo Marco Puche <br>
<<a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>
<br>
<a moz-do-not-send="true" class="moz-txt-link-rfc2396E"
href="mailto:guillermo.marco@sistemasgenomicos.com"><mailto:guillermo.marco@sistemasgenomicos.com></a>>
wrote: <br>
<br>
Hello, <br>
<br>
I recently updated to ensembl73 database. I've found
the <br>
following problem with Conservation plugin: <br>
<br>
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. <br>
<br>
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. <br>
<br>
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. <br>
<br>
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. <br>
<br>
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. <br>
<br>
(...) <br>
<br>
-------------------- WARNING ---------------------- <br>
<br>
MSG: Unable to find method_link_species_set with
method_link_type of Conservation_score and species_set_tag
value of mammals <br>
<br>
FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm
LINE: 567 <br>
<br>
CALLED BY: vep_config/Plugins/Conservation.pm LINE:
82 <br>
<br>
Date (localtime) = Mon Oct 7 12:36:33 2013 <br>
<br>
Ensembl API version = 73 <br>
<br>
--------------------------------------------------- <br>
<br>
2013-10-07 12:36:33 - Failed to instantiate plugin
Conservation: Failed to fetch MLSS for Conservation_score
and mammals <br>
<br>
<br>
Thank you. <br>
<br>
Best regards, <br>
Guillermo. <br>
<br>
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