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Hi Will,<br>
<br>
I'm querying local Ensembl DB (76, GRCh38).<br>
As you said maybe the problem is due to downloaded cache, on
previous releases I had only one cache as there was only on human
assembly available.<br>
For release 76 I've the following two directories with their
respective caches:<br>
<ul>
<li>/share/references/vep/homo_sapiens/76_GRCh38/</li>
<li>/share/references/vep/homo_sapiens/76_GRCh37/</li>
</ul>
I'm using these options related to cache when using VEP script:<br>
dir_cache /share/references/vep<br>
assembly GRCh38<br>
<br>
I wasn't using assembly flag until this vep release. I thought I
could have both caches and switch between them with assembly flag.
Anyways, maybe the problem is in directory structure, and
GRCh37/GRCh38 directories should be on same level inside "76"
directory.<br>
<br>
I guess having the correct directory structure will solve the
problem.<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 07/10/14 13:51, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX017=hbAMkeCa0KM4qwXud71NyLNutVTWrDAXfKVF9u9Q@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>I suspect the issue is to do with database connections.</div>
<div><br>
</div>
<div>If you are running your plugin with the VEP in offline mode
(--offline), then you will be unable to retrieve data from the
databases without instantiating your own registry instance and
adaptors within the plugin.</div>
<div><br>
</div>
<div>If you are running the VEP using --cache or --database you
shouldn't have this issue; just make sure that your cache
version and the version of the database you are connecting to
match, and that the assemblies also match.</div>
<div><br>
</div>
<div>If I run, for example:</div>
<div><br>
</div>
<div>perl -I vep_plugins/ <a moz-do-not-send="true"
href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a>
-cache -port 3337 -dir ~/.vep/77/GRCh37/ -force -i
example_GRCh37.vcf -plugin Interpro_fixed<br>
</div>
<div><br>
</div>
<div>it runs without an issue. Or similarly for the GRCh38
example:</div>
<div><br>
</div>
<div>perl -I vep_plugins/ <a moz-do-not-send="true"
href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a>
-cache -dir ~/.vep/77/ -force -i example_GRCh38.vcf -plugin
Interpro_fixed<br>
</div>
<div><br>
</div>
<div>In both these cases the VEP will use <a
moz-do-not-send="true" href="http://ensembldb.ensembl.org">ensembldb.ensembl.org</a>
to retrieve data; the first example uses port 3337 to connect
to the GRCh37 mirror, and the second the default (3306) port
to connect to the latest GRCh38 mirror.</div>
<div><br>
</div>
<div>HTH</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 3 October 2014 16:20, 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 text="#000066" bgcolor="#FFFFFF"> Dear developers,<br>
<br>
I'm experiencing some VEP plugin errors on Ensembl 76+.<br>
<br>
I've uploaded both plugins failing to this public
repository: <a moz-do-not-send="true"
href="https://github.com/guillermomarco/vep_plugins"
target="_blank">https://github.com/guillermomarco/vep_plugins</a><br>
<br>
I've been looking for API changes in
<a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1Utils_1_1BaseVepPlugin.html#a2d966d465a2bbc2a067417cc4978e304"
target="_blank">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1Utils_1_1BaseVepPlugin.html#a2d966d465a2bbc2a067417cc4978e304</a>
but I can't really find why I'm getting the following
errors:<br>
<br>
<pre>Plugin 'Interpro_fixed' went wrong: Can't call method "translation" on an undefined value at Interpro_fixed.pm line 107</pre>
<pre>Plugin 'Gene_description' went wrong: Can't call method "description" on an undefined value at Gene_description.pm line 78.
</pre>
It's like hashes are empty:<br>
<br>
<table>
<tbody>
<tr>
<td style="padding:0px
10px;font-family:Consolas,'Liberation
Mono',Menlo,Courier,monospace;font-size:12px;color:rgb(51,51,51);vertical-align:top;white-space:pre-wrap;overflow:visible">
<span style="color:rgb(0,128,128)">$gene</span> <span
style="font-weight:bold">=</span> <span
style="color:rgb(0,128,128)">$config</span><span
style="font-weight:bold">-></span><span>{</span><span
style="color:rgb(51,51,51)">ga</span><span>}</span><span
style="font-weight:bold">-></span><span
style="color:rgb(51,51,51)">fetch_by_transcript_stable_id</span><span>(</span><span
style="color:rgb(0,128,128)">$transcript_id</span><span>);</span></td>
</tr>
<tr>
<td style="padding:0px
10px;width:50px;min-width:50px;font-family:Consolas,'Liberation
Mono',Menlo,Courier,monospace;font-size:12px;line-height:18px;color:rgba(0,0,0,0.298039);vertical-align:top;text-align:right;border-style:solid;border-color:rgb(238,238,238);border-width:0px
1px 0px 0px"><br>
</td>
<td style="padding:0px
10px;font-family:Consolas,'Liberation
Mono',Menlo,Courier,monospace;font-size:12px;color:rgb(51,51,51);vertical-align:top;white-space:pre-wrap;overflow:visible">
<span style="color:rgb(0,128,128)">$gene_desc</span>
<span style="font-weight:bold">=</span> <span
style="color:rgb(0,128,128)">$gene</span><span
style="font-weight:bold">-></span><span
style="color:rgb(51,51,51)">description</span><span>;</span></td>
</tr>
</tbody>
</table>
<br>
<table>
<tbody>
<tr>
<td style="padding:0px
10px;font-family:Consolas,'Liberation
Mono',Menlo,Courier,monospace;font-size:12px;color:rgb(51,51,51);vertical-align:top;white-space:pre-wrap;overflow:visible">
<span style="font-weight:bold">my</span> <span
style="color:rgb(0,128,128)">$slice_adaptor</span>
<span style="font-weight:bold">=</span> <span
style="color:rgb(0,128,128)">$config</span><span
style="font-weight:bold">-></span><span>{</span><span
style="color:rgb(51,51,51)">reg</span><span>}</span><span
style="font-weight:bold">-></span><span
style="color:rgb(51,51,51)">get_adaptor</span><span>((</span><span
style="color:rgb(0,128,128)">$config</span><span
style="font-weight:bold">-></span><span>{</span><span
style="color:rgb(51,51,51)">species</span><span>}),</span>
<span style="color:rgb(223,80,0)">'core'</span><span>,</span>
<span style="color:rgb(223,80,0)">'Transcript'</span><span>);</span></td>
</tr>
<tr>
<td style="padding:0px
10px;width:50px;min-width:50px;font-family:Consolas,'Liberation
Mono',Menlo,Courier,monospace;font-size:12px;line-height:18px;color:rgba(0,0,0,0.298039);vertical-align:top;text-align:right;border-style:solid;border-color:rgb(238,238,238);border-width:0px
1px 0px 0px"><br>
</td>
<td style="padding:0px
10px;font-family:Consolas,'Liberation
Mono',Menlo,Courier,monospace;font-size:12px;color:rgb(51,51,51);vertical-align:top;white-space:pre-wrap;overflow:visible">
<span style="font-weight:bold">my</span> <span
style="color:rgb(0,128,128)">$tr</span> <span
style="font-weight:bold">=</span> <span
style="color:rgb(0,128,128)">$slice_adaptor</span><span
style="font-weight:bold">-></span><span
style="color:rgb(51,51,51)">fetch_by_stable_id</span><span>(</span><span
style="color:rgb(0,128,128)">$Transcript</span><span>);</span></td>
</tr>
<tr>
<td style="padding:0px
10px;width:50px;min-width:50px;font-family:Consolas,'Liberation
Mono',Menlo,Courier,monospace;font-size:12px;line-height:18px;color:rgba(0,0,0,0.298039);vertical-align:top;text-align:right;border-style:solid;border-color:rgb(238,238,238);border-width:0px
1px 0px 0px"><br>
</td>
<td style="padding:0px
10px;font-family:Consolas,'Liberation
Mono',Menlo,Courier,monospace;font-size:12px;color:rgb(51,51,51);vertical-align:top;white-space:pre-wrap;overflow:visible">
<span style="font-weight:bold">my</span> <span
style="color:rgb(0,128,128)">$translation</span>
<span style="font-weight:bold">=</span> <span
style="color:rgb(0,128,128)">$tr</span><span
style="font-weight:bold">-></span><span
style="color:rgb(51,51,51)">translation</span><span>;</span></td>
</tr>
</tbody>
</table>
<br>
I suspect of <span style="color:rgb(0,128,128)">$config</span><span
style="font-weight:bold">-></span><span>{</span><span
style="color:rgb(51,51,51)">ga</span><span>} and </span><span
style="color:rgb(0,128,128)">$config</span><span
style="font-weight:bold">-></span><span>{</span><span
style="color:rgb(51,51,51)">reg</span><span>} are the
cause of this problem, because I still see </span><span><span
style="color:rgb(51,51,51)"><span
style="color:rgb(51,51,51)">fetch_by_transcript_stable_id</span><span>
and </span>fetch_by_stable_id</span><span></span>
methods on Ensembl API.<br>
<br>
Thanks !<br>
<br>
<br>
Best regards,<br>
Guillermo.<br>
</span> </div>
<br>
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<br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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</pre>
</blockquote>
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