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Please do not send in duplicate emails to both Ensembl helpdesk and
Ensembl dev as it means that multiple people are working on your
query, wasting their time.<br>
<br>
<div class="moz-cite-prefix">On 18/03/2015 07:32, namchul ghim
wrote:<br>
</div>
<blockquote
cite="mid:CANi7z4cBuHZuaewZfum_aiaghBUfwcfF5VXHkpQAynYA+fvaEA@mail.gmail.com"
type="cite">
<div dir="ltr">
<div style="font-size:12.8000001907349px">After installing
Ensembl_v79, I annotated vep cache with GRch37. </div>
<div style="font-size:12.8000001907349px">When doing so I got a
following message: <br>
Can't call method "impact" on an undefined value at
/mnt/lustre/Tools/VEP/src/ensembl-tools-release-79/scripts/variant_effect_predictor <br>
/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2379.</div>
<div style="font-size:12.8000001907349px"><br>
</div>
<div style="font-size:12.8000001907349px">When I checked the
following source file, there is no definition of imapct()
function. There is only function name in the same line.</div>
<div style="font-size:12.8000001907349px">Isn't that a bug?</div>
<div style="font-size:12.8000001907349px"><br>
</div>
<div style="font-size:12.8000001907349px">Also, in same
condition, annotating only vep cache with GRCh38 version was
successful.</div>
<div style="font-size:12.8000001907349px"><br>
</div>
<div style="font-size:12.8000001907349px">What is going on?</div>
<div style="font-size:12.8000001907349px"><br>
</div>
<div style="font-size:12.8000001907349px">Additionally, when I
was annotating vep cache with GRCh38 version, there is a
warning message in cache file.</div>
<div style="font-size:12.8000001907349px">The warning message is
as follow:</div>
<span style="font-size:12.8000001907349px">
<div>WARNING: Could not find variation cache for
22:51000001-52000000</div>
<div>WARNING: Could not find variation cache for
22:51000001-52000000</div>
<div>WARNING: Could not find variation cache for
22:51000001-52000000</div>
<div>WARNING: Could not find variation cache for
22:51000001-52000000</div>
<div>WARNING: Could not find cache for 22:51000001-52000000</div>
<div>WARNING: Could not find cache for 22:51000001-52000000</div>
<div><br>
</div>
</span>
<div style="font-size:12.8000001907349px">When I checked the
actual cache folder, there is no file in such range. Is this
something I should consider or can I ignore this message?</div>
<div style="font-size:12.8000001907349px"><br>
</div>
<div style="font-size:12.8000001907349px">For your information,
the vep cahce is downloaded in this location:</div>
<div style="font-size:12.8000001907349px"><a
moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/release-79/variation/VEP/homo_sapiens_vep_79_GRCh38.tar.gz"
target="_blank">ftp://ftp.ensembl.org/pub/release-79/variation/VEP/homo_sapiens_vep_79_GRCh38.tar.gz</a></div>
<div style="font-size:12.8000001907349px"><br>
</div>
<div style="font-size:12.8000001907349px">Thank you very much!</div>
</div>
<br>
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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