<div dir="ltr">Hi Alison,<div><br></div><div>It looks from the the path in your error message that your API is still version 85.</div><div><br></div><div>If you are running the new (ensembl-vep) code, you should use the latest (release/87) version of the ensembl, ensembl-variation and ensembl-funcgen API checkouts. The INSTALL.pl script will download a set of these within the ensembl-vep directory for you to use, or you may use git to update the directories from the path in your error message.</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 15 February 2017 at 09:12, MEYNERT Alison <span dir="ltr"><<a href="mailto:alison.meynert@igmm.ed.ac.uk" target="_blank">alison.meynert@igmm.ed.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">




<div dir="ltr">
<div id="m_-8037915299930075515divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif" dir="ltr">
<p>I've been running the new VEP package on the v87 GRCh37 downloaded cache, and get a warning for just one of the lines in my input VCF.</p>
<p><br>
</p>
<p></p>
<p style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">20<span style="white-space:pre-wrap">
</span>34067454<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap">
</span>AT<span style="white-space:pre-wrap"> </span>A</span></p>
<br>
<p></p>
<p></p>
<p style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">WARNING: 63631 : Use of uninitialized value $cdna_position in pattern match (m//) at /exports/igmm/software/pkg/<wbr>el7/libs/ensembl_api/85/<wbr>ensembl-variation/modules/Bio/<wbr>EnsEMBL/Variation/<wbr>TranscriptVariationAllele.pm
 line 1901, <GEN4> line 57651.</span></p>
<p style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">Use of uninitialized value $cdna_coord in concatenation (.) or string at /exports/igmm/software/pkg/<wbr>el7/libs/ensembl_api/85/<wbr>ensembl-variation/modules/Bio/<wbr>EnsEMBL/Variation/<wbr>TranscriptVariationAllele.pm
 line 1933, <GEN4> line 57651.</span></p>
<p style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">Use of uninitialized value $exon_start_coord in addition (+) at /exports/igmm/software/pkg/<wbr>el7/libs/ensembl_api/85/<wbr>ensembl-variation/modules/Bio/<wbr>EnsEMBL/Variation/<wbr>TranscriptVariationAllele.pm line 703,
 <GEN4> line 57651.</span></p>
<br>
<p></p>
<p>When I try inputting this variant to the GRCh37 web interface, it works. I also didn't get any warnings when running the old VEP package on the v86 GRCh37 downloaded cache, and get the following hits:</p>
<p><br>
</p>
<p></p>
<p style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">ENSG00000126001<span style="white-space:pre-wrap">
</span>ENST00000342580<span style="white-space:pre-wrap"> </span>intron_variant</span></p>
<p style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">ENSG00000126001<span style="white-space:pre-wrap">
</span>ENST00000397527<span style="white-space:pre-wrap"> </span>intron_variant</span></p>
<p style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">ENSG00000126001</span><span style="font-variant-ligatures:no-common-ligatures;white-space:pre-wrap">
</span><span style="font-variant-ligatures:no-common-ligatures">ENST00000425096</span><span style="font-variant-ligatures:no-common-ligatures;white-space:pre-wrap">
</span><span style="font-variant-ligatures:no-common-ligatures">downstream_gene_variant</span><br>
</p>
<p style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">ENSG00000126001<span style="white-space:pre-wrap">
</span>ENST00000425934<span style="white-space:pre-wrap"> </span>downstream_gene_variant</span></p>
<p style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures"></span></p>
<p style="margin-right:0px;margin-left:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures"><span style="font-family:Menlo;font-size:11px;font-variant-ligatures:no-common-ligatures">ENSG00000126001</span><span style="font-family:Menlo;font-size:11px;font-variant-ligatures:no-common-ligatures;white-space:pre-wrap">
</span><span style="font-family:Menlo;font-size:11px;font-variant-ligatures:no-common-ligatures">ENST00000461386</span><span style="font-family:Menlo;font-size:11px;font-variant-ligatures:no-common-ligatures;white-space:pre-wrap">
</span><span style="font-family:Menlo;font-size:11px;font-variant-ligatures:no-common-ligatures">downstream_gene_variant</span></span></p>
<div>ENSG00000230155<span style="white-space:pre-wrap"> </span>ENST00000416260<span style="white-space:pre-wrap">
</span>intron_variant,non_coding_<wbr>transcript_variant<br>
</div>

<p></p>
<div>ENSG00000230155<span style="white-space:pre-wrap"> </span>ENST00000444933<span style="white-space:pre-wrap">
</span>intron_variant,non_coding_<wbr>transcript_variant<br>
</div>

<p></p>
<p style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">ENSG00000230155<span style="white-space:pre-wrap">
</span>ENST00000453914<span style="white-space:pre-wrap"> </span>intron_variant,non_coding_<wbr>transcript_variant</span></p>
<p style="margin:0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<br>
</p>
<p></p>
<p><span style="font-size:12pt">Cheers,</span><br>
</p>
<p>Alison</p><span class="HOEnZb"><font color="#888888">
<p><br>
</p>
<div id="m_-8037915299930075515Signature">
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