<HTML xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<HEAD><!-- Template generated by Exclaimer Mail Disclaimers on 03:49:08 pondělí, 25 dubna 2016 -->
<STYLE type=text/css>P.027b080b-4fe1-442b-af78-4a4c31036de8 {
MARGIN: 0cm 0cm 0pt
}
LI.027b080b-4fe1-442b-af78-4a4c31036de8 {
MARGIN: 0cm 0cm 0pt
}
DIV.027b080b-4fe1-442b-af78-4a4c31036de8 {
MARGIN: 0cm 0cm 0pt
}
TABLE.027b080b-4fe1-442b-af78-4a4c31036de8Table {
MARGIN: 0cm 0cm 0pt
}
DIV.Section1 {
page: Section1
}
</STYLE>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="Generator" content="Microsoft Word 14 (filtered medium)" />
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:Verdana;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
span.StylE-mailovZprvy19
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 70.85pt 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</HEAD>
<BODY lang="CS" link="blue" vlink="purple">
<P class=027b080b-4fe1-442b-af78-4a4c31036de8>
<div class="WordSection1">
<p class="MsoNormal"><span style=font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D>Great, thank you, it works now.<o:p></o:p></span></p>
<p class="MsoNormal"><span style=font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D>Bara<o:p></o:p></span></p>
<p class="MsoNormal"><span style=font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style=font-size:10.0pt;font-family:"Tahoma","sans-serif">From:</span></b><span style=font-size:10.0pt;font-family:"Tahoma","sans-serif"> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org]
<b>On Behalf Of </b>Will McLaren<br />
<b>Sent:</b> Monday, April 25, 2016 3:28 PM<br />
<b>To:</b> Ensembl developers list<br />
<b>Subject:</b> Re: [ensembl-dev] local installation VEP - error in GMAF, EUR_MAF, EA_MAF<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">Hello,<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Apologies, the initial release 84 of VEP had a bug in that affects newer (>=5.18) versions of Perl.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">A fix [1] has already been applied to the ensembl-variation GitHub repository, you can use INSTALL.pl to update VEP's API installation with the fixed version.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Regards<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Will McLaren<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Ensembl Variation<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">[1] : <a href="https://github.com/Ensembl/ensembl-variation/commit/e0b3b5129f67d51ac1beb2c0771291903154bcdf">https://github.com/Ensembl/ensembl-variation/commit/e0b3b5129f67d51ac1beb2c0771291903154bcdf</a><o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On 25 April 2016 at 14:01, Honysová Barbora <<a href="mailto:Barbora.Honysova@gennet.cz" target="_blank">Barbora.Honysova@gennet.cz</a>> wrote:<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style=mso-margin-top-alt:auto;mso-margin-bottom-alt:auto>Hello,<o:p></o:p></p>
<p class="MsoNormal" style=mso-margin-top-alt:auto;mso-margin-bottom-alt:auto>after the installation of VEP84 (API and databases) with cache and plugins I have run variant effect predictor like usually. When I have checked my results returned, I have encountered
the internal error when using a flag <b>--gmaf --maf_1kg --maf_exac --maf_esp</b> that no data have been received back into the final .txt file. If I try to run the same script, the version VEP83, using the databases and cache for version 83, I obtain the
correct data. When running VEP84 and databases and cache 83, no results in these columns appear. If I use plugin dbNSFP, the corresponding values are received as well. But our internal database setup of data coming from NGS is not bulit to cope with different
format using plugins.<o:p></o:p></p>
<p class="MsoNormal" style=mso-margin-top-alt:auto;mso-margin-bottom-alt:auto>So, please, do you know what is going on or where to look for this error?<o:p></o:p></p>
<p class="MsoNormal" style=mso-margin-top-alt:auto;mso-margin-bottom-alt:auto>Thanks, Bara<o:p></o:p></p>
</div>
<p> <o:p></o:p></p>
<p><span style=font-size:10.0pt;font-family:"Arial","sans-serif">Ing. Barbora Honysová</span><o:p></o:p></p>
<p><span style=font-size:10.0pt;font-family:"Arial","sans-serif">Odborný VŠ pracovník v laboratorních metodách na oddělení molekulárně genetické laboratoře - konzultant</span><o:p></o:p></p>
<p><span style=font-size:10.0pt;font-family:"Arial","sans-serif">GENNET, s.r.o.</span><o:p></o:p></p>
<p> <o:p></o:p></p>
<p><span style=font-size:10.0pt;font-family:"Arial","sans-serif">Kostelní 9, 170 00 Praha 7<br />
Tel: <a href="tel:%2B420%20222%20313%20000" target="_blank">+420 222 313 000</a></span><o:p></o:p></p>
<p><span style=font-size:10.0pt;font-family:"Arial","sans-serif"><a href="http://www.gennet.cz" target="_blank">www.gennet.cz</a><o:p></o:p></span></p>
<p> <o:p></o:p></p>
<p><o:p></o:p></p>
<p> <o:p></o:p></p>
<p style=margin:0cm;margin-bottom:.0001pt;line-height:115%><strong><i><span lang="EN-GB" style=font-size:11.0pt;line-height:115%;color:#0090D6>Where excellence meets hope</span></i></strong><span lang="EN-GB" style=font-size:7.5pt;line-height:115%;font-family:"Calibri","sans-serif";color:#7F7F7F><o:p></o:p></span></p>
<p class="MsoNormal" style=text-align:justify;line-height:115%><span lang="EN-GB" style=font-size:7.5pt;line-height:115%;color:black> </span><span lang="EN-GB" style=color:#7F7F7F><o:p></o:p></span></p>
<p class="MsoNormal" style=text-align:justify><span lang="EN-GB" style=font-size:7.0pt;color:#7F7F7F>Tento e-mail včetně jeho případných příloh je určen výlučně pro adresáta uvedeného v záhlaví e-mailové zprávy. Disclaimer je k nahlédnutí
<a href="http://www.gennet.cz/disclaimer/" target="_blank">zde</a> GENNET s.r.o. je českou společností registrovanou pod IČ 27080234 se sídlem Kostelní 9, Praha 7.</span><span lang="EN-GB" style=color:#7F7F7F><o:p></o:p></span></p>
<p class="MsoNormal" style=text-align:justify><span lang="EN-GB" style=font-size:7.0pt;color:#7F7F7F> </span><span lang="EN-GB" style=color:#7F7F7F><o:p></o:p></span></p>
<p class="MsoNormal" style=text-align:justify><span lang="EN-GB" style=font-size:7.0pt;color:#7F7F7F>This email communication including any attachments is intended solely for the user of the email address to which it was addressed. Please click
<a href="http://www.gennet.cz/disclaimer/" target="_blank">here</a> to see our disclaimer. GENNET is a Czech limited liability company (VAT ID CZ699004108). Its registered office is at Kostelni 9, Prague, Czech Republic.</span><span lang="EN-GB" style=color:#7F7F7F><o:p></o:p></span></p>
<p class="MsoNormal" style=text-align:justify><span lang="EN-GB" style=color:#7F7F7F> <o:p></o:p></span></p>
<p class="MsoNormal" style=text-align:justify><span lang="EN-GB" style=font-size:7.0pt;color:#F79646>Před vytištěním této zprávy vezměte v úvahu životní prostředí / Please don't print this email unless you really need to.</span><span lang="EN-GB" style=color:#7F7F7F><o:p></o:p></span></p>
<p class="MsoNormal"><span style=font-size:7.5pt;font-family:"Calibri","sans-serif";color:#7F7F7F> </span><span style=font-size:7.5pt;font-family:"Verdana","sans-serif";color:#BABABA>
<o:p></o:p></span></p>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal" style=margin-bottom:12.0pt><br />
</p></div></div></div></P>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8> </P>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><FONT size=2 face=Arial></FONT><span style='font-family:Arial; font-size:x-small; '>Ing. </span><span style='font-family:Arial; font-size:x-small; '>Barbora</span><FONT size=2 face=Arial> </FONT><span style='font-family:Arial; font-size:x-small; '>Honysová</span><FONT size=2 face=Arial></FONT><span style='font-family:Arial; font-size:x-small; '></span></P>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><span style='font-family:Arial; font-size:x-small; '>Odborný VŠ pracovník v laboratorních metodách na oddělení molekulárně genetické laboratoře - konzultant</span></P>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><FONT size=2 face=Arial>GENNET, s.r.o.</FONT></P>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><FONT size=2 face=Arial></FONT> </P>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"><span style='font-family:Arial; font-size:x-small; '></span>Kostelní 9, 170 00 Praha 7<br>Tel: +420 222 313 000</SPAN></P>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"><span style='font-family:Arial; font-size:x-small; '></span></P></SPAN><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'">
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><A href="http://www.gennet.cz">www.gennet.cz</A></P></SPAN><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"></SPAN>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"></P></SPAN>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"></SPAN></P>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"></SPAN></P>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"></SPAN> </P>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"></SPAN></P>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"></SPAN></P>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"><IMG id=IMG1 border=0 src="cid:image90cf74.GIF@84d95641.4ebb2db7" width=200 height=28 /></SPAN></P>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"></SPAN> </P><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"><FONT color=#bababa size=1 face=Verdana><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"><FONT color=#bababa size=1 face=Verdana><SPAN style="FONT-SIZE: 7.5pt; FONT-FAMILY: 'Calibri','sans-serif'; COLOR: #7f7f7f; LINE-HEIGHT: 115%"><SPAN lang=EN-GB style="FONT-SIZE: 7.5pt; FONT-FAMILY: 'Verdana','sans-serif'; COLOR: #bababa; mso-ansi-language: EN-GB; mso-bidi-font-family: Arial"></SPAN><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><o:p>
<P class=b3a921a9-d8f4-46e1-98b0-c11d889f9370 style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"><STRONG><I><SPAN lang=EN-GB style="FONT-SIZE: 11pt; COLOR: #0090d6; mso-ansi-language: EN-GB; mso-bidi-font-size: 13.5pt">Where
excellence meets hope</SPAN></I></STRONG><SPAN lang=EN-GB style="FONT-SIZE: 10pt; COLOR: #0090d6; mso-ansi-language: EN-GB; mso-bidi-font-size: 12.0pt"><o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style='FONT-SIZE: 7.5pt; FONT-FAMILY: "Times New Roman","serif"; LINE-HEIGHT: 115%; mso-ansi-language: EN-GB'><o:p><FONT color=#000000> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: normal"><SPAN style='FONT-SIZE: 7pt; FONT-FAMILY: "Times New Roman","serif"; COLOR: #7f7f7f; mso-themecolor: text1; mso-themetint: 128'>Tento
e-mail včetně jeho případných příloh je určen výlučně pro adresáta uvedeného
v záhlaví e-mailové zprávy. Disclaimer je k nahlédnutí </SPAN><SPAN style='FONT-SIZE: 7pt; TEXT-DECORATION: none; FONT-FAMILY: "Times New Roman","serif"; COLOR: #7f7f7f; mso-themecolor: text1; mso-themetint: 128; text-underline: none'></SPAN><SPAN style='FONT-SIZE: 7pt; FONT-FAMILY: "Times New Roman","serif"; COLOR: #7f7f7f; mso-themecolor: text1; mso-themetint: 128'><A href="http://www.gennet.cz/disclaimer/">zde</A> GENNET s.r.o. je českou
společností registrovanou pod IČ 27080234 se sídlem Kostelní 9, Praha
7.</SPAN></P>
<P class=MsoNormal style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: normal"><SPAN style='FONT-SIZE: 7pt; FONT-FAMILY: "Times New Roman","serif"; COLOR: #7f7f7f; mso-themecolor: text1; mso-themetint: 128'><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: normal"><SPAN style='FONT-SIZE: 7pt; FONT-FAMILY: "Times New Roman","serif"; COLOR: #7f7f7f; mso-themecolor: text1; mso-themetint: 128'>This
email communication including any attachments is intended solely for the user of
the email address to which it was addressed. Please click <A href="http://www.gennet.cz/disclaimer/">here</A></SPAN><A href="http://www.gennet.cz/disclaimer.html"><SPAN style='FONT-SIZE: 7pt; FONT-FAMILY: "Times New Roman","serif"; COLOR: #7f7f7f; mso-themecolor: text1; mso-themetint: 128'></SPAN></A><SPAN style='FONT-SIZE: 7pt; FONT-FAMILY: "Times New Roman","serif"; COLOR: #7f7f7f; mso-themecolor: text1; mso-themetint: 128'>
to see our disclaimer. GENNET is a Czech limited liability company (VAT ID
CZ699004108). Its registered office is at Kostelni 9, Prague, Czech
Republic.</SPAN></P>
<P class=MsoNormal style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: normal"><SPAN style='FONT-SIZE: 7pt; FONT-FAMILY: "Times New Roman","serif"; COLOR: #7f7f7f; mso-themecolor: text1; mso-themetint: 128'></SPAN> </P>
<P class=MsoNormal style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: normal"><SPAN style='FONT-SIZE: 7pt; FONT-FAMILY: "Times New Roman","serif"; COLOR: #f79646; mso-themecolor: accent6'>Před
vytištěním této zprávy vezměte v úvahu životní prostředí / </SPAN><SPAN lang=EN-GB style='FONT-SIZE: 7pt; FONT-FAMILY: "Times New Roman","serif"; COLOR: #f79646; mso-ansi-language: EN-GB; mso-themecolor: accent6'>Please
don't print this email unless you really need to</SPAN><SPAN style='FONT-SIZE: 7pt; FONT-FAMILY: "Times New Roman","serif"; COLOR: #f79646; mso-themecolor: accent6'>.</SPAN><SPAN style='FONT-SIZE: 7pt; FONT-FAMILY: "Times New Roman","serif"; COLOR: #7f7f7f; mso-themecolor: text1; mso-themetint: 128'><o:p></o:p></SPAN></P>
<P class=b3a921a9-d8f4-46e1-98b0-c11d889f9370 style="MARGIN: 0cm 0cm 0pt"></o:p></SPAN> </P></SPAN></FONT></SPAN><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"><FONT color=#bababa size=1 face=Verdana>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8></FONT></SPAN></FONT></SPAN><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'"></SPAN> </P>
<P class=027b080b-4fe1-442b-af78-4a4c31036de8><div class="WordSection1"><div><div><p class="MsoNormal" style=margin-bottom:12.0pt>_______________________________________________<br />
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br />
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">
http://lists.ensembl.org/mailman/listinfo/dev</a><br />
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
</P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P>
<P></P></FONT></SPAN>
<P></P></FONT></SPAN>
<P></P>
<P></P>
<P></P>
<P></P></SPAN></SPAN></FONT></SPAN></FONT></SPAN>
<P></P>
<P></P></SPAN></SPAN></FONT></SPAN></FONT></SPAN>
<P></P>
<P></P></SPAN></SPAN></FONT></SPAN></FONT></SPAN>
<P></P>
<P></P></o:p></SPAN></SPAN></FONT></SPAN></FONT></SPAN></P></P></BODY>
</HTML>