<html>
<head>
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
</head>
<body>
<p>Hi</p>
<p>Using a cache is the most efficient way to use VEP. However some
VEP options require a connection to a database e.g. to look up the
position when using an identifier (e.g. a dbSNP rsid) or to look
up reference feature locations. <br>
<br>
The Ensembl REST VEP endpoint /vep/human/hgvs should work with a
core database and an empty variation database provided none of the
options used require information from the variation database that
is not in the cache. <br>
<br>
The Ensembl REST VEP endpoint /vep/human/id that uses an rsid,
does require a variation database.<br>
<br>
As the number of variants for human have increased loading the
MySQL database is not trivial. The schema provided uses MyISAM
storage engine and this is the storage engine on the Ensembl
public MySQL Servers. <br>
<br>
Did the load using the MyISAM storage engine fail on data import
or on the index creation?<br>
Is there a particular file/table that caused problems? I suggest
maybe trying to load the file in parts.</p>
<p>Regards<br>
Helen <br>
</p>
<div class="moz-cite-prefix">On 08/09/2020 01:19, Sage Hornung
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:20200908002101.0351611AD01_F56CE6DB@hh-mx4.ebi.ac.uk">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<meta name="Generator" content="Microsoft Word 15 (filtered
medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]-->
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri",sans-serif;}size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
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]-->
<div class="WordSection1">
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal">I have asked a few questions recently about
setting up an ensemble rest and an ensemble database. I
appreciate the all the help.
<br>
<br>
<o:p></o:p></p>
<p class="MsoNormal">I was able to get all the Ensembl data
imported after a couple weeks but unfortunately its already
corrupted one or more of my InnoDB tables.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I previously asked I am not opposed to
using the cached data and I ended up adding it but one of the
rest endpoints supposedly ignores and bypasses the cache. This
one in particular
<a href="https://grch37.rest.ensembl.org/vep/human/hgvs"
moz-do-not-send="true">https://grch37.rest.ensembl.org/vep/human/hgvs</a>.
We are only using a few endpoints and the whole point of this
was to speed some of these requests up for ourselves.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Our MySQL database server has 14GB ram and
4 cores and 2TB of storage. I followed the directions on the
Ensembl website for importing the data but the only way I was
able to get the larger tables to import was changing the
storage engine to InnoDB. Im not sure if this was the best
choice because its seems the MyISAM engine is better for read
data. But this is the only way I was able to get it to
successfully import the data.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I guess my question is was this a good
idea? Is there any specific settings I should be using when
configuring MySQL? I have used a few tools online and most say
my settings are good/ok doe my configuration. The
homo_sapiens_variation_100_37 is the only one that’s giving me
issues and only with the tables greater than 25GB. Some of
these tables are massive I am looking for any tips or
suggestions when dealing with them.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank You,<o:p></o:p></p>
<p class="MsoNormal">Sage Hornung<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"
style="mso-line-height-alt:12.05pt;text-autospace:none"><b><span
style="font-size:14.0pt;color:#004A97">Sage Hornung</span></b><span
style="font-size:14.0pt;color:#004A97"><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:7.0pt;line-height:12.05pt;text-autospace:none">
<i><span style="font-size:12.0pt;color:#004A97">Software
Engineer </span></i><span
style="font-size:12.0pt;color:#004A97"><o:p></o:p></span></p>
<p class="MsoNormal"
style="line-height:12.05pt;text-autospace:none"><b><span
style="color:#424242">NeoGenomics Laboratories, Inc.</span></b><span
style="color:#424242"><o:p></o:p></span></p>
<p class="MsoNormal"
style="line-height:12.05pt;text-autospace:none"><span
style="color:#424242">2131 Faraday Avenue, Carlsbad, CA
92008<o:p></o:p></span></p>
<p class="MsoNormal"
style="line-height:12.05pt;text-autospace:none"><b><span
style="color:#424242">Phone:
</span></b><span style="color:#424242">760.516.5114<o:p></o:p></span></p>
<p class="MsoNormal"
style="line-height:12.05pt;text-autospace:none"><b><span
style="color:#424242">Cell:
</span></b><span style="color:#424242">760.755.3930<o:p></o:p></span></p>
<p class="MsoNormal"
style="line-height:12.05pt;text-autospace:none"><a
href="mailto:sage.hornung@neogenomics.com"
moz-do-not-send="true">sage.hornung@neogenomics.com</a><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><a
href="http://neogenomics.com/" moz-do-not-send="true"><span
style="color:#004A97">neogenomics.com</span></a><span
style="color:#004A97"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><a
href="http://neogenomics.com/" moz-do-not-send="true"><span
style="color:#5B9BD5;text-decoration:none"><img
style="width:1.25in;height:.5208in" id="Picture_x0020_1"
src="cid:part4.A78CB2A0.CA8AFE1F@ebi.ac.uk"
alt="cid:image001.png@01D27B05.09A580E0" class=""
width="120" height="50" border="0"></span></a><span
style="color:#5B9BD5"><o:p></o:p></span></p>
<p class="MsoNormal"><a
href="https://www.linkedin.com/company/neogenomics-laboratories/"
moz-do-not-send="true"><span
style="color:#5B9BD5;text-decoration:none"><img
style="width:.3125in;height:.3125in"
id="Picture_x0020_2"
src="cid:part6.1546AC01.C89F5BB2@ebi.ac.uk"
alt="cid:image002.png@01D2789A.338CAE00" class=""
width="30" height="30" border="0"></span></a><span
style="color:#5B9BD5">
</span><a href="https://twitter.com/NeoGenomics"
moz-do-not-send="true"><span
style="color:#5B9BD5;text-decoration:none"><img
style="width:.3125in;height:.3125in"
id="Picture_x0020_3"
src="cid:part8.A1C4654D.F4D502D0@ebi.ac.uk"
alt="cid:image003.png@01D2789A.338CAE00" class=""
width="30" height="30" border="0"></span></a><span
style="color:#5B9BD5"> </span><a
href="https://www.youtube.com/channel/UCBa0vLyn1ZO7tW-RyJOrxPA"
moz-do-not-send="true"><span
style="color:#5B9BD5;text-decoration:none"><img
style="width:.3125in;height:.3125in"
id="Picture_x0020_4"
src="cid:part10.44EF89CB.A722D8FD@ebi.ac.uk"
alt="cid:image004.png@01D2789A.338CAE00" class=""
width="30" height="30" border="0"></span></a><span
style="color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
This communication and its attachments contain confidential
information and is intended only for the named addressee. If you
are not the named addressee you should not disseminate, distribute
or copy this communication. Please notify the sender immediately
if you have received this communication by mistake and delete or
destroy this communication. Communications cannot be guaranteed to
be secured or error-free as information could be intercepted,
corrupted, lost, destroyed, arrive late or incomplete, or contain
viruses. The sender therefore does not accept liability for any
errors or omissions in the contents of this communication which
arise as a result of transmission. If verification is required
please request a hard-copy version. NeoGenomics Laboratories,
12701 Commonwealth Dr, Fort Myers, FL 33913,
<a class="moz-txt-link-freetext" href="http://www.neogenomics.com">http://www.neogenomics.com</a> (2020)
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
</body>
</html>