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<p>Hi</p>
<p>Sorry there was a typo, the version for the variation database
should have been 100, i.e. homo_sapiens_variation_100_37</p>
<p>Regards<br>
Helen<br>
</p>
<div class="moz-cite-prefix">On 04/11/2020 14:11, Helen Schuilenburg
wrote:<br>
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<p>Hi</p>
<p>From the log provided the database
homo_sapiens_variation_100_37 is not being loaded.<br>
<br>
This database is used by the variant_recoder to return the id.<br>
<br>
From the logs homo_sapiens_core_100_37 is loaded.<br>
<br>
Please can you check that the homo_sapiens_variation_101_37 can
be accessed using the configuration<br>
provided in ensembl_rest.conf (Model::Registry section) and
used to access homo_sapiens_core_100_37</p>
<p>The variation database can also be queried to check that the id
in the local variation database e.g.</p>
<p>select v.name <br>
from variation v, variation_feature vf <br>
where v.variation_id = vf.variation_id <br>
and name = 'rs80358450';<br>
<br>
name: rs80358450<br>
1 row in set (0.25 sec)</p>
<p>Regards<br>
Helen<br>
</p>
<div class="moz-cite-prefix">On 03/11/2020 17:16, Sage Hornung
wrote:<br>
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<div class="WordSection1">
<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am making the following call (To
localhost though not Ensembl) <span
style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#505050;background:white"><a
href="%20http:/grch37.rest.ensembl.org%20/variant_recoder/human/13:g.32893310A%3eG?content-type=application/json&fields=hgvsg,id"
moz-do-not-send="true"> http://grch37.rest.ensembl.org
/variant_recoder/human/13:g.32893310A>G?content-type=application/json&fields=hgvsg,id</a>
to a local ensemble setup. But I don’t get an ID back in
the response. I loaded the ensembl_stable_ids_100 database
but its was the one I found here <a
href="ftp://ftp.ensembl.org/pub/release-100/mysql/"
moz-do-not-send="true">ftp://ftp.ensembl.org/pub/release-100/mysql/</a>.
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#505050;background:white"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#505050;background:white">Here
is what I get back using my local Ensembl REST and
Ensembl DB . If I change to your DB it gives the ID
back. Any idea what I am going wrong? Or how this should
be configured differently? I am making my changes in the
ensembl_rest.conf file<o:p></o:p></span></p>
<p class="MsoNormal"
style="line-height:13.5pt;background:#FFFFFE"><span
style="font-size:9.0pt;font-family:Consolas;color:black">[<o:p></o:p></span></p>
<p class="MsoNormal"
style="line-height:13.5pt;background:#FFFFFE"><span
style="font-size:9.0pt;font-family:Consolas;color:black"> {<o:p></o:p></span></p>
<p class="MsoNormal"
style="line-height:13.5pt;background:#FFFFFE"><span
style="font-size:9.0pt;font-family:Consolas;color:black"> </span><span
style="font-size:9.0pt;font-family:Consolas;color:#A31515">"hgvsg"</span><span
style="font-size:9.0pt;font-family:Consolas;color:black">: [<o:p></o:p></span></p>
<p class="MsoNormal"
style="line-height:13.5pt;background:#FFFFFE"><span
style="font-size:9.0pt;font-family:Consolas;color:black"> </span><span
style="font-size:9.0pt;font-family:Consolas;color:#A31515">"NC_000013.10:g.32893310A>G"</span><span
style="font-size:9.0pt;font-family:Consolas;color:black">,<o:p></o:p></span></p>
<p class="MsoNormal"
style="line-height:13.5pt;background:#FFFFFE"><span
style="font-size:9.0pt;font-family:Consolas;color:black"> </span><span
style="font-size:9.0pt;font-family:Consolas;color:#A31515">"LRG_293:g.8694A>G"</span><span
style="font-size:9.0pt;font-family:Consolas;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"
style="line-height:13.5pt;background:#FFFFFE"><span
style="font-size:9.0pt;font-family:Consolas;color:black"> ],<o:p></o:p></span></p>
<p class="MsoNormal"
style="line-height:13.5pt;background:#FFFFFE"><span
style="font-size:9.0pt;font-family:Consolas;color:black"> </span><span
style="font-size:9.0pt;font-family:Consolas;color:#A31515">"input"</span><span
style="font-size:9.0pt;font-family:Consolas;color:black">: </span><span
style="font-size:9.0pt;font-family:Consolas;color:#0451A5">"13:g.32893310A>G"</span><span
style="font-size:9.0pt;font-family:Consolas;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"
style="line-height:13.5pt;background:#FFFFFE"><span
style="font-size:9.0pt;font-family:Consolas;color:black"> }<o:p></o:p></span></p>
<p class="MsoNormal"
style="line-height:13.5pt;background:#FFFFFE"><span
style="font-size:9.0pt;font-family:Consolas;color:black">]<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I do see that pointing to the ensemble DB
gives this when starting up the REST server <o:p></o:p></p>
<p class="MsoNormal">Species 'homo_sapiens' loaded from
database 'homo_sapiens_core_100_37'<o:p></o:p></p>
<p class="MsoNormal">Species 'homo_sapiens' loaded from
database 'homo_sapiens_cdna_100_37'<o:p></o:p></p>
<p class="MsoNormal">Species 'homo_sapiens' loaded from
database 'homo_sapiens_otherfeatures_100_37'<o:p></o:p></p>
<p class="MsoNormal">Species 'homo_sapiens' loaded from
database 'homo_sapiens_rnaseq_100_37'<o:p></o:p></p>
<p class="MsoNormal">homo_sapiens_variation_100_37 loaded<o:p></o:p></p>
<p class="MsoNormal">homo_sapiens_funcgen_100_37 loaded<o:p></o:p></p>
<p class="MsoNormal">ensembl_compara_100 loaded<o:p></o:p></p>
<p class="MsoNormal">No ancestral database found<o:p></o:p></p>
<p class="MsoNormal">ensembl_ontology_100 loaded<o:p></o:p></p>
<p class="MsoNormal">No taxonomy database found<o:p></o:p></p>
<p class="MsoNormal">No ensembl_metadata database found<o:p></o:p></p>
<p class="MsoNormal">No production database or adaptor found<o:p></o:p></p>
<p class="MsoNormal">ensembl_stable_ids_100 loaded<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">But it only finds the homo_sapiens_core
DB when I point to my local DB (I definitely have the
variation DB loaded )<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Will only load v100 databases<o:p></o:p></p>
<p class="MsoNormal">Species 'homo_sapiens' loaded from
database 'homo_sapiens_core_100_37'<o:p></o:p></p>
<p class="MsoNormal">No variation databases found<o:p></o:p></p>
<p class="MsoNormal">No funcgen databases found<o:p></o:p></p>
<p class="MsoNormal">No Compara databases found<o:p></o:p></p>
<p class="MsoNormal">No ancestral database found<o:p></o:p></p>
<p class="MsoNormal">No ontology database found<o:p></o:p></p>
<p class="MsoNormal">No taxonomy database found<o:p></o:p></p>
<p class="MsoNormal">No ensembl_metadata database found<o:p></o:p></p>
<p class="MsoNormal">No production database or adaptor found<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>
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