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<p>Dear Rares,<br>
<br>
Then this might be something to do with some elements of the
Ensembl API being in a different version (i.e. not "release/94"):
do you have ensembl-vep and the other ensembl APIs in version 94 ?<br>
</p>
<p>To check the installer VEP version:</p>
cd <path_to_ensembl-vep>/ensembl-vep<br>
git branch | grep \* | cut -d ' ' -f2
<p>And the following command will list the versions of the other
Ensembl APIs installed for VEP (ensembl, ensembl-variation,
ensembl-funcgen,ensembl-io):</p>
<p>grep release <path_to_ensembl-vep>/ensembl-vep/.version/*</p>
<p>For instance you should see:</p>
<p>.version/ensembl:release 94<br>
.version/ensembl-funcgen:release 94<br>
.version/ensembl-io:release 94<br>
.version/ensembl-variation:release 94</p>
<p><br>
</p>
<p>Best regards,<br>
</p>
<pre class="moz-signature" cols="72">Laurent</pre>
<div class="moz-cite-prefix">On 29/10/2018 16:40, Rares Vernica
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CALQ9KxCdrNkfbX_R0jOexerhRt1LefgRPaxQFqJNQmPfvLuqug@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">
<div>Hi Laurent,</div>
<div><br>
</div>
<div><span style="font-family:monospace,monospace">--refseq</span>
is intentional and I do have the Refseq cache.</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Rares<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Mon, Oct 29, 2018 at 2:26 AM Laurent Gil <<a
href="mailto:lgil@ebi.ac.uk" moz-do-not-send="true">lgil@ebi.ac.uk</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<p>Dear Rares,<br>
<br>
<font face="Helvetica, Arial, sans-serif">Looking at you
command line, it seems that you only have the cache for
the Ensembl transcripts but you are using the flag
"--refseq" in combination with the flag "--cache", which
means that VEP is looking for the Refseq transcript
cache repository: ~/.vep/homo_sapiens_<b>refseq</b>/94_GRCh37/.<br>
If you don't have it, you will need to install it: <a
href="ftp://ftp.ensembl.org/pub/release-94/variation/VEP/homo_sapiens_refseq_vep_94_GRCh37.tar.gz"
target="_blank" moz-do-not-send="true">ftp://ftp.ensembl.org/pub/release-94/variation/VEP/homo_sapiens_refseq_vep_94_GRCh37.tar.gz</a></font></p>
<p><font face="Helvetica, Arial, sans-serif">You can do it
via the VEP installer or you can install it manually in
few steps:<br>
</font></p>
<pre class="m_1207750113062935992code m_1207750113062935992sh_sh m_1207750113062935992sh_sourceCode"><span class="m_1207750113062935992sh_keyword">cd <font face="Helvetica, Arial, sans-serif">~</font></span><span class="m_1207750113062935992sh_variable"></span><span class="m_1207750113062935992sh_symbol">/.</span>vep
<span class="m_1207750113062935992sh_keyword">curl </span><span class="m_1207750113062935992sh_name">-O</span> <font face="Helvetica, Arial, sans-serif"><a class="m_1207750113062935992moz-txt-link-freetext" href="ftp://ftp.ensembl.org/pub/release-94/variation/VEP/homo_sapiens_refseq_vep_94_GRCh37.tar.gz" target="_blank" moz-do-not-send="true">ftp://ftp.ensembl.org/pub/release-94/variation/VEP/homo_sapiens_refseq_vep_94_GRCh37.tar.gz</a></font>
<span class="m_1207750113062935992sh_keyword">tar </span>xzf <font face="Helvetica, Arial, sans-serif">homo_sapiens_refseq_vep_94_GRCh37.tar.gz</font>
</pre>
<p><br>
</p>
<p>Best regards,<br>
</p>
<pre class="m_1207750113062935992moz-signature" cols="72">Laurent</pre>
<div class="m_1207750113062935992moz-cite-prefix">On
29/10/2018 04:07, Rares Vernica wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">
<div>Hello,</div>
<div><br>
</div>
<div>I'm having trouble with the public database when
using the <span
style="font-family:monospace,monospace">GRCh37</span>
assembly. This is what I run:</div>
<div><br>
</div>
<div style="margin-left:40px"><span
style="font-family:monospace,monospace">> ./vep
--cache --refseq --assembly GRCh37 --fasta
~/.vep/homo_sapiens/94_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz
--input_file 1.tsv --port 3337<br>
<br>
-------------------- WARNING
----------------------<br>
MSG: homo_sapiens is not a valid species name
(check DB and API version)<br>
FILE: Bio/EnsEMBL/Registry.pm LINE: 1334<br>
CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 1109<br>
Date (localtime) = Mon Oct 29 03:49:22 2018<br>
Ensembl API version = 94<br>
---------------------------------------------------<br>
<br>
-------------------- EXCEPTION
--------------------<br>
MSG: Can not find internal name for species
'homo_sapiens'<br>
STACK Bio::EnsEMBL::Registry::get_adaptor
/usr/local/src/ensembl-vep/Bio/EnsEMBL/Registry.pm:1111<br>
STACK Bio::EnsEMBL::VEP::BaseVEP::get_adaptor
/usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:307<br>
STACK
Bio::EnsEMBL::VEP::BaseVEP::get_database_assembly
/usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:419<br>
STACK
Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection
/usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:123<br>
STACK Bio::EnsEMBL::VEP::Runner::init
/usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:118<br>
STACK Bio::EnsEMBL::VEP::Runner::run
/usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194<br>
STACK toplevel ./vep:224<br>
Date (localtime) = Mon Oct 29 03:49:22 2018<br>
Ensembl API version = 94<br>
---------------------------------------------------</span></div>
<div><br>
</div>
<div>It works with <span
style="font-family:monospace,monospace">--online</span>
but I would like to use the <a
href="https://uswest.ensembl.org/info/docs/tools/vep/vep_formats.html#id"
target="_blank" moz-do-not-send="true"><i>Variant
identifiers</i></a> input format and that does
not work with <span
style="font-family:monospace,monospace">--offline</span>.</div>
<div><br>
</div>
<div>Any ideas what I'm doing wrong?</div>
<div><br>
</div>
<div>Thanks!</div>
<div>Rares<br>
</div>
</div>
</div>
<br>
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<pre class="m_1207750113062935992moz-quote-pre">_______________________________________________
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</pre>
</blockquote>
</div>
</blockquote>
</div>
<br>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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