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<p>Hi Ivan, <br>
</p>
<p>We have updated our cache files for GRCh37 and this should
resolve the issue. Can you please try the installation again and
let us know if you are still facing issues? </p>
<p>Thanks and regards,</p>
<p>Likhitha<br>
</p>
<div class="moz-cite-prefix">On 10/11/2022 02:25, Adzhubey, Ivan,PHD
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:20221110022806.3021A11ADD7_36C61B6B@hh-mx4.ebi.ac.uk">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Hi,
<div class="moz-text-html" lang="x-unicode">
<div class="moz-text-html" lang="x-unicode">
<p>It looks like installation for <span
style="color:#000000;background-color:#ffffff;">
108_GRCh37 is broken:</span></p>
<p><span style="font-family:monospace">$ perl INSTALL.pl -a c
-s homo_sapiens -y GRCh37 -c /data/vep --NO_HTSLIB
--NO_TEST<br>
- getting list of available cache files<br>
- downloading <a class="moz-txt-link-freetext"
href="https://urldefense.proofpoint.com/v2/url?u=https-3A__ftp.ensembl.org_pub_release-2D108_variation_indexed-5Fvep-5Fcache_homo-5Fsapiens-5Fvep-5F108-5FGRCh37.tar.gz&d=DwMGaQ&c=WO-RGvefibhHBZq3fL85hQ&r=fpFYsQD9efuj6qk0TjK1MbUTPI07tTdDii-uM88QGpo&m=uEeAtmcBVmdX_pYTuAZvb2qERdaRosoAWop6hummx2YX5fU9PHe2Eg2QxKw-9-aA&s=aJ4A-kNCHvqTdpd3zD-IdHQPMtNEscAdIhnVin8ADK4&e="
moz-do-not-send="true">
https://ftp.ensembl.org/pub/release-108/variation/indexed_vep_cache/homo_sapiens_vep_108_GRCh37.tar.gz</a><br>
- unpacking homo_sapiens_vep_108_GRCh37.tar.gz<br>
- converting cache, this may take some time but will
allow VEP to look up variants and frequency data much
faster<br>
- use CTRL-C to cancel if you do not wish to convert this
cache now (you may run convert_cache.pl later)<br>
ERROR: Version 108_GRCh37 not found<br>
WARNING: Failed to run convert script<br>
<br>
All done</span></p>
<p>For some reason, it attempts to run indexing script and
fails, even though the caches downloaded were already
indexed. Caches are in fact downloaded & installed
successfully, or at least it looks like they did. I have not
run actual tests yet.</p>
<p>Update: In fact, caches are successfully downloaded,
checked and uncompressed into the tmp directory but then
deleted for no apparent reason, hence installation failed
completely. Probably triggered by the "ERROR: Version
108_GRCh37 not found", see above but what it means is
unclear.<br>
</p>
<p>Also, there is no way to install FASTA sequence since it
will first remove all cache files installed previously. And
if I try the other way round it refuses to download caches
*after* FASTA sequence has been downloaded because cache
directory already exists.</p>
<p><span style="font-family:monospace">$ perl INSTALL.pl -a f
-s homo_sapiens -y GRCh37 -c /data/vep --NO_HTSLIB
--NO_TEST<br>
<br>
WARNING: Changing URL for GRCh37<br>
- downloading
Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz<br>
- extracting data<br>
- attempting to index<br>
Indexing failed - VEP will attempt to index the file the
first time you use it<br>
<br>
The FASTA file should be automatically detected by the VEP
when using --cache or --offline.<br>
If it is not, use "--fasta
/data/vep/homo_sapiens/108_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa"<br>
<br>
<br>
All done<br>
</span></p>
<p><span style="font-family:monospace">$ perl INSTALL.pl -a c
-s homo_sapiens -y GRCh37 -c /data/vep --NO_HTSLIB
--NO_TEST<br>
- getting list of available cache files<br>
<br>
WARNING: It looks like you already have the cache for
homo_sapiens GRCh37 (v108) installed.<br>
<br>
Delete the folder /data/vep/homo_sapiens/108_GRCh37 and
re-run INSTALL.pl if you want to re-install<br>
- skipping homo_sapiens<br>
<br>
All done<br>
</span></p>
<p>I had to first move .fa file out of the <span
style="color:#000000;background-color:#ffffff;">
108_GRCh37</span> folder, delete empty folder, re-install
caches and then move .fa file back and index it manually.
Not a big deal but it took me some time to figure out what's
going on. Does not seems to be an intended behavior, so I
assume this is due to some bug(s) in INSTALL.pl script.</p>
<p>Thanks,</p>
<p>Ivan<br>
</p>
<div class="moz-cite-prefix">On 10/20/22 06:08, Louisse Paola
Mirabueno wrote:<br>
</div>
<blockquote type="cite"
cite="mid:62fb78ba-ccb6-2c4b-0caf-dd4da05c0ed2@ebi.ac.uk">
Hi all,<br>
<br>
We are pleased to announce that the latest <a
moz-do-not-send="true">Ensembl</a> and <a
moz-do-not-send="true">Ensembl Genomes</a> updates have
been released!<br>
<br>
Highlights of this release include:<br>
<ul>
<li>Changes in the human default tracks</li>
<li>New genomes added in <a moz-do-not-send="true">Ensembl
Plants</a> and <a moz-do-not-send="true">Ensembl
Metazoa</a></li>
<li>Addition of mitochondrial annotation for Tasmanian
devil</li>
<li>New and additional data reported by VEP</li>
</ul>
<br>
The release blog post with all news can be viewed <a
moz-do-not-send="true">here</a>.<br>
<br>
<br>
For the latest news from the Ensembl project visit our <a
moz-do-not-send="true">blog</a>. Thank you all!<br>
<br>
<br>
All the best,<br>
<br>
Louisse (on behalf of the Ensembl team) <br>
<fieldset class="moz-mime-attachment-header"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
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</pre>
</blockquote>
</div>
<div class="moz-cite-prefix">On 10/20/22 06:08, Louisse Paola
Mirabueno wrote:<br>
</div>
<blockquote type="cite"
cite="mid:62fb78ba-ccb6-2c4b-0caf-dd4da05c0ed2@ebi.ac.uk">
Hi all,<br>
<br>
We are pleased to announce that the latest <a
moz-do-not-send="true">Ensembl</a> and <a
moz-do-not-send="true">Ensembl Genomes</a> updates have been
released!<br>
<br>
Highlights of this release include:<br>
<ul>
<li>Changes in the human default tracks</li>
<li>New genomes added in <a moz-do-not-send="true">Ensembl
Plants</a> and <a moz-do-not-send="true">Ensembl
Metazoa</a></li>
<li>Addition of mitochondrial annotation for Tasmanian devil</li>
<li>New and additional data reported by VEP</li>
</ul>
<br>
The release blog post with all news can be viewed <a
moz-do-not-send="true">here</a>.<br>
<br>
<br>
For the latest news from the Ensembl project visit our <a
moz-do-not-send="true">blog</a>. Thank you all!<br>
<br>
<br>
All the best,<br>
<br>
Louisse (on behalf of the Ensembl team) </blockquote>
<pre class="moz-signature" cols="72">--
Ivan Adzhubey, Ph.D.
Research Associate
Dept of Biomedical Informatics
Harvard Medical School
10 Shattuck Street, Suite 514
Boston, MA 02115
tel: (617) 432-2144
fax: (617) 432-0693
web: <a class="moz-txt-link-freetext" href="http://genetics.bwh.harvard.edu/wiki/sunyaevlab/" moz-do-not-send="true">http://genetics.bwh.harvard.edu/wiki/sunyaevlab/</a></pre>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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