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<p><font face="monospace">Hi </font>Likhitha,</p>
<p>Thank you for the prompt response and for fixing the GRCh37 caches on the download server. I have tested install script again tonight and the caches installed fine, no errors reported this time and all cache files were in place. I will get back to you if
I notice any further issues with the GRCh37 annotations.<br>
</p>
<p>Best,</p>
<p>Ivan<br>
</p>
<div class="moz-cite-prefix">On 11/10/22 08:25, Likhitha Surapaneni wrote:<br>
</div>
<blockquote type="cite" cite="mid:20221110132548.68EA062B239_36CFBDCB@hh-mx3.ebi.ac.uk">
<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">
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>
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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>
</div>
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</pre>
</blockquote>
<pre class="moz-signature" signature-switch-id="a81c2e3d-93ba-45a3-8c1c-e0989879af97" cols="72">--
Ivan Adzhubey, Ph.D.
Research Associate
Division of Genetics, Dept of Medicine
Brigham & Women's Hospital
New Research Building, Room 0464C
77 Avenue Louis Pasteur
Boston, MA 02115
tel.: (617) 525-4728
fax: (617) 525-4705
web: <a class="moz-txt-link-freetext" href="http://genetics.bwh.harvard.edu/wiki/sunyaevlab/">http://genetics.bwh.harvard.edu/wiki/sunyaevlab/</a></pre>
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