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<p>Thank you Will! Indeed I had a problem with ensembl-compara API
local install.</p>
<p>Regards,<br>
Guillermo<br>
</p>
<br>
<div class="moz-cite-prefix">On 03/08/2017 04:48 PM, Will McLaren
wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX286Yz1gc+buikNciowsdAhyD+EJxoEbJa7mGmkK7bvtg@mail.gmail.com"
type="cite">
<div dir="ltr">OK, next thing to check is that your
ensembl-compara API checkout is up to date (it should be on
release/87).
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 8 March 2017 at 15:25, Guillermo
Marco Puche <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000066">
<p>Hi Will,</p>
My bad that '-host' was a typo when posting command to dev
mail list. I've actually tested it with both local
database and remote database and I'm getting the same
error. However this is the corrected command I'm testing
right now:<br>
<pre><a moz-do-not-send="true" href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i test.vcf -o test_out.vcf -config /home/ensembl_test/87.conf -dir_plugins /home/ensembl_test -dir_cache /share/references/vep -host <b><a moz-do-not-send="true" href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a></b> -fork 4
</pre>
Regards,<br>
Guillermo.
<div>
<div class="h5"><br>
<br>
<div class="m_3196108687984264710moz-cite-prefix">On
03/08/2017 04:13 PM, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>You have nothing following your "-host" entry
in your command line; odd that this doesn't
cause any other errors, but probably the root of
your issue.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 7 March 2017 at 08:25,
Guillermo Marco Puche <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@<wbr>sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000066"> Dear
devs,<br>
<br>
I'm having trouble running Conservation
plugin on latest Ensembl 87 version. Here's
the log:<br>
<br>
<pre><a moz-do-not-send="true" href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i test.vcf -o test_out.vcf -config /home/ensembl_test/87.conf -dir_plugins /home/ensembl_test -dir_cache /share/references/vep -host -fork 4</pre>
<pre>2017-03-07 09:15:31 - Read configuration from /home/ensembl_test/87.conf
2017-03-07 09:15:44 - Read existing cache info
2017-03-07 09:15:44 - Auto-detected FASTA file in cache directory<b>
</b><b>2017-03-07 09:18:27 - Failed to instantiate plugin Conservation: Failed to connect to compara database</b>
2017-03-07 09:18:34 - Starting...
2017-03-07 09:18:34 - Detected format of input file as vcf
2017-03-07 09:18:34 - Read 51 variants into buffer
2017-03-07 09:18:34 - Calculating consequences
2017-03-07 09:18:36 - Writing output
2017-03-07 09:18:36 - Processed 51 total variants (26 vars/sec, 26 vars/sec total)
2017-03-07 09:18:36 - Finished!</pre>
<br>
I've cloned it from VEP plugin repo just to
be sure I've latest version. I've tested it
against both local Ensembl DB installation
and remote host both failing.<br>
<br>
This is my config file:<br>
<br>
cache 1<br>
plugin Conservation<br>
force_overwrite 1<br>
no_escape 1<br>
no_progress 0<br>
no_stats 1<br>
hgvs 1<br>
canonical 1<br>
symbol 1<br>
ccds 1<br>
check_existing 1<br>
allele_number 1<br>
check_alleles 1<br>
domains 1<br>
gmaf 1<br>
maf_1kg 1<br>
maf_esp 1<br>
numbers 1<br>
uniprot 1<br>
biotype 1<br>
tsl 1<br>
pubmed 1<br>
polyphen b<br>
regulatory 1<br>
sift b<br>
xref_refseq 1<br>
vcf 1<br>
<br>
Regards,<br>
Guillermo.<br>
</div>
<br>
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