<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 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">
Dear devs,<br>
<br>
I'm having trouble running Conservation plugin on latest Ensembl 87
version. Here's the log:<br>
<br>
<pre><a 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>
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<br></blockquote></div><br></div>