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<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>ensembldb.ensembl.org</b> -fork 4
</pre>
Regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 03/08/2017 04:13 PM, Will McLaren
wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX3ZiQuahGc+Yz6bAM8D8V0X1_tFptYZ_wUuR-mCPzmgig@mail.gmail.com"
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@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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</blockquote>
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</blockquote>
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