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Hi again,<br>
The installation of the API went fine, I no longer have
the instentiation problem. However, I do get an error when using the
api:<br>
<br>
[15-08-13 15:59:09]
kchennen@kc-Dell-XPS-L702X:/opt/apps/bioinfo/ensembl-tools/scripts/variant_effect_predictor
<br>
[30:30] > ./variant_effect_predictor.pl --dir cache -i
example_GRCh37.vcf
<br>
2015-08-13 16:01:17 - Read configuration from cache/vep.ini<br>
#----------------------------------#<br>
# ENSEMBL VARIANT EFFECT PREDICTOR #<br>
#----------------------------------#<br>
<br>
version 81<br>
<br>
By Will McLaren (<a class="moz-txt-link-abbreviated" href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>)<br>
<br>
Configuration options:<br>
<br>
##<br>
assembly GRCh37<br>
cache 1<br>
core_type core<br>
dir cache<br>
dir_plugins cache/Plugins<br>
force_overwrite 1<br>
fork 2<br>
host ensembldb.ensembl.org<br>
input_file example_GRCh37.vcf<br>
no_stats 1<br>
offline 1<br>
plugin Conservation,GERP_CONSERVATION_SCORE,mammals<br>
port 3337<br>
species homo_sapiens<br>
stats HASH(0x3e68338)<br>
stats_text 1<br>
terms SO<br>
verbose 1<br>
<br>
--------------------<br>
<br>
2015-08-13 16:01:17 - Read existing cache info<br>
2015-08-13 16:01:17 - Auto-detected FASTA file in cache directory<br>
2015-08-13 16:01:17 - Checking/creating FASTA index<br>
2015-08-13 16:02:56 - Loaded plugin: Conservation<br>
2015-08-13 16:02:56 - Starting...<br>
2015-08-13 16:02:56 - Detected format of input file as vcf<br>
2015-08-13 16:02:56 - Read 173 variants into buffer<br>
2015-08-13 16:02:56 - Calculating consequences<br>
[>
] [ 0% ]<br>
Plugin 'Conservation' went wrong: Can't call method
"fetch_normalized_slice_projection" on an undefined value at
/opt/apps/bioinfo/ensembl-api/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/ConservationScoreAdaptor.pm
line 204, <GEN1> line 175.<br>
<br>
<br>
<br>
<br>
Thanks<br>
Kirsley<br>
<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 13/08/2015 15:46, Will McLaren
wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX3m48h5FjHpEcgq7LiaKJ_J-zeLTZa=3kUUz_fyFd9Oqg@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Kirsley,
<div><br>
</div>
<div>The only parameter you have to change for GRCh37 is the
port, by adding "--port 3337" to your VEP command. The plugin
will only work when using --cache (recommended) or --database;
it will not work with --offline.</div>
<div><br>
</div>
<div>You also need the ensembl-compara API installed, which is
not installed by the VEP installer script. </div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="https://github.com/Ensembl/ensembl-compara">https://github.com/Ensembl/ensembl-compara</a><br>
</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/api/api_installation.html">http://www.ensembl.org/info/docs/api/api_installation.html</a><br>
</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 13 August 2015 at 14:36, Kirsley
Chennen <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:kchennen@unistra.fr" target="_blank">kchennen@unistra.fr</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="#000000"> Hi Will,<br>
Am still having the same issue with the latest
version of the Convervation.pm plugin :<br>
<br>
2015-08-13 15:31:17 - Failed to instantiate plugin
Conservation: Failed to connect to compara database<br>
<br>
<br>
Do we have to the config for the database in the vep.ini
file?<br>
<br>
# reconnect to DB without species param<br>
my $config = $self->{config};<br>
$reg->load_registry_from_db(<br>
-host => $config->{host},<br>
-user => $config->{user},<br>
-pass => $config->{password},<br>
-port => $config->{port},<br>
-db_version => $config->{db_version},<br>
-no_cache => $config->{no_slice_cache},<br>
);<br>
<br>
If that's so, what are the parameters for the GRCh37 human
assembly?<br>
<br>
Regards<span class="HOEnZb"><font color="#888888"><br>
Kirsley</font></span>
<div>
<div class="h5"><br>
<br>
<br>
<div>On 13/08/2015 14:46, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>Thanks for the report, I've pushed a fix to
the plugin on GitHub.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 13 August 2015 at
12:36, 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 text="#000066" bgcolor="#FFFFFF"> Dear
devs,<br>
<br>
I'm using latest version of VEP Conservation
plugin available in github. However it's not
working for me:<br>
<br>
2015-08-13 13:35:17 - Failed to instantiate
plugin Conservation: Failed to connect to
compara database<br>
<br>
Is this a bug?<br>
<br>
Regards,<br>
Guillermo.<br>
<div><br>
</div>
</div>
<br>
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