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Oups! My mistake! Works like a charm now. However, it seems rather
slow with the database connection. I've just tested an alternative
which looks much faster by using the bigwig file with the custom
annotation option. My question is do we get the same results for
indel if we do the average of the values returned by "overlap"
annotation type parameter?<br>
<br>
Thanks<br>
Kirsley<br>
<br>
<br>
<div class="moz-cite-prefix">On 13/08/2015 16:19, Will McLaren
wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX3wdkJGe095ZMZ25TBDgQVKi02C0QNuyjd0VOAV6Kezqw@mail.gmail.com"
type="cite">
<div dir="ltr">You have "offline 1" in your config.
<div><br>
</div>
<div>Remove this and you shouldn't see the problem.</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 13 August 2015 at 15:08, 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> 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] > ./<a moz-do-not-send="true"
href="http://variant_effect_predictor.pl"
target="_blank">variant_effect_predictor.pl</a> --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 moz-do-not-send="true"
href="mailto:wm2@ebi.ac.uk" target="_blank">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 <a moz-do-not-send="true"
href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a><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<span class="HOEnZb"><font color="#888888"><br>
Kirsley</font></span>
<div>
<div class="h5"><br>
<br>
<br>
<br>
<br>
<div>On 13/08/2015 15:46, Will McLaren wrote:<br>
</div>
<blockquote 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"
target="_blank">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"
target="_blank">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><font color="#888888"><br>
Kirsley</font></span>
<div>
<div><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>
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