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Hi<br>
<br>
Sorry to be a pain but I have found a couple of <i>very minor</i>
errors in the VEP script. <br>
<br>
In the readme file it says to use --registry_file as the flag
whereas in the code you are loading $config->{registry}<br>
Naturally all you have to do to fix this is to change the flag in
the config file to --registry but it might save other people the
time finding the problem. I spotted this when i found it was taking
this long to run the script (i thought 7 minutes to run 20 variants
was extremely slow so I guessed i was using the external database
but even in the old script you can do 100 annotations a minute
against the external db????)<br>
<br>
workspace/snp$ variant_effect_predictor.pl --config config.txt<br>
#----------------------------------#<br>
# ENSEMBL VARIANT EFFECT PREDICTOR #<br>
#----------------------------------#<br>
<br>
version 2.0<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>
config config.txt<br>
input_file input.vep<br>
output_file vep_output.txt<br>
registry_file registry.txt<br>
species homo_sapiens<br>
terms display<br>
verbose <br>
<br>
--------------------<br>
<br>
2011-05-05 12:26:33 - Starting...<br>
2011-05-05 12:28:48 - Processed 10 variants<br>
2011-05-05 12:33:36 - Processed 20 variants<br>
<br>
<br>
But this is back to normal speed when i changed the config file to
--registry. <br>
<br>
There is another small error after that. See the output<br>
<br>
Configuration options:<br>
<br>
config config.txt<br>
input_file input.vep<br>
output_file vep_output.txt<br>
registry registry.txt<br>
species homo_sapiens<br>
terms display<br>
verbose <br>
<br>
--------------------<br>
<br>
2011-05-05 13:01:21 - Loading DB config from registry file
registry.txt<br>
2011-05-05 13:01:21 - Starting...<br>
2011-05-05 13:01:24 - Processed 10 variants<br>
2011-05-05 13:01:27 - Processed 20 variants<br>
2011-05-05 13:01:34 - Processed 30 variants<br>
<br>
<br>
note i am running in verbose mode and this code never runs<br>
<br>
if($config->{verbose}) {<br>
<br>
# get a meta container adaptors to check version<br>
my $core_mca = $reg->get_adaptor($config->{species},
'core', 'metacontainer');<br>
my $var_mca = $reg->get_adaptor($config->{species},
'variation', 'metacontainer');<br>
<br>
if($core_mca && $var_mca) {<br>
debug(<br>
"Connected to core version ",
$core_mca->get_schema_version, " database ",<br>
"and variation version ",
$var_mca->get_schema_version, " database"<br>
);<br>
}<br>
}<br>
<br>
<br>
This is because $config->verbose = '' so i changed it to
if(defined($config->{verbose})) to get the output<br>
<br>
cheers<br>
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