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-------- Original Message --------
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Subject: </th>
<td>Variant Effect Predictor script</td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Date: </th>
<td>Wed, 23 May 2012 14:34:33 +0200</td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">From: </th>
<td>Qi Weihong <a class="moz-txt-link-rfc2396E" href="mailto:weihong.qi@fgcz.ethz.ch"><weihong.qi@fgcz.ethz.ch></a></td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">To: </th>
<td><a class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a> <a class="moz-txt-link-rfc2396E" href="mailto:dev@ensembl.org"><dev@ensembl.org></a></td>
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<div style="direction: ltr;font-family: Tahoma;color:
#000000;font-size: 10pt;">Dear Ensembl development team,<br>
<br>
Recently I installed the VEP script version 2.5 using the install
perl script. It runs well with human datasets. But I could not
run the script against arabidopsis. Could you please help me out?<br>
<br>
The command line was "perl variant_effect_predictor.pl -i
test.vcf --format vcf -o test.vep -genomes -species
arabidopsis_thaliana", which was followed the suggestions from the
help page
<a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/variation/vep/vep_script.html#help."
target="_blank">
http://www.ensembl.org/info/docs/variation/vep/vep_script.html#help.</a>
<br>
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The error messages were:<br>
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-------------------- WARNING ----------------------<br>
MSG: arabidopsis_thaliana is not a valid species name (check DB
and API version)<br>
FILE: Bio/EnsEMBL/Registry.pm LINE: 1172<br>
CALLED BY:
src/variant_effect_predictor/variant_effect_predictor.pl LINE:
653<br>
Ensembl API version = 67<br>
---------------------------------------------------<br>
<br>
-------------------- WARNING ----------------------<br>
MSG: arabidopsis_thaliana is not a valid species name (check DB
and API version)<br>
FILE: Bio/EnsEMBL/Registry.pm LINE: 1172<br>
CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 957<br>
Ensembl API version = 67<br>
---------------------------------------------------<br>
<br>
-------------------- EXCEPTION --------------------<br>
MSG: Can not find internal name for species 'arabidopsis_thaliana'<br>
STACK Bio::EnsEMBL::Registry::get_adaptor
/misc/ngseq/src/variant_effect_predictor/Bio/EnsEMBL/Registry.pm:959<br>
STACK main::get_adaptors
/usr/local/ngseq/src/variant_effect_predictor/variant_effect_predictor.pl:1054<br>
STACK main::configure
/usr/local/ngseq/src/variant_effect_predictor/variant_effect_predictor.pl:766<br>
STACK toplevel
/usr/local/ngseq/src/variant_effect_predictor/variant_effect_predictor.pl:66<br>
Ensembl API version = 67<br>
<br>
Many thanks,<br>
<br>
Weihong<br>
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