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<font face="Menlo" style="font-size: 11px;">Hi, </font>
<div><font face="Menlo" style="font-size: 11px;">I am having trouble with variant_effect_predictor.pl. I am using this script to predict the effect of the SNP’s of wheat(Triticum aestivum) exome capture. I installed the tool as explained in the tutorial. <a href="http://useast.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html">http://useast.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html</a></font></div>
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<div><font face="Menlo" style="font-size: 11px;"><font color="#222222">The test data sets runs perfectly fine with human cache but when I run the script with Triticum aestivum cache I get the following error. The cache for Triticum aestivum is in directory </font><span style="background-color: rgb(255, 255, 255);"><font color="#555555"><span style="line-height: 16px;">$HOME/.vep.
I </span></font><font color="#555555"><span style="line-height: 16px;">downloaded the prebuilt cache, other species(Plants, triticum_asetivum_vep_25_IWGSC2.tar.gz). Then I moved it to ~ /.vep/. I followed </span></font></span><font color="#555555"><span style="line-height: 16px;">instructions
from </span></font><a href="http://useast.ensembl.org/info/docs/tools/vep/script/vep_cache.html">http://useast.ensembl.org/info/docs/tools/vep/script/vep_cache.html</a>.</font></div>
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<div style="color: rgb(34, 34, 34);"><font face="Menlo" style="font-size: 11px;">Here is the error I was getting.</font></div>
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">perl <a href="http://variant_effect_predictor.pl/" target="_blank" style="color: rgb(17, 85, 204);">variant_effect_predictor.<wbr>pl</a> -i /berber/radhika/seq_for_assaf/<wbr>mpileup_on_rmdup/Zavitan_var.<wbr>flt_d6_a4.vcf
--species triticum_aestivum --cache</div>
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-------------------- WARNING ----------------------</div>
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MSG: triticum_aestivum is not a valid species name (check DB and API version)</div>
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FILE: Bio/EnsEMBL/Registry.pm LINE: 1200</div>
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CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 985</div>
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Date (localtime) = Thu Jan 29 11:42:51 2015</div>
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Ensembl API version = 78</div>
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<span style="font-family: Menlo; font-size: 11px;">------------------------------<wbr>---------------------</span> </div>
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">-------------------- EXCEPTION --------------------</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">MSG: Can not find internal name for species 'triticum_aestivum'</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">STACK Bio::EnsEMBL::Registry::get_<wbr>adaptor /home/radhika/ensembl-tools-<wbr>release-78/scripts/variant_<wbr>effect_predictor/Bio/EnsEMBL/<wbr>Registry.pm:987</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">STACK main::connect_to_dbs <a href="http://variant_effect_predictor.pl:1161/" target="_blank" style="color: rgb(17, 85, 204);">variant_<wbr>effect_predictor.pl:1161</a></div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">STACK main::configure <a href="http://variant_effect_predictor.pl:766/" target="_blank" style="color: rgb(17, 85, 204);">variant_<wbr>effect_predictor.pl:766</a></div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">STACK toplevel <a href="http://variant_effect_predictor.pl:140/" target="_blank" style="color: rgb(17, 85, 204);">variant_effect_<wbr>predictor.pl:140</a></div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Date (localtime) = Thu Jan 29 11:42:51 2015</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Ensembl API version = 78</div>
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">I highly appreciate help.</div>
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Thank you!</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Radhika</div>
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