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Hi Will,
<div>Thank you very much. It worked.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Radhika</div>
<div>
<div>
<div>On Feb 4, 2015, at 4:17 AM, Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div dir="ltr">Hello,
<div><br>
</div>
<div>Ensembl Genomes use different software version numbers to Ensembl; you should be able to use your wheat cache using --cache_version 25, e.g.</div>
<div><br>
</div>
<div><span style="font-size:12.8000001907349px">perl </span><a href="http://variant_effect_predictor.pl/" target="_blank" style="font-size:12.8000001907349px">variant_effect_predictor.pl</a> -<span style="font-size:12.8000001907349px">i </span><span class="im" style="font-size:12.8000001907349px">/berber/radhika/seq_for_assaf/pileup_on_rmdup/Zavitan_var.flt_d6_a4.vcf --species
triticum_aestivum --cache --cache_version 25 --genomes</span><br>
</div>
<div><span class="im" style="font-size:12.8000001907349px"><br>
</span></div>
<div><span class="im" style="font-size:12.8000001907349px">Regards</span></div>
<div><span class="im" style="font-size:12.8000001907349px"><br>
</span></div>
<div><span class="im" style="font-size:12.8000001907349px">Will McLaren</span></div>
<div><span class="im" style="font-size:12.8000001907349px">Ensembl Variation</span></div>
<div><br>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On 3 February 2015 at 22:09, Radhika Bartaula <span dir="ltr">
<<a href="mailto:rb11@wildcats.unh.edu" target="_blank">rb11@wildcats.unh.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Magali,
<div>Thank you very much for quick response. I did try with the -genomes option but still getting the error below. </div>
<div>
<div style="margin:0px;font-size:11px;font-family:Menlo"><br>
</div>
<div style="margin:0px;font-size:11px;font-family:Menlo">UNIVERSAL->import is deprecated and will be removed in a future perl at /home/radhika/ensembl-tools-release-78/scripts/variant_effect_predictor/Bio/Tree/TreeFunctionsI.pm line 94.</div>
<div style="margin:0px;font-size:11px;font-family:Menlo"><br>
</div>
<div style="margin:0px;font-size:11px;font-family:Menlo">ERROR: No cache found for triticum_aestivum, version 78</div>
</div>
<div style="margin:0px;font-size:11px;font-family:Menlo"><br>
</div>
<div style="margin:0px;font-size:11px;font-family:Menlo">Based on the comments found at the link, I thought it might be because of the version issue.</div>
<div style="margin:0px;font-size:11px;font-family:Menlo"><a href="http://comments.gmane.org/gmane.science.biology.ensembl.devel/9198" target="_blank">http://comments.gmane.org/gmane.science.biology.ensembl.devel/9198</a></div>
<div style="margin:0px;font-size:11px;font-family:Menlo"><br>
</div>
<div style="margin:0px;font-size:11px;font-family:Menlo">So, I changed the version to 77, this is the error I get when I change the version.</div>
<div style="margin:0px;font-size:11px;font-family:Menlo"><br>
</div>
<div style="margin:0px;font-size:11px;font-family:Menlo">perl <a href="http://variant_effect_predictor.pl/" target="_blank">
variant_effect_predictor.pl</a> -i /berber/radhika/seq_for_assaf/mpileup_on_rmdup/Zavitan_var.flt_d6_a4.vcf -genomes --species triticum_aestivum --cache -db_version 77</div>
<div style="margin:0px;font-size:11px;font-family:Menlo"><br>
</div>
<div style="margin:0px;font-size:11px;font-family:Menlo">UNIVERSAL->import is deprecated and will be removed in a future perl at /home/radhika/ensembl-tools-release-78/scripts/variant_effect_predictor/Bio/Tree/TreeFunctionsI.pm line 94.</div>
<div style="margin:0px;font-size:11px;font-family:Menlo"><br>
</div>
<div style="margin:0px;font-size:11px;font-family:Menlo">For triticum_aestivum_core_24_77_1 there is a difference in the software release (78) and the database release (77). You should update one of these to ensure that your script does not crash.</div>
<div style="margin:0px;font-size:11px;font-family:Menlo">For triticum_aestivum_variation_24_77_1 there is a difference in the software release (78) and the database release (77). You should update one of these to ensure that your script does not crash.</div>
<div style="margin:0px;font-size:11px;font-family:Menlo">ERROR: No cache found for triticum_aestivum, version 77</div>
<div style="margin:0px;font-size:11px;font-family:Menlo"><br>
</div>
<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>
<div style="margin:0px;font-size:11px;font-family:Menlo"><br>
</div>
<div style="margin:0px;font-size:11px;font-family:Menlo"><br>
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<div>
<div>On Feb 3, 2015, at 4:46 PM, <<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>> <<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>> wrote:</div>
<br>
<blockquote type="cite"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Public</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">database
server</span></blockquote>
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