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<p class="MsoNormal">Hi ,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I am using the latest version (v71) and using the VCF format (VCFv4.1) generated from GATK.</p>
<p class="MsoNormal">The script breaks down when I use the –regulatory flag while it runs fine when I remove the flag.</p>
<p class="MsoNormal">Also, it runs fine even with –regulatory for some VCF while it gives error with others, which is strange because all the VCF have been generated from the same pipeline.</p>
<p class="MsoNormal">The script exits with the following error :</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">2013-04-18 16:28:54 - Read existing cache info</p>
<p class="MsoNormal">2013-04-18 16:28:54 - Starting...</p>
<p class="MsoNormal">2013-04-18 16:28:54 - Read 2125 variants into buffer</p>
<p class="MsoNormal">2013-04-18 16:28:54 - Reading transcript data from cache and/or database</p>
<p class="MsoNormal">[==================================================================================================================================] [ 100% ]</p>
<p class="MsoNormal">2013-04-18 16:30:39 - Retrieved 50462 transcripts (0 mem, 52330 cached, 0 DB, 1868 duplicates)</p>
<p class="MsoNormal">2013-04-18 16:30:39 - Reading regulatory data from cache and/or database</p>
<p class="MsoNormal">[========> ] [ 7% ]Can't call method "isa" on unblessed reference at EnsemblAPI_71/ensembl-tools/scripts/variant_effect_predictor/Bio/EnsEMBL/Funcgen/DBSQL/BaseFeatureAdaptor.pm
line 133, <GEN0> line 2125.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">This is the command : </p>
<p class="MsoNormal">perl EnsemblAPI_71/ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl -cache -i input.vcf -o VEP_output -species mus_musculus -format vcf --force -sift b –regulatory</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I have attached a test VCF file which is producing this error.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Can you please help me in fixing this error</p>
<p class="MsoNormal">I will appreciate any kind of help.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Thank you</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><span style="color:black">Sid</span></p>
<p class="MsoNormal">Bioinformatics</p>
<p class="MsoNormal">MRC Harwell</p>
<p class="MsoNormal">Mammalian Genetics Unit</p>
<p class="MsoNormal">Harwell Science and Innovation Campus Oxfordshire</p>
<p class="MsoNormal">OX11 0RD, UK</p>
<p class="MsoNormal"> </p>
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