<div dir="ltr">Hi G.<div><br></div><div>This error is returned because you have an unsupported version of Perl, as well as not having the latest version of <a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a></div><div><br></div><div>Ensembl and VEP support a minimum Perl version of 5.10; this error will occur on 5.8.x versions.</div><div><br></div><div>However, a patch was put in to the ensembl-tools repo to suppress this error:</div><div><br></div><div><a href="https://github.com/Ensembl/ensembl-tools/commit/aaa06ff9e02faa7c10b8f5ea33b1883cec137714">https://github.com/Ensembl/ensembl-tools/commit/aaa06ff9e02faa7c10b8f5ea33b1883cec137714</a><br></div><div><br></div><div>You should have this patched version if you downloaded ensembl-tools after Dec 21st 2015.</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 21 April 2016 at 14:45, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">







<p><span>Hi Ensembl team,</span></p><p><span>I have installed VEP script release 84 and found the error below when running it. Your help will be appreciated.</span></p><p><span>Thanks,</span></p><p>G.<br></p><p><span><b>[ggaw84@hpclogin2 variant_annotation]$ ./<a href="http://ping_ensembl_v84.pl" target="_blank">ping_ensembl_v84.pl</a> </b></span></p><p><span><b>








</b></span></p><p><span>Installation is good. Connection to Ensembl works and you can query the human core database</span></p><p><span><b>[ggaw84@hpclogin2 variant_annotation]$ ./<a href="http://variant_effect_predictor_v84.pl" target="_blank">variant_effect_predictor_v84.pl</a> -i example_GRCh38.vcf --database</b></span></p>
<p><span>Bareword found where operator expected at ./<a href="http://variant_effect_predictor_v84.pl" target="_blank">variant_effect_predictor_v84.pl</a> line 997, near "s/\_$//r"</span></p>
<p><span>syntax error at ./<a href="http://variant_effect_predictor_v84.pl" target="_blank">variant_effect_predictor_v84.pl</a> line 997, near "s/\_$//r"</span></p>
<p><span>Execution of ./<a href="http://variant_effect_predictor_v84.pl" target="_blank">variant_effect_predictor_v84.pl</a> aborted due to compilation errors.</span></p>
<p><span><b>[ggaw84@hpclogin2 variant_annotation]$ grep -n . <a href="http://variant_effect_predictor_v81.pl" target="_blank">variant_effect_predictor_v81.pl</a> | grep -b5 -a5 '^997'</b></span></p>
<p><span>992:    }</span></p>
<p><span>993:    </span></p>
<p><span>994:    # warn user DB will be used for SIFT/PolyPhen/HGVS/frequency/LRG</span></p>
<p><span>995:    if(defined($config->{cache})) {</span></p>
<p><span>996:        </span></p>
<p><span>997:        # these two def depend on DB</span></p>
<p><span>998:        foreach my $param(grep {defined $config->{$_}} qw(hgvs lrg check_sv check_ref)) {</span></p>
<p><span>999:            debug("INFO: Database will be accessed when using --$param") unless defined($config->{quiet}) or ($param =~ /hgvs|check_ref/ and defined($config->{fasta}));</span></p>
<p><span>1000:        }</span></p>
<p><span>1001:        </span></p>
<p><span>1002:        debug("INFO: Database will be accessed when using --check_frequency with population ".$config->{freq_pop}) if !defined($config->{quiet}) and defined($config->{check_frequency}) && $config->{freq_pop} !~ /1kg.*(all|afr|amr|asn|eur)/i;</span></p><div><br></div>
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