<div dir="ltr">Hi Michael,<div><br></div><div>I'm not sure why this error is occurring, but the VEP stores a reference to the slice adaptor which you can access from your plugin as:</div><div><br></div><div>$self->{config}->{sa}</div>
<div><br></div><div>There are a number of adaptors stored in this way; the references are created in the get_adaptors sub-routine in <a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a></div><div><br>
</div><div>The second warning is nothing to worry about. The line:</div><div><br></div><div>Bio::EnsEMBL::Utils::Exception::verbose(1999)<br></div><div><br></div><div>in <a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a> should suppress this warning from happening, but currently this happens after the sub-routine configure_plugins is run, so if your plugin creates an adaptor with no_slice_cache enabled you will see the warning.</div>
<div><br></div><div>I'll update the script so the warning gets suppressed before configure_plugins runs.</div><div><br></div><div>Cheers</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On 14 November 2013 22:56, Michael Yourshaw <span dir="ltr"><<a href="mailto:myourshaw@ucla.edu" target="_blank">myourshaw@ucla.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"><font face="Monaco" size="1">I normally use a local copy of the mySQL database to process large datasets. Some of my plugins make calls to the Ensembl database via the Perl API.</font><div>
<font face="Monaco" size="1"><br></font><font face="Monaco" size="1">VEP runs normally without the cache.<br></font><div><font face="Monaco" size="1"><br></font></div><div>I want to take advantage of some of the options available only through the cache, such as <span style="font-family:Monaco;font-size:10px">maf_esp, and possibly improve throughput, but still get everything not in the cache from the local database.</span><div>
<font face="Monaco" size="1"><br></font></div><div><div><font face="Monaco" size="1">I have downloaded and installed the homo_sapiens_73 cache, and use these parameters:</font></div><div><div style="margin:0px;font-size:10px;font-family:Monaco">
<span style="white-space:pre-wrap"> </span>cache=1</div><div style="margin:0px"><div style="font-family:Monaco;font-size:10px;margin:0px"><span style="white-space:pre-wrap"> </span>dir_cache=/scratch1/tmp/myourshaw/ensembl/.vep/</div>
<div style="font-family:Monaco;font-size:10px;margin:0px">-—offline is not on</div><div style="font-family:Monaco;font-size:10px;margin:0px"><br></div><div style="font-family:Monaco;font-size:10px;margin:0px">There are two problems when I turn on the cache.</div>
<div style="font-family:Monaco;font-size:10px;margin:0px"><br></div><div style="font-family:Monaco;font-size:10px;margin:0px">First, some of my plugins get an error in Bio::EnsEMBL::DBSQL::GeneAdaptor in the fetch_nearest_Gene_by_Feature sub at the line</div>
<div style="font-family:Monaco;font-size:10px;margin:0px"><span style="white-space:pre-wrap"> </span>my $seq_region_id = $feat->slice->adaptor->get_seq_region_id($feat->slice);</div><div style="font-family:Monaco;font-size:10px;margin:0px">
<br></div><div style="font-family:Monaco;font-size:10px;margin:0px">The error is</div><div style="font-family:Monaco;font-size:10px;margin:0px"><span style="white-space:pre-wrap"> </span>Can't call method "get_seq_region_id" on an undefined value at /share/apps/myourshaw/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm line 1978.</div>
<div style="font-family:Monaco;font-size:10px;margin:0px"><br></div><div style="font-family:Monaco;font-size:10px;margin:0px">Specifically, $feat->slice->adapter is undef</div><div style="font-family:Monaco;font-size:10px;margin:0px">
<br></div><div style="font-family:Monaco;font-size:10px;margin:0px">The call in my code that triggers this is:</div><div style="font-family:Monaco;font-size:10px;margin:0px">sub run {</div><div style="margin:0px"><div style="margin:0px">
<font face="Monaco" size="1"> my ($self, $bvfoa, $line_hash) = @_;</font></div><div><div><font face="Monaco" size="1"> if($bvfoa->isa('Bio::EnsEMBL::Variation::RegulatoryFeatureVariationAllele')){</font></div>
<div><span style="font-family:Monaco;font-size:x-small"> my $feature = $bvfoa->regulatory_feature;</span></div><div><span style="font-family:Monaco;font-size:x-small"><span style="white-space:pre-wrap"> </span># </span><span style="font-family:Monaco;font-size:10px">At this point, $feature->slice->adapter is undef and the next line fails</span></div>
<div><font face="Monaco" size="1"> my $nearest_genes = $config->{ga}->fetch_nearest_Gene_by_Feature($feature);</font></div><div><font face="Monaco" size="1"> my $gene = @{$nearest_genes}[0];</font></div>
<div><font face="Monaco" size="1"> }</font></div><div><br></div></div></div></div><div><div><font face="Monaco" size="1">Second, I get the following warning when VEP initializes. Is this related to the first problem? Should I be concerned?</font></div>
<div><div style="margin:0px;font-size:10px;font-family:Monaco"><span style="white-space:pre-wrap"> </span>MSG: You are using the API without caching most recent features. Performance might be affected.</div><div style="margin:0px;font-size:10px;font-family:Monaco">
<span style="white-space:pre-wrap"> </span>FILE: EnsEMBL/DBSQL/BaseFeatureAdaptor.pm LINE: 76</div><div style="margin:0px;font-size:10px;font-family:Monaco"><span style="white-space:pre-wrap"> </span>CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 1043</div>
<div style="margin:0px;font-size:10px;font-family:Monaco"><span style="white-space:pre-wrap"> </span>Date (localtime) = Thu Nov 14 11:52:27 2013</div><div style="margin:0px;font-size:10px;font-family:Monaco"><span style="white-space:pre-wrap"> </span>Ensembl API version = 73</div>
</div><div><br></div><div><div><span style="border-collapse:separate;font-size:12px;border-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:12px;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:12px;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:10px;white-space:normal;font-family:'Lucida Grande';word-spacing:0px"><p class="MsoNormal">
<font face="'Devanagari MT'" size="7"><span style="font-size:27px"><font face="'Lucida Grande'" size="3"><span style="font-size:12px"><br></span></font><font size="5"><span style="font-size:18px">ॐ</span></font></span></font></p>
</span><p></p><p style="margin-top:0px;margin-right:0px;margin-bottom:6px;margin-left:0px;line-height:19px;font:normal normal normal 16px/normal Helvetica"><span style="font-family:'Lucida Grande';font-size:10px">Michael Yourshaw</span></p>
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<span style="letter-spacing:0px">Department of Human Genetics, Nelson Lab</span></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 10px/normal 'Lucida Grande'">
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