<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div><br></div><div><br></div><div>Hello Ensembl and Will,</div><div><br></div><div>I’m running into trouble when I am trying to <b>create / update my cache files</b> for VEP. </div><div><br></div><div>My best guess currently is, that the problem is either related to the ensembl code, or related to storing references with <b>Storable.pm</b> - I’m using version <b>$VERSION = ‘2.41’ of this module.</b></div><div><br></div><div><b>Here’s how to reproduce the error :</b></div><div><br></div><div><div><font face="Menlo">perl ensembl-tools-release-74/scripts/variant_effect_predictor/variant_effect_predictor.pl \</font></div><div><font face="Menlo"> -build all -dir tmp --verbose --host <HOST> --user <USER> --pass <SECRET> --port 3326</font></div></div><div><font face="Menlo"><br></font></div><div><font face="Menlo">ERROR: </font></div><div><font face="Menlo"><br></font></div><div><div style="font-family: Menlo;">2015-03-02 20:56:27 - Connected to core version 74 database and variation version 74 database</div><div style="font-family: Menlo;"><br></div><div style="font-family: Menlo;">Can't store CODE items at …/perl/5.18.2/x86_64-linux-2.6-rhel6/lib/5.18.2/x86_64-linux-thread-multi/Storable.pm line 304, at </div><div style="font-family: Menlo;">variant_effect_predictor/e74_api/ensembl-variation-release-74/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 4261.</div><div style="font-family: Menlo;"><br></div><div style="font-family: Menlo;"><br></div><div>So reading trough <a href="http://perldoc.perl.org/Storable.html#CODE-REFERENCES">http://perldoc.perl.org/Storable.html#CODE-REFERENCES</a> suggests to serialize code-references with B::Deparse. I’ve added 2 lines to the variant_effect_predictor.pl script: </div><div style="font-family: Menlo;"><br></div><div style="font-family: Menlo;"><span style="color: rgb(0, 104, 139); font-family: monospace; font-size: 12.4800004959106px; background-color: rgb(238, 238, 221);">$Storable::Eval=1; </span></div><div style="font-family: Menlo;"><div><span style="color: rgb(0, 104, 139); font-family: monospace; font-size: 12.4800004959106px; background-color: rgb(238, 238, 221);">$Storable::Deparse=1; </span></div></div><div style="font-family: Menlo;"><br></div><div style="font-family: Menlo;"><br></div><div>Now, the script writes the binary cache files - however, the next problem occurs when I try to read them. </div><div><br></div><div>Depending on which version of the Ensembl API I am using, I get these error messages: </div><div style="font-family: Menlo;"><br></div><div style="font-family: Menlo;"><b>e75: </b></div><div style="font-family: Menlo;"><br></div><div style="font-family: Menlo;"><div>2015-03-02 21:42:33 - Reading cached adaptor data</div><div>code sub {</div><div> package Bio::EnsEMBL::DBSQL::DBConnection;</div><div> use strict;</div><div> $args[0];</div><div>} caused an error: Global symbol "@args" requires explicit package name at (eval 108) line 4</div></div><div style="font-family: Menlo;"><br></div><div style="font-family: Menlo;"><br></div><div style="font-family: Menlo;"><b>e74:</b></div><div style="font-family: Menlo;"><div>2015-03-02 21:47:40 - Reading cached adaptor data</div><div>code sub {</div><div> package Bio::EnsEMBL::DBSQL::DBConnection;</div><div> use strict;</div><div> $arg;</div><div>} caused an error: Global symbol "$arg" requires explicit package name at (eval 130) line 4, at /gne/research/apps/ensembl/ensembl-74/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 4281.</div><div><br></div><div>I’ve tried various work-arounds and different ensembl versions, but did not succeed. Any help welcome.</div><div><br></div><div><br></div><div>The database I am currently working on is an e67 core which has been patched up to e74 ( so i can’t use the e74 cache files from the web). </div><div><br></div><div>I tried to build indices with e77 but did not succeed either. </div></div><div style="font-family: Menlo;"><br></div><div style="font-family: Menlo;"><br></div><div style="font-family: Menlo;">Any help welcome </div><div style="font-family: Menlo;"><br></div><div style="font-family: Menlo;"> Jan Vogel </div><div style="font-family: Menlo;"><br></div></div></body></html>