[ensembl-dev] VEP cache file creation for e74

Jan Vogel jan.vogel at gmail.com
Tue Mar 3 05:55:29 GMT 2015



Hello Ensembl and Will,

I’m running into trouble when I am trying to create / update my cache files for VEP. 

My best guess currently is, that the problem is either related to the ensembl code, or related to storing references with Storable.pm - I’m using version $VERSION = ‘2.41’ of this module.

Here’s how to reproduce the error :

perl  ensembl-tools-release-74/scripts/variant_effect_predictor/variant_effect_predictor.pl \
       -build all -dir tmp --verbose --host <HOST> --user <USER> --pass <SECRET> --port 3326

ERROR: 

2015-03-02 20:56:27 - Connected to core version 74 database and variation version 74 database

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 
variant_effect_predictor/e74_api/ensembl-variation-release-74/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 4261.


So reading trough http://perldoc.perl.org/Storable.html#CODE-REFERENCES suggests to serialize code-references with B::Deparse. I’ve added 2 lines to the variant_effect_predictor.pl script: 

$Storable::Eval=1; 
$Storable::Deparse=1; 


Now, the script writes the binary cache files - however, the next problem occurs when I try to read them. 

Depending on which version of the Ensembl API I am using, I get these error messages: 

e75: 

2015-03-02 21:42:33 - Reading cached adaptor data
code sub {
    package Bio::EnsEMBL::DBSQL::DBConnection;
    use strict;
    $args[0];
} caused an error: Global symbol "@args" requires explicit package name at (eval 108) line 4


e74:
2015-03-02 21:47:40 - Reading cached adaptor data
code sub {
    package Bio::EnsEMBL::DBSQL::DBConnection;
    use strict;
    $arg;
} caused an error: Global symbol "$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.

I’ve tried various work-arounds and different ensembl versions, but did not succeed. Any help welcome.


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). 

I tried to build indices with e77 but did not succeed either. 


Any help welcome 

   Jan Vogel 

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