[ensembl-dev] Variant Effect Predictor 2.2 A global symbol error

[Daniel Sobral]

Hi Saeed,

These lines probably affect variation predictions in Transcription 
Factor binding sites.

The error is coming from a variable that is exported by 
Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor,  from which 
MotifFeatureAdaptor inherits.

I would think there is something wrong with your ensembl instalation or 
PERL5LIB  because I try the same and I don't get errors. All ensembl 
modules need to be checked out from the same release (64).
Try a fresh cvs checkout.

The PERL5LIB I used to test:
PERL5LIB=$ENS_SRC/bioperl-live/:$ENS_SRC/ensembl/modules/:$ENS_SRC/ensembl-variation/modules/:$ENS_SRC/ensembl-functgenomics/modules/

Hope it helps,
Daniel

On 28/09/2011 11:31, Saeed Al Turki wrote:
> Hi,
>
> I trying to run VEP 2.2 with Ensembl API 64 but I ran into this error:
>
> $ perl variant_effect_predictor_2.2.pl  --help
>
> ------------------------------
> Global symbol "%true_tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 69.
> Global symbol "%tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 70.
> Global symbol "%true_tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 70.
> Global symbol "%tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 99.
> Global symbol "%tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 107.
> Global symbol "%true_tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 107.
> Global symbol "%tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 135.
> Global symbol "%tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 149.
> Global symbol "%true_tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 149.
> Global symbol "%tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 184.
> Global symbol "%true_tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 184.
> Global symbol "%tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 215.
> Global symbol "%tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 227.
> Global symbol "%true_tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 227.
> Global symbol "%tables" requires explicit package name at
> /software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
> line 271.
> Compilation failed in require at variant_effect_predictor_2.2.pl line 480.
> BEGIN failed--compilation aborted at variant_effect_predictor_2.2.pl line
> 480.
> ------------------------------
> If I comment lines from 479 to 483 , the script seems to work but I don't
> know how this would affect the final output.
>
> What do you think the cause of the error? Is it save to keep lines 479-483
> commented out?
>
> Cheers,
> Saeed
>
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