[ensembl-dev] 'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor' cannot be found.

[Diana Lemos]

Hello Calum,


Can you please share what you have in your PERL5LIB? (echo $PERL5LIB)



Kind Regards,

Diana




On 30/06/2021 16:19, Tattersfield,Calum (BIDMC - Friedman-Clin Trial 
Nephrol SF) wrote:
>
> Bash on Linux version 7 with Perl/5.24.0. Attempting to access 1000 
> Genomes population frequencies using example script from
>
>
> https://www.ensembl.info/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/ 
> <https://www.ensembl.info/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/>
>
>
> The API version used is 104.
>
>
> Error message is
>
> 'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor'  cannot be found.
>
>
> Exception is
>
> 'Can't locate Bio/DB/HTS/Tabix.pm in @INC'
>
>
> BEGIN failed--compilation aborted at 
> /src/ensembl-io/modules/Bio/EnsEMBL/IO/TabixParser.pm line 41.
>
> BEGIN failed--compilation aborted at 
> /src/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/VCF4Tabix.pm line 42.
>
> Compilation failed in require at 
> /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm 
> line 82.
> BEGIN failed--compilation aborted at 
> /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm 
> line 82.
> Compilation failed in require at 
> /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VCFCollectionAdaptor.pm 
> line 98.
> BEGIN failed--compilation aborted at 
> /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VCFCollectionAdaptor.pm 
> line 98.
> Compilation failed in require at (eval 875) line 2.
>
>
> I have been unable to clone tabix from github, but their page says it 
> has been moved to htslib. I made htslib following api installation 
> instructions here:
>
> https://useast.ensembl.org/info/docs/api/api_installation.html 
> <https://useast.ensembl.org/info/docs/api/api_installation.html>
>
>
> Thanks,
>
> Calum
>
>
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