[ensembl-dev] 'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor' cannot be found.
Tattersfield,Calum (BIDMC - Friedman-Clin Trial Nephrol SF)
ctatters at bidmc.harvard.edu
Wed Jun 30 16:19:32 BST 2021
Bash on Linux version 7 with Perl/5.24.0. Attempting to access 1000 Genomes population frequencies using example script from
The API version used is 104.
Error message is
'Bio::EnsEMBL::Variation::DBSQL::VCFCollectionAdaptor' cannot be found.
'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:
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