[ensembl-dev] import_vcf.pl - ERROR: Could not get population adaptor

Phil Dagosto PDagosto at edgebio.com
Tue Mar 5 20:59:43 GMT 2013

I'm trying to import a VCF file into my local Ensembl variation database.

The version of the API I'm using is 70.

Here are the contents of  my registry file:

use Bio::EnsEMBL::Utils::ConfigRegistry;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;

new Bio::EnsEMBL::DBSQL::DBAdaptor(
  -host    => 'local_ensembl',
  -user    => 'test',
  -pass    => '123',
  -port    => '3306',
  -species => 'Homo sapiens',
  -group   => 'variation',
  -dbname  => 'homo_sapiens_variation_70_37'

my @aliases = ( 'H_Sapiens', 'human' );

  -species => 'Homo sapiens',
  -alias   => \@aliases


The import_vcf .pl script is being run with the following command-line parameters:

--input_file indel.final.vcf --registry registry.pl --source 'edgebio' --population 'test' --test 100

The output is:

2013-03-05 15:54:33 - Session ID is 64494fac5e75b495bfb5907137f45cbf
2013-03-05 15:54:40 - Connected to database homo_sapiens_variation_70_37 on local_ensembl as user test
ERROR: Could not get population adaptor

Is there something I need to add to my Registry file so that the population adaptor can be found?



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