[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' );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => 'Homo sapiens',
-alias => \@aliases
);
1;
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?
Thanks,
Phil
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