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<div>Dear ENSEMBL developers,</div>
<div><br>
</div>
<div>When I try to download VCF file to the locally installed database using the following command:</div>
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</div>
<div>perl ./import_vcf.pl -i ./<span style="font-size: 10pt;">common_all.vcf.gz</span><span style="font-size: 10pt;"> -db VCFdump -u atchourb --password abcd1234 --source dbSNP --population general</span></div>
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<div>I get the following message:</div>
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<div>Use of qw(...) as parentheses is deprecated at /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 1564.</div>
<div>2013-02-22 16:33:54 - Session ID is a9703281edc05675ba906f396b0586fb</div>
<div>human is not a valid species name for this instance</div>
<div>Use of uninitialized value $species in hash element at /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 958.</div>
<div>Use of uninitialized value $species in hash element at /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 969.</div>
<div>ERROR: Could not get population adaptor</div>
<div><br>
</div>
<div>What is the way to get the population adapter? Are there more detailed instructions on how to download de novo VCF file to a database with <span style="font-size: 10pt;">import_vcf.pl?</span></div>
<div><span style="font-size: 10pt;"><br>
</span></div>
<div><span style="font-size: 10pt;">Another question refers to usage of the registry file, which I never managed to get working:</span></div>
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</span></div>
<div>
<div>use strict;</div>
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</div>
<div>use Bio::EnsEMBL::Utils::ConfigRegistry;</div>
<div>use Bio::EnsEMBL::DBSQL::DBAdaptor;</div>
<div>use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;</div>
<div><br>
</div>
<div>new Bio::EnsEMBL::DBSQL::DBAdaptor(</div>
<div> -user => 'atchourb',</div>
<div> -pass => 'abcd1234',</div>
<div> -host => 'localhost',</div>
<div> -port => '3306',</div>
<div> -dbname => 'VCFdump'</div>
<div>);</div>
<div><br>
</div>
<div>my @aliases = ( 'H_Sapiens', 'human' );</div>
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<div>Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(</div>
<div> -species => 'Homo sapiens',</div>
<div> -alias => \@aliases</div>
<div>);</div>
</div>
<div><span style="font-size: 10pt;"><br>
</span></div>
<div><span style="font-size: 10pt;">after running the program I get the following message:</span></div>
<div><span style="font-size: 10pt;"><br>
</span></div>
<div><span style="font-size: 10pt;">
<div>Use of qw(...) as parentheses is deprecated at /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 1564.</div>
<div>2013-02-22 16:40:30 - Session ID is dd2fc7598559030f21bfcc9bc529162f</div>
<div>./registry.conf did not return a true value at /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 360.</div>
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<div>Thanks for any suggestions!</div>
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</span></div>
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