<div dir="ltr">Hello,<div><br></div><div>I'd recommend that you use the registry file rather than specifying the connection parameters on the command line.</div><div><br></div><div>The problem with your registry file is that it does not return a true value; all registry files must end with:</div>
<div><br></div><div>1;</div><div><br></div><div style>as it is interpreted as a Perl module, and all Perl modules must return a true value.</div><div style><br></div><div style>The DBAadaptor your file is creating should also be a Variation DBAdaptor, and must have the species name specified in it.</div>
<div style><br></div><div style>Depending on your use case, you may also need to connect to a core database; this should be specified as a non-variation DBAdaptor, as you had before, but it should also have the species name included.</div>
<div style><br></div><div style>So, your registry file should look like:</div><div style><br></div><div style><div style="font-family:Tahoma;font-size:13px">use strict;</div><div style="font-family:Tahoma;font-size:13px">
<br></div><div style="font-family:Tahoma;font-size:13px">use Bio::EnsEMBL::Utils::ConfigRegistry;</div><div style="font-family:Tahoma;font-size:13px">use Bio::EnsEMBL::DBSQL::DBAdaptor;</div><div style="font-family:Tahoma;font-size:13px">
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;</div><div style="font-family:Tahoma;font-size:13px"><br></div><div style="font-family:Tahoma;font-size:13px"><div>new Bio::EnsEMBL::DBSQL::DBAdaptor(</div><div> -species => 'Homo_sapiens',</div>
<div> -user => 'atchourb',</div><div> -pass => 'abcd1234',</div><div> -host => 'localhost',</div><div> -port => '3306',</div><div> -dbname => 'my_core_database'</div>
<div>);</div></div><div style="font-family:Tahoma;font-size:13px"><br></div><div style="font-family:Tahoma;font-size:13px">new Bio::EnsEMBL::Variation::DBSQL::DBAdaptor(</div><div style="font-family:Tahoma;font-size:13px">
-species => 'Homo_sapiens',</div><div style="font-family:Tahoma;font-size:13px"> -user => 'atchourb',</div><div style="font-family:Tahoma;font-size:13px"> -pass => 'abcd1234',</div>
<div style="font-family:Tahoma;font-size:13px"> -host => 'localhost',</div><div style="font-family:Tahoma;font-size:13px"> -port => '3306',</div><div style="font-family:Tahoma;font-size:13px">
-dbname => 'VCFdump'</div><div style="font-family:Tahoma;font-size:13px">);</div><div style="font-family:Tahoma;font-size:13px"><br></div><div style="font-family:Tahoma;font-size:13px">my @aliases = ( 'H_Sapiens', 'human' );</div>
<div style="font-family:Tahoma;font-size:13px"><br></div><div style="font-family:Tahoma;font-size:13px">Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(</div><div style="font-family:Tahoma;font-size:13px"> -species => 'Homo sapiens',</div>
<div style="font-family:Tahoma;font-size:13px"> -alias => \@aliases</div><div style="font-family:Tahoma;font-size:13px">);</div></div><div><br><div>1;</div></div><div><br></div><div style>There's a slightly better example of a registry file (with the main ensembldb parameters entered) here:</div>
<div style><br></div><div style><a href="http://www.ensembl.org/info/docs/variation/vep/vep_script.html#local">http://www.ensembl.org/info/docs/variation/vep/vep_script.html#local</a><br></div><div style><br></div><div style>
Hope this helps!</div><div style><br></div><div style>Will McLaren</div><div style>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 22 February 2013 23:52, Tchourbanov, Alexander Y - (atchourb) <span dir="ltr"><<a href="mailto:atchourb@email.arizona.edu" target="_blank">atchourb@email.arizona.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">
<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>
<div><br>
</div>
<div>perl ./<a href="http://import_vcf.pl" target="_blank">import_vcf.pl</a> -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>
<div><br>
</div>
<div>I get the following message:</div>
<div><br>
</div>
<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"><a href="http://import_vcf.pl" target="_blank">import_vcf.pl</a>?</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>
<div><span style="font-size:10pt"><br>
</span></div>
<div>
<div>use strict;</div>
<div><br>
</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>
<div><br>
</div>
<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>
<div><br>
</div>
<div>Thanks for any suggestions!</div>
<div><br>
</div>
</span></div>
</div>
</div>
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<br></blockquote></div><br></div>