[ensembl-dev] Unable to connect to Compara->homology

Casper Shyr casper at cmmt.ubc.ca
Wed Mar 19 23:46:57 GMT 2014


Hello,
   I am having a problem creating the adaptor to the Ensembl compara’s homology database.
My code:
my $homology_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Multi', 'compara', 'Homology');  die "homology  adaptor fail\n" if !defined $homology_adaptor;

My output:
-------------------- WARNING ----------------------
MSG: 'Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor' cannot be found.
Exception Can't locate feature.pm in @INC (@INC contains: /usr/local/src/ensembl-75/ensembl-funcgen/modules /usr/local/src/ensembl-75/ensembl-variation/modules /usr/local/src/ensembl-75/ensembl-compara/modules /usr/local/src/ensembl-75/ensembl/modules /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignedMember.pm line 75.
BEGIN failed--compilation aborted at /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignedMember.pm line 75.
Compilation failed in require at /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignedMemberSet.pm line 86.
BEGIN failed--compilation aborted at /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignedMemberSet.pm line 86.
Compilation failed in require at (eval 234) line 3.
	...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
BEGIN failed--compilation aborted at /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/Homology.pm line 76.
Compilation failed in require at /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm line 24.
BEGIN failed--compilation aborted at /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm line 24.
Compilation failed in require at (eval 233) line 3.


FILE: Bio/EnsEMBL/Registry.pm LINE: 1040
CALLED BY: get_paralogs.pl  LINE: 45
Date (localtime)    = Wed Mar 19 16:38:34 2014
Ensembl API version = 75
---------------------------------------------------

Additional notes:
1) I have already checked that the compara is installed and in my script, I already linked to the modules using:
use lib '/usr/local/src/ensembl-75/ensembl-compara/modules’;
use Bio::EnsEMBL::Registry;

2) The following code works:
my $gene_member_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Multi', 'compara', 'GeneMember'); die "gene member adaptor fail\n" if !defined $gene_member_adaptor;
It seems that I can connect to GeneMember for compara no problem, but fails when I replace “GeneMember" with “Homology"

Any suggestion is greatly appreciated! Thanks!
Casper Shyr
PhD Candidate, Centre for Molecular Medicine and Therapeutics
University of British Columbia
casper at cmmt.ubc.ca



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