[ensembl-dev] MSG: Could not get adaptor Slice for mycobacterium_tuberculosis variation

[Tal Shmaya]

Hi,

I'm trying to populate a database I've created, with some of my own vcf
files. I've created the tables in the database using the "--sql
ensembl-variation/sql/table.sql" option and am using the
ensembl-variation/scripts/import/import_vcf.pl to ingest a dummy vcf file
(1.0002.vcf).
I also populated the seq_resion table with some dummy data (1,'1',1).
I've attached the command I'm running with the error I'm getting
(import_vcf_error.txt), as well as the registry file and the ensembl_init
file.
Could you please clarify why do I need the adaptor Slice?
I've tried creating a slice adaptor in my ensembl_init file but it didn't
help.

Ensembl version: 86
mysql version: 5.5.52.
OS: Debian

Let me know if there's any more details I can provide,
Thanks! :)
Tal
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$ perl ensembl-variation/scripts/import/import_vcf.pl -r registry -i ~/1.0002.vcf --population NA --source GCDD --species 'mycobacterium_tuberculosis'
UNIVERSAL->import is deprecated and will be removed in a future perl at /usr/local/share/perl/5.20.2/Bio/Tree/TreeFunctionsI.pm line 94.
2016-11-09 16:13:40 - Session ID is 57ba9d87411c117b6872676c600d0428
2016-11-09 16:13:40 - Connected to database mycobacterium_tuberculosis_86_1 on localhost as user root
For mycobacterium_tuberculosis_86_1 there is a difference in the software release (86) and the database release (84). You should update one of these to ensure that your script does not crash.
2016-11-09 16:13:40 - Reading from file /home/tshmaya/1.0002.vcf
2016-11-09 16:13:40 - Parsing header line

-------------------- WARNING ----------------------
MSG: Could not find Slice adaptor in the registry for mycobacterium_tuberculosis variation

FILE: EnsEMBL/DBSQL/DBAdaptor.pm LINE: 992
CALLED BY: Variation/DBSQL/VariationFeatureAdaptor.pm  LINE: 1286
Date (localtime)    = Wed Nov  9 16:13:40 2016
Ensembl API version = 86
---------------------------------------------------

-------------------- EXCEPTION --------------------
MSG: Could not get adaptor Slice for mycobacterium_tuberculosis variation

STACK Bio::EnsEMBL::DBSQL::DBAdaptor::AUTOLOAD /home/tshmaya/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm:996
STACK Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::_objs_from_sth /home/tshmaya/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm:1286
STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch /home/tshmaya/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:488
STACK Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::_fetch_all_by_coords /home/tshmaya/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm:1226
STACK main::variation_feature ensembl-variation/scripts/import/import_vcf.pl:2006
STACK main::main ensembl-variation/scripts/import/import_vcf.pl:802
STACK toplevel ensembl-variation/scripts/import/import_vcf.pl:85
Date (localtime)    = Wed Nov  9 16:13:40 2016
Ensembl API version = 86
---------------------------------------------------

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