[ensembl-dev] Error on cache mismatch

[Stefan Gräf]

Hi Will,

Looks like this bug sneaked in again with v79:

All best,
 Stefan

-------------------- WARNING ----------------------
MSG: homo_sapiens is not a valid species name (check DB and API version)
FILE: Bio/EnsEMBL/Registry.pm LINE: 1200
CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 985
Date (localtime)    = Fri Mar 13 16:13:37 2015
Ensembl API version = 79
---------------------------------------------------

-------------------- EXCEPTION --------------------
MSG: Can not find internal name for species 'homo_sapiens'
STACK Bio::EnsEMBL::Registry::get_adaptor
/home/cbrcmod/scratch/modules/out/modulebin/VEP/79/perl/Bio/EnsEMBL/Registry.pm:987
STACK main::connect_to_dbs
/home/cbrcmod/scratch/modules/out/modulebin/VEP/79/bin/
variant_effect_predictor.pl:1191
STACK main::configure
/home/cbrcmod/scratch/modules/out/modulebin/VEP/79/bin/
variant_effect_predictor.pl:780
STACK toplevel /home/cbrcmod/scratch/modules/out/modulebin/VEP/79/bin/
variant_effect_predictor.pl:141
Date (localtime)    = Fri Mar 13 16:13:37 2015
Ensembl API version = 79
---------------------------------------------------


On 4 December 2014 at 10:51, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi Konrad,
>
> Thanks for finding this, I've pushed a fix to 77 and 78
> (ensembl-variation).
>
> In general though, I would advise against mixing different software and
> cache releases if you can avoid it.
>
> Cheers
>
> Will
>
> On 4 December 2014 at 01:18, Konrad Karczewski <konradk at broadinstitute.org
> > wrote:
>
>> Hi VEP crew,
>>
>> I've been trying to use newer versions of VEP (77/78) with older versions
>> of the cache (74) and seem to be running into some issues (stack trace
>> below). Any ideas?
>>
>> Thanks!
>> -Konrad
>>
>> -------------------- EXCEPTION --------------------
>> MSG: Can not find internal name for species 'homo_sapiens'
>> STACK Bio::EnsEMBL::Registry::get_adaptor
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Registry.pm:987
>> STACK Bio::EnsEMBL::DBSQL::DBAdaptor::AUTOLOAD
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/DBSQL/DBAdaptor.pm:1016
>> STACK Bio::EnsEMBL::Translation::get_all_Attributes
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Translation.pm:995
>> STACK Bio::EnsEMBL::Translation::get_all_SeqEdits
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Translation.pm:1069
>> STACK
>> Bio::EnsEMBL::Variation::BaseTranscriptVariation::_selenocysteine_positions
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/BaseTranscriptVariation.pm:733
>> STACK Bio::EnsEMBL::Variation::TranscriptVariationAllele::peptide
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm:248
>> STACK Bio::EnsEMBL::Variation::TranscriptVariation::pep_allele_string
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariation.pm:230
>> STACK Bio::EnsEMBL::Variation::TranscriptVariation::_prefetch_for_vep
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariation.pm:436
>> STACK Bio::EnsEMBL::Variation::Utils::VEP::whole_genome_fetch_transcript
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:3143
>> STACK Bio::EnsEMBL::Variation::Utils::VEP::whole_genome_fetch
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:2997
>> STACK Bio::EnsEMBL::Variation::Utils::VEP::vf_list_to_cons
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1387
>> STACK Bio::EnsEMBL::Variation::Utils::VEP::get_all_consequences
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1271
>> STACK main::main
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/
>> variant_effect_predictor.pl:280
>> STACK toplevel
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/
>> variant_effect_predictor.pl:144
>> Date (localtime)    = Wed Dec  3 20:13:21 2014
>> Ensembl API version = 77
>> ---------------------------------------------------
>>
>>
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>
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