[ensembl-dev] Error on cache mismatch

[Will McLaren]

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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