[ensembl-dev] Error on cache mismatch

[Will McLaren]

Hi Stefan,

The 79 databases were only brought online to ensembldb.ensembl.org earlier
today; this was probably the cause of your error, but it should work OK now.

We are also experiencing delays getting our FTP site up, which carries the
VEP 79 cache files; we hope to make this available soon.

Thanks for your patience

Will McLaren
Ensembl Variation



On 13 March 2015 at 16:24, Stefan Gräf <sg550 at cam.ac.uk> wrote:

> 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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