[ensembl-dev] VEP version 73 fasta file error

[Will McLaren]

Hi David,

Are you able to provide a line or more of input that recreates the issue?

This would help greatly with debugging the problem.

Regards

Will McLaren
Ensembl Variation


On 5 February 2014 12:00, David Blaney <David.Blaney at ogt.com> wrote:

> Dear Developers,
>
>
>
> I am running version 73 of the VEP script and API. I am running the script
> in offline mode, cache only with the HGVS option selected and a fastq file
> specified (see snippet from config below):
>
>
>
> #######     cache stuff   #############
>
> cache                                                    1
>
> dir_plugins                                          /NGS_Tools/vep/Plugins
>
> dir_cache
> /ReferenceData/vep_cache
>
> # cache_region_size       1MB
>
> offline                                   1
>
> # skip_db_check                              1
>
> fasta
> /ReferenceData/vep_cache/homo_sapiens/73/Homo_sapiens.GRCh37.73.dna.primary_assembly.fa
>
>
>
> when running the program I get the following warning (with trace, some
> line numbers may have changed in my vep script due to adding the libs for
> the modules):
>
>
>
> Use of uninitialized value in reverse at
> /NGS_Tools/v73/ensembl/modules/Bio/EnsEMBL/Utils/Sequence.pm line 81.
>
> at /NGS_Tools/v73/ensembl/modules/Bio/EnsEMBL/Utils/Sequence.pm line 81.
>
>         Bio::EnsEMBL::Utils::Sequence::reverse_comp(SCALAR(0x56bd200))
> called at (eval 68)[/NGS_Tools/VEP-latest/variant_effect_predictor.pl:1031]
> line 22
>
>         Bio::EnsEMBL::Slice::seq(Bio::EnsEMBL::Slice=HASH(0x97811d0))
> called at
> /NGS_Tools/v73/ensembl-variation/modules//Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 580
>
>
> Bio::EnsEMBL::Variation::TranscriptVariationAllele::hgvs_transcript(Bio::EnsEMBL::Variation::TranscriptVariationAllele=HASH(0x971c890))
> called at
> /NGS_Tools/v73/ensembl-variation/modules//Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 1854
>
>         Bio::EnsEMBL::Variation::Utils::VEP::tva_to_line(HASH(0x54c0f18),
> Bio::EnsEMBL::Variation::TranscriptVariationAllele=HASH(0x971c890)) called
> at
> /NGS_Tools/v73/ensembl-variation/modules//Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 1659
>
>
> Bio::EnsEMBL::Variation::Utils::VEP::vf_to_consequences(HASH(0x54c0f18),
> Bio::EnsEMBL::Variation::VariationFeature=HASH(0x5c67ba0)) called at
> /NGS_Tools/v73/ensembl-variation/modules//Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 1425
>
>
> Bio::EnsEMBL::Variation::Utils::VEP::vf_list_to_cons(HASH(0x54c0f18),
> ARRAY(0x5006550)) called at
> /NGS_Tools/v73/ensembl-variation/modules//Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 985
>
>
> Bio::EnsEMBL::Variation::Utils::VEP::get_all_consequences(HASH(0x54c0f18),
> ARRAY(0x53023d0)) called at /NGS_Tools/VEP-latest/
> variant_effect_predictor.pl line 364
>
>         main::main(HASH(0x54c0f18)) called at /NGS_Tools/VEP-latest/
> variant_effect_predictor.pl line 202
>
>
>
> Could you please shed some light on what is going on? I have not yet
> figured out if this warning has any effect on the output.
>
>
>
> Many thanks,
>
> David Blaney
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140205/1a57a24b/attachment.html>