[ensembl-dev] VEP version 73 fasta file error
David Blaney
David.Blaney at ogt.com
Wed Feb 5 12:00:39 GMT 2014
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
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