[ensembl-dev] VEP version 73 fasta file error

[Duarte Molha]

Dear Will

David works with me...  Here is an example line where this is happening:

#CHROM             POS        ID            REF         ALT         QUAL    FILTER   INFO      FORMAT              SS_sample
5              98216956             .               CTT         C             16.9698 .                AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1M2D;DP=7;DPB=22.2692;DPRA=0;EPP=7.35324;EPPR=11.6962;GTI=0;LEN=2;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.88252;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=121;RO=4;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=del;technology.ILLUMINA=1;BVAR              GT:DP:RO:QR:AO:QA:GL                0/1:7:4:121:2:63:-5,0,-5


Best regards

Duarte



From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: 05 February 2014 13:02
To: Ensembl developers list
Subject: Re: [ensembl-dev] VEP version 73 fasta file error

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<mailto: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<http://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<http://variant_effect_predictor.pl> line 364
        main::main(HASH(0x54c0f18)) called at /NGS_Tools/VEP-latest/variant_effect_predictor.pl<http://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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