[ensembl-dev] VEP version 73 fasta file error
Will McLaren
wm2 at ebi.ac.uk
Wed Feb 5 16:36:45 GMT 2014
OK, good to know.
I wonder if there's some way of checking the integrity of the index...
Will
On 5 February 2014 16:28, David Blaney <David.Blaney at ogt.com> wrote:
> Hi Will,
>
>
>
> Sorted it, I solved the problem by deleting the index to the v73 FASTA
> file and therefore forcing VEP to recreate the index. This in turn resolved
> the problem.
>
>
>
> Thanks again,
>
> David
>
>
>
> *From:* dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] *On
> Behalf Of *Will McLaren
> *Sent:* 05 February 2014 16:09
>
> *To:* Ensembl developers list
> *Subject:* Re: [ensembl-dev] VEP version 73 fasta file error
>
>
>
> I can't recreate the problem; I'm using API v73, VEP 73, the 73 main cache
> (NOT RefSeq) and the same 73 FASTA file you describe.
>
>
>
> My output:
>
>
>
> > perl variant_effect_predictor.pl -i duarte.vcf -offline -force -hgvs
> -fasta /[path]/73/Homo_sapiens.GRCh37.73.dna.primary_assembly.fa
>
> > cat variant_effect_output.txt
>
> ## ENSEMBL VARIANT EFFECT PREDICTOR v73
>
> ## Output produced at 2014-02-05 16:07:25
>
> ## Connected to
>
> ## Using cache in /nfs/users/nfs_w/wm2/.vep/homo_sapiens/73
>
> ## Using API version 73, DB version ?
>
> ## Extra column keys:
>
> ## DISTANCE : Shortest distance from variant to transcript
>
> ## HGVSc : HGVS coding sequence name
>
> ## HGVSp : HGVS protein sequence name
>
> #Uploaded_variation Location Allele Gene Feature
> Feature_type Consequence cDNA_position CDS_position
> Protein_position Amino_acids Codons Existing_variation Extra
>
> 5_98216957_TT/- 5:98216957-98216958 - ENSG00000153922
> ENST00000284049 Transcript intron_variant,feature_truncation -
> - -
>
> - - -
> HGVSc=ENST00000284049.3:c.2964+25_2964+26delAA
>
> 5_98216957_TT/- 5:98216957-98216958 - ENSG00000153922
> ENST00000511628 Transcript
> non_coding_exon_variant,nc_transcript_variant,feature_truncation
> 592-593 - - - - -
> HGVSc=ENST00000511628.1:n.592_593delAA
>
> 5_98216957_TT/- 5:98216957-98216958 - ENSG00000153922
> ENST00000505982 Transcript downstream_gene_variant - - -
> - -
>
> - DISTANCE=1880
>
>
>
> I get no warning messages, only the usual output.
>
>
>
> Are you using any other options besides those described in your config
> file?
>
>
>
> Are you using the RefSeq cache, or the default human one?
>
>
>
> Will
>
> On 5 February 2014 14:34, Duarte Molha <Duarte.Molha at ogt.com> wrote:
>
> 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> 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
>
>
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