[ensembl-dev] VEP version 73 fasta file error
David Blaney
David.Blaney at ogt.com
Wed Feb 5 16:28:59 GMT 2014
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<http://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<mailto: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> [mailto: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
_______________________________________________
Dev mailing list Dev at ensembl.org<mailto:Dev at ensembl.org>
Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
Ensembl Blog: http://www.ensembl.info/
_______________________________________________
Dev mailing list Dev at ensembl.org<mailto: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/d252e022/attachment.html>
More information about the Dev
mailing list