[ensembl-dev] VEP version 73 fasta file error

Will McLaren wm2 at ebi.ac.uk
Wed Feb 5 16:08:45 GMT 2014


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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