[ensembl-dev] VEP return error

[Will McLaren]

If you can find a line of input that reproduces the error, then I can run
it through a debug process here.

That would be great!

Thanks

Will


On 30 November 2012 10:01, KingWai Lau <KingWai.Lau at icr.ac.uk> wrote:

> Hi,****
>
> ** **
>
> Unfortunately, we are stuck with Ensemble 65. By now, I tried VEP 2.2 –
> 2.7, they return the same error. Any there anything I can do/provide so
> that you can help?****
>
> ** **
>
> Best,****
>
> King Wai****
>
> ** **
>
> *From:* dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] *On
> Behalf Of *Will McLaren
> *Sent:* 30 November 2012 09:51
> *To:* Ensembl developers list
> *Subject:* Re: [ensembl-dev] VEP return error****
>
> ** **
>
> Hello,****
>
> ** **
>
> Have you tried updating your API installation?****
>
> ** **
>
> I seem to recall at least one other user encountering this problem (though
> I can't seem to find reference to it in my email records), and I think it
> was fixed by a patch to the API.****
>
> ** **
>
> I would also recommend that you always use the latest version of the
> script - this is now 2.7. If you use 2.7 you _must_ have the appropriate
> version of the API installed - for 2.7 this is 69. You can see the
> corresponding versions here:
> http://www.ensembl.org/info/docs/variation/vep/vep_script.html#download***
> *
>
> ** **
>
> To make it easier, you can run the INSTALL.pl script supplied in the
> script download archive, which will install/update the API to the
> appropriate version for the script.****
>
> ** **
>
> Regards****
>
> ** **
>
> Will McLaren****
>
> Ensembl Variation****
>
> ** **
>
> On 30 November 2012 09:16, KingWai Lau <KingWai.Lau at icr.ac.uk> wrote:****
>
> Dear sir/Madam,****
>
>  ****
>
> We are having difficulty to use variant effect predictor. We have Ensembl
> API 65, homo_sapiens_vep_65_sift_polyphen.tar.gz, VEP v2.3. we use the
> following command, and got an error. We have tried VEP 2.4, 2.6. Do you
> have any ideas how to solve it?****
>
>  ****
>
>  ****
>
>  ****
>
> perl variant_effect_predictor.pl --host ensembldb.ensembl.org --user
> anonymous --port 5306 --db_version 65 --cache --dir /vep --sift b
> --polyphen b --ccds --hgvs --hgnc --regulatory --canonical --protein
> --check_existing --check_alleles --quiet --no_progress --force_overwrite
> --format vcf --custom FACT5728.vcf.gz,samtools,vcf,exact,0 --input_file
> FACT5728.vcf -o FACT5728.csv****
>
> 2012-11-29 17:17:20 - Retrieved 5000 custom annotations (5000 samtools)***
> *
>
>  ****
>
> -------------------- EXCEPTION --------------------****
>
> MSG: Sequence NNNNNNNNNNNNNNNNNNN contains invalid characters: Only Aa Cc
> Gg Tt accepted STACK
> Bio::EnsEMBL::Funcgen::BindingMatrix::relative_affinity
> /home/apps/ensembl/ensembl65/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/BindingMatrix.pm:296
> ****
>
> STACK
> Bio::EnsEMBL::Variation::MotifFeatureVariationAllele::motif_score_delta
> /home/apps/ensembl/ensembl65/ensembl-variation/modules/Bio/EnsEMBL/Variation/MotifFeatureVariationAllele.pm:169
> ****
>
> STACK Bio::EnsEMBL::Variation::Utils::VEP::vf_to_consequences
> /home/apps/ensembl/ensembl65/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm:927
> ****
>
> STACK Bio::EnsEMBL::Variation::Utils::VEP::get_all_consequences
> /home/apps/ensembl/ensembl65/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm:816
> ****
>
> STACK main::main
> /home/cancgene/klau/software/vep/2.3/variant_effect_predictor/
> variant_effect_predictor.pl:161****
>
> STACK toplevel
> /home/cancgene/klau/software/vep/2.3/variant_effect_predictor/
> variant_effect_predictor.pl:66****
>
> Ensembl API version = 65****
>
>  ****
>
>
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> ** **
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> Company Limited by Guarantee, Registered in England under Company No.
> 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>
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> the message is received by anyone other than the addressee, please return
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