[ensembl-dev] VEP return error

Fri Nov 30 10:11:03 GMT 2012

I don't know how to capture the line. Are there any way I can capture the error and work my way back, please advice.

King Wai

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: 30 November 2012 10:05
To: Ensembl developers list
Subject: Re: [ensembl-dev] VEP return error

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<mailto: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> [mailto: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<mailto: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<http://variant_effect_predictor.pl> --host ensembldb.ensembl.org<http://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<http://variant_effect_predictor.pl:161>

STACK toplevel /home/cancgene/klau/software/vep/2.3/variant_effect_predictor/variant_effect_predictor.pl:66<http://variant_effect_predictor.pl:66>

Ensembl API version = 65

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