[ensembl-dev] VEP return error

KingWai Lau KingWai.Lau at icr.ac.uk
Fri Nov 30 09:16:51 GMT 2012

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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