[ensembl-dev] Warning message in from VariationFeature.pm

[Duarte Molha]

Hi Devs

 I have been trying to run a VCF file by the variant annotation script and
I've been getting a warning message that I have never before encountered..

 I was wondering if someone could let me know if it is something I am doing
wrong…

 The message is :

 *Can't call method "expand" on an undefined value at
<sic>/Bio/EnsEMBL/Variation/VariationFeature.pm line 471*

**

* *

Here are the configuration options I am using:



Configuration options:

 ###

allow_non_variant    1

cache                1

canonical            1

ccds                 1

check_alleles        1

check_existing       1

config               vep_human.ini

core_type            core

custom
./vep_additional_annotations/Somatic_variation_phenotypes.bed.gz,Somatic,bed,exact
./vep_additional_annotations/dbsnp135_ensembl_variation_phenotype.bed.gz,dbsnp135,bed,exact

db_version           72

dir                  /ReferenceData/vep_cache

dir_cache            /ReferenceData/vep_cache

dir_plugins          ./Plugins

domains              1

force_overwrite      1

fork                 5

gmaf                 1

hgnc                 1

host                 ensembldb.ensembl.org

individual           all

input_file           All_BOTH_SNPINDELfilter_PASSED.vcf

maf_1kg              1

numbers              1

output_file          All_BOTH_SNPINDELfilter_PASSED.ann

plugin
OGT_NHBLI_MAF,/ReferenceData/NHLBI_EVS/NHLBI_OGT.gz
OGT_selected_VCF_fields_output  Blosum62        Carol   OGT_Condel,b
OGT_Grantham    TSSDistance     Downstream

polyphen             b

port                 5306

protein              1

regulatory           1

sift                 b

species              homo_sapiens

stats                HASH(0x4370ad8)

terms                SO

verbose              1



I would be very grateful for your help.

 Duarte Molha
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