[ensembl-dev] VEP error when using --regulatory flag

Siddharth Sethi s.sethi at har.mrc.ac.uk
Fri Apr 19 10:16:08 BST 2013


Hi ,

I am using the latest version (v71) and using the VCF format (VCFv4.1) generated from GATK.
The script breaks down when I use the -regulatory flag while it runs fine when I remove the flag.
Also, it runs fine even with -regulatory for some VCF while it gives error with others, which is strange because all the VCF have been generated from the same pipeline.
The script exits with the following error :

2013-04-18 16:28:54 - Read existing cache info
2013-04-18 16:28:54 - Starting...
2013-04-18 16:28:54 - Read 2125 variants into buffer
2013-04-18 16:28:54 - Reading transcript data from cache and/or database
[==================================================================================================================================]  [ 100% ]
2013-04-18 16:30:39 - Retrieved 50462 transcripts (0 mem, 52330 cached, 0 DB, 1868 duplicates)
2013-04-18 16:30:39 - Reading regulatory data from cache and/or database
[========>                                                                                                                         ]    [ 7% ]Can't call method "isa" on unblessed reference at EnsemblAPI_71/ensembl-tools/scripts/variant_effect_predictor/Bio/EnsEMBL/Funcgen/DBSQL/BaseFeatureAdaptor.pm line 133, <GEN0> line 2125.


This is the command :
perl EnsemblAPI_71/ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl -cache -i input.vcf -o VEP_output -species mus_musculus -format vcf --force -sift b -regulatory

I have attached a test VCF file which is producing this error.

Can you please help me in fixing this error
I will appreciate any kind of help.

Thank you

Sid
Bioinformatics
MRC Harwell
Mammalian Genetics Unit
Harwell Science and Innovation Campus Oxfordshire
OX11 0RD, UK



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