VEP tool

Question

[Shweta]

I am using VEP tool for variant annotation, I ran the VEP command : ./vep -i sample.vcf -o out.txt --offline but it shows the following error :

-------------------- EXCEPTION --------------------
MSG: ERROR: Cache directory /home/shweta/.vep/homo_sapiens not found

STACK Bio::EnsEMBL::VEP::CacheDir::dir /home/shweta/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:305
STACK Bio::EnsEMBL::VEP::CacheDir::init /home/shweta/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:219
STACK Bio::EnsEMBL::VEP::CacheDir::new /home/shweta/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /home/shweta/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:116
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /home/shweta/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:92
STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /home/shweta/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:170
STACK Bio::EnsEMBL::VEP::Runner::init /home/shweta/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:128
STACK Bio::EnsEMBL::VEP::Runner::run /home/shweta/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:199
STACK toplevel ./vep:46
Date (localtime)    = Sun Apr  9 00:25:17 2023
Ensembl API version = 109

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what to do to resolve this error?

Answer 1

[ATpoint]

First hit for google "vep cache not found" (as by the first line of the error" points to VEP cache issues

Please check it and come back if not working. Please google your error messages first, often this was asked before.