Dear all,
I am trying to run VEP in Hail, but I keep running into this exception:
MSG: Could not open index file /path/Homo_sapiens.GRCh38.dna.primary_assembly.fa.index: No such file or directory
STACK Bio::DB::IndexedBase::_open_index /path/tools/vep/ensembl-tools-release-85/scripts/variant_effect_predictor/Bio/DB/IndexedBase.pm:666
STACK Bio::DB::IndexedBase::_index_files /path/tools/vep/ensembl-tools-release-85/scripts/variant_effect_predictor/Bio/DB/IndexedBase.pm:643
STACK Bio::DB::IndexedBase::index_file /path/tools/vep/ensembl-tools-release-85/scripts/variant_effect_predictor/Bio/DB/IndexedBase.pm:484
STACK Bio::DB::IndexedBase::new /path/tools/vep/ensembl-tools-release-85/scripts/variant_effect_predictor/Bio/DB/IndexedBase.pm:364
STACK Bio::EnsEMBL::Variation::Utils::FastaSequence::_get_fasta_db /path/tools/vep/ensembl-tools-release-85/scripts/variant_effect_predictor/Bi
o/EnsEMBL/Variation/Utils/FastaSequence.pm:314
STACK Bio::EnsEMBL::Variation::Utils::FastaSequence::setup_fasta /path/tools/vep/ensembl-tools-release-85/scripts/variant_effect_predictor/Bio/
EnsEMBL/Variation/Utils/FastaSequence.pm:196
STACK main::configure /path/tools/vep/variant_effect_predictor/variant_effect_predictor.pl:835
STACK toplevel /path/tools/vep/variant_effect_predictor/variant_effect_predictor.pl:146
I hope that this is not a naive question, but I have confirmed that the index file Homo_sapiens.GRCh38.dna.primary_assembly.fa.index
is on the correct path, I am just not sure why VEP is not able to detect that. Can I get advice as to how I can troubleshoot this? Thank you very much!