VEP cache issues

Question

[storm1907]

Hello,

I need some help with VEP cache files.

So, I downloaded cache file as written in this manual with https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#cache

with curl -O ftp://ftp.ensembl.org/pub/release-102/variation/vep/homo_sapiens_vep_102_GRCh38.tar.gz

I have file homo_sapiens_vep_102_GRCh38.tar.gz in my ~/.vep directory

However, when running script, I got the error

 -------------------- EXCEPTION --------------------
MSG: ERROR: Cache directory /mnt/home/baiba01/vep/homo_sapiens not found
STACK Bio::EnsEMBL::VEP::CacheDir::dir /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:311
STACK Bio::EnsEMBL::VEP::CacheDir::init /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227
STACK Bio::EnsEMBL::VEP::CacheDir::new /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91
STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:170
STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:132
STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:203
STACK toplevel /opt/vep/src/ensembl-vep/vep:228
Date (localtime)    = Thu Jan 28 13:16:06 2021
Ensembl API version = 101

How can I run that cache from ~/.vep?

Thank you!

[13554221497]

hi , just do something like this ln -sf homo_sapiens_refseq homo_sapiens

Answer 1

[Emily]

The file structure should be: .vep/homo_sapiens/102_GRCh38/..

You definitely need to unzip your cache (but don't unzip any more of the zipped files in the cache), but I can't remember if it makes the homo_sapiens folder for you or if you need to make it yourself.

[storm1907]

well, when I run

tar xzf homo_sapiens_vep_102_GRCh38.tar.gz

I got this:

gzip: stdin: unexpected end of file
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now

[Emily]

It may have gotten corrupted on download. Perhaps delete and try again.