VEP Could not get current species list - using predefined list instead

Question

[Filago]

Hello,

when installing VEP cache file with INSTALL.pl, I receive the following error:

"Could not get current species list - using predefined list instead"

Any idea whats going on here / how to solve this?

Many thanks in advance!

Answer 1

[Ben Moore]

Hi Filago,

Do you have other Ensembl repositories installed on your machine? This error message will show up if other Ensembl API elements with different versions are found in your $PATH.

[Filago]

Many thanks for your answer!

How can I check, which elements are in my Path? How could I delete potential multiple VEP installations?

Many Thanks!

[Ben Moore]

I would recommend go through the troubleshooting for the Ensembl API installation: https://www.ensembl.org/info/docs/api/api_installation.html https://www.ensembl.org/info/docs/api/debug_installation_guide.html

Then going through VEP: https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html

However, you can use echo $PERL5LIB to check if ensembl-variation and other repos are correctly pointed to your PERL5LIB bash.