<div dir="ltr"><div dir="ltr"><div>Hello,</div><div><br></div><div>I'm having trouble with the public database when using the <span style="font-family:monospace,monospace">GRCh37</span> assembly. This is what I run:</div><div><br></div><div style="margin-left:40px"><span style="font-family:monospace,monospace">> ./vep --cache --refseq --assembly GRCh37 --fasta ~/.vep/homo_sapiens/94_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz --input_file 1.tsv --port 3337<br><br>-------------------- WARNING ----------------------<br>MSG: homo_sapiens is not a valid species name (check DB and API version)<br>FILE: Bio/EnsEMBL/Registry.pm LINE: 1334<br>CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 1109<br>Date (localtime)    = Mon Oct 29 03:49:22 2018<br>Ensembl API version = 94<br>---------------------------------------------------<br><br>-------------------- EXCEPTION --------------------<br>MSG: Can not find internal name for species 'homo_sapiens'<br>STACK Bio::EnsEMBL::Registry::get_adaptor /usr/local/src/ensembl-vep/Bio/EnsEMBL/Registry.pm:1111<br>STACK Bio::EnsEMBL::VEP::BaseVEP::get_adaptor /usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:307<br>STACK Bio::EnsEMBL::VEP::BaseVEP::get_database_assembly /usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:419<br>STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:123<br>STACK Bio::EnsEMBL::VEP::Runner::init /usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:118<br>STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194<br>STACK toplevel ./vep:224<br>Date (localtime)    = Mon Oct 29 03:49:22 2018<br>Ensembl API version = 94<br>---------------------------------------------------</span></div><div><br></div><div>It works with <span style="font-family:monospace,monospace">--online</span> but I would like to use the <a href="https://uswest.ensembl.org/info/docs/tools/vep/vep_formats.html#id"><i>Variant identifiers</i></a> input format and that does not work with <span style="font-family:monospace,monospace">--offline</span>.</div><div><br></div><div>Any ideas what I'm doing wrong?</div><div><br></div><div>Thanks!</div><div>Rares<br></div></div></div>