I'm using the VEP (Variant Effect Predictor) standalone Perl script to annotate some variants, it connects to the Ensembl MySql database. I used the same script before and I didn't have any problems. But now I'm getting this error:
DBI connect('host=ensembldb.ensembl.org;port=3337','anonymous',...) failed: Lost connection to MySQL server at 'reading authorization packet', system error: 110 at /home/sara/Documenti/bin/vep/ensembl-vep/Bio/EnsEMBL/Registry.pm line 1769. -------------------- EXCEPTION -------------------- MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3337; check your settings & DBI error message: Lost connection to MySQL server at 'reading authorization packet', system error: 110 STACK Bio::EnsEMBL::Registry::load_registry_from_db /home/sara/Documenti/bin/vep/ensembl-vep/Bio/EnsEMBL/Registry.pm:1769 STACK Bio::EnsEMBL::VEP::BaseVEP::registry /home/sara/Documenti/bin/vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:252 STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /home/sara/Documenti/bin/vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:120 STACK Bio::EnsEMBL::VEP::Runner::init /home/sara/Documenti/bin/vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:118 STACK Bio::EnsEMBL::VEP::Runner::run /home/sara/Documenti/bin/vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194 STACK toplevel /home/sara/Documenti/bin/vep/ensembl-vep/vep:224 Date (localtime) = Thu Aug 2 11:30:01 2018
Using port 3306 instead of port 3337 everything works fine. But I need to use port 3337 in order to use human GRCh37 reference genome, while port 3306 is for GRCh38.
The same thing happens if I try to use this mysql command:
mysql --host=ensembldb.ensembl.org --port=3337 --user=anonymous
I'm working form Ubuntu 16.04.4 LTS and the firewall is inactive. There is a firewall in the middle, but the network administrator told me that port 3337 is open.
Any suggestions on what can be the problem?