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?
Thank you for your answer. Yes, I am able to connect to UCSC's MySQL server. This is the output of mysql status:
So do you suggest it is an issue on Ensembl end? But I emailed them and they said they cannot see a reason on their side why I would be able to establish a connection, but then loose it. So I really don't understand what can be the problem...
I am going to assume that your firewall is not filtering outbound connections so it is possible that port 3337 is indeed blocked by your firewall. Try this to see if the port can be reached from your machine.
Indeed, if I do as you suggest, it seems that port 3337 can't be reached from my machine.
This is the output of "nc -zv 127.0.0.1":
But if my ubuntu firewall is inactive and the network administrator said that the firewall in the middle is not blocking port 3337, I don't understand what else can be blocking the port, is there something I'm missing? I'm sorry but I'm quite newby.
I suggest contacting your network admin and telling them (respectfully) about this result. Also tell them that you are able to connect with UCSC DB without any issues. So what could the problem be with Ensembl.
I assume
nc
with other Ensembl port (3306) works?Thank you very much for your help, I will do as you suggest.
Yes, nc with the other port works perfectly: