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Old 08-02-2018, 05:42 AM   #1
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Location: Italy

Join Date: Apr 2018
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Default Failed connection with Ensembl VEP script on port 3337

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(';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/ line 1769.

-------------------- EXCEPTION -------------------- MSG: Cannot connect to the Ensembl MySQL server at; 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/ STACK Bio::EnsEMBL::VEP::BaseVEP::registry /home/sara/Documenti/bin/vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/ STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /home/sara/Documenti/bin/vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/ STACK Bio::EnsEMBL::VEP::Runner::init /home/sara/Documenti/bin/vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/ STACK Bio::EnsEMBL::VEP::Runner::run /home/sara/Documenti/bin/vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/ 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.

I'm working form Ubuntu 16.04.4 LTS and the firewall is inactive.

Any suggestions on what can be the problem?
sc_123 is offline   Reply With Quote

ensembl, grch37, mysql, perl, vep

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