SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
dexseq_prepare script error with Ensembl human gtf aleadam Bioinformatics 7 08-16-2017 04:06 AM
Recommendation for which short read aligner to port to FPGA rhplane Bioinformatics 2 02-24-2014 01:30 PM
TopHat2 failed to read known junctions from GTF file (from ensembl or UCSC) Alex234 RNA Sequencing 4 08-05-2013 08:31 AM

Reply
 
Thread Tools
Old 08-02-2018, 05:42 AM   #1
sc_123
Junior Member
 
Location: Italy

Join Date: Apr 2018
Posts: 2
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('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.

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
Reply

Tags
ensembl, grch37, mysql, perl, vep

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:49 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO