[ensembl-dev] Ensembl API not responding?

Simon Andrews simon.andrews at babraham.ac.uk
Wed Nov 27 13:16:22 GMT 2024


I'm trying to run some scripts against the Ensembl perl API.  I used to run these on a old server and I've now moved to a new one so I'm setting things up again.

I've got all of the necessary Perl modules installed, but I can't get the registry to load.  Even a basic:

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
      -host => 'ensembldb.ensembl.org',
      -user => 'anonymous',
      -verbose => 1
);

hangs, seemingly indefinitely.  I checked and I can make a manual mysql connection to ensembldb.ensembl.org, but just doing a "show databases" took well over a minute to return:

$ mysql -u anonymous -h ensembldb.ensembl.org
Welcome to the MariaDB monitor.  Commands end with ; or \g.
Your MySQL connection id is 228387134
Server version: 5.6.33 MySQL Community Server (GPL)

Copyright (c) 2000, 2018, Oracle, MariaDB Corporation Ab and others.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

MySQL [(none)]> show databases;
...results appear...
23330 rows in set (1 min 17.741 sec)

I'm guessing this is why the registry isn't loading.  Am I using the correct db still?  Is anyone able to check why the performance is so slow or whether something is broken please.

Thanks

Simon.
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