Could not connect to database, Too many connections

[GACGAMA]

Describe the issue

Ensembl does not start running on GRCh37

System

• VEP version: 113
• VEP Cache version: 113
• OS: CentOS
• tabix installed: Yes

Full VEP command line

singularity exec -H /scratch4/nsobrei2/references/ensembl_113_grch37 /scratch4/nsobrei2/singularities/vep_113_GRCh37.sif vep --cache --dir_cache /scratch4/nsobrei2/references/ensembl_113_grch37 -i  vcf --species homo_sapiens --assembly GRCh37  --buffer_size 5000 --failed 1 --flag_pick_allele --format vcf --input_file "\$filepathsstarR1"  --output_file $OUT_PATH/"\$filenames"_vep.vcf.gz --vcf --compress_output bgzip --force_overwrite --af_gnomade --af_gnomadg --fork $THREADS

Full error message

-------------------- EXCEPTION --------------------
MSG: Could not connect to database homo_sapiens_core_113_37 as user anonymous using [DBI:mysql:database=homo_sapiens_core_113_37;host=ensembldb.ensembl.org;port=3337] as a locator:
DBI connect('database=homo_sapiens_core_113_37;host=ensembldb.ensembl.org;port=3337','anonymous',...) failed: Too many connections at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/DBSQL/DBConnection.pm line 260.

STACK Bio::EnsEMBL::DBSQL::DBConnection::connect /opt/vep/src/ensembl-vep/Bio/EnsEMBL/DBSQL/DBConnection.pm:276
STACK Bio::EnsEMBL::DBSQL::DBConnection::db_handle /opt/vep/src/ensembl-vep/Bio/EnsEMBL/DBSQL/DBConnection.pm:673
STACK Bio::EnsEMBL::DBSQL::DBConnection::prepare /opt/vep/src/ensembl-vep/Bio/EnsEMBL/DBSQL/DBConnection.pm:701
STACK Bio::EnsEMBL::DBSQL::SliceAdaptor::prepare /opt/vep/src/ensembl-vep/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm:2567
STACK Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_all /opt/vep/src/ensembl-vep/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm:999
STACK Bio::EnsEMBL::VEP::BaseVEP::chr_lengths /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:562
STACK Bio::EnsEMBL::VEP::BaseVEP::get_slice /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:413
STACK Bio::EnsEMBL::VEP::InputBuffer::finish_annotation /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/InputBuffer.pm:488
STACK Bio::EnsEMBL::VEP::Runner::_buffer_to_output /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:411
STACK (eval) /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:671
STACK Bio::EnsEMBL::VEP::Runner::_forked_process /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:665
STACK Bio::EnsEMBL::VEP::Runner::_forked_buffer_to_output /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:496
STACK Bio::EnsEMBL::VEP::Runner::next_output_line /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:367
STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:208
STACK toplevel /opt/vep/src/ensembl-vep/vep:46
Date (localtime)    = Fri Feb  7 14:16:16 2025
Ensembl API version = 113
---------------------------------------------------
Died in forked process 3410937

Data files (if applicable)

Unnanotated GRCh19 vcf

[nakib103]

Hi @GACGAMA,

Are you still facing this issue? I was unable to re-produce the issue.

Best regards,
Nakib

[GACGAMA]

Seems like this was solved by itself. Maybe there was some instability with the ensembl servers.
But then I tried again today with other samples and I got the same error!

MSG: Could not connect to database homo_sapiens_core_113_37 as user anonymous using [DBI:mysql:database=homo_sapiens_core_113_37;host=ensembldb.ensembl.org;port=3337] as a locator:
DBI connect('database=homo_sapiens_core_113_37;host=ensembldb.ensembl.org;port=3337','anonymous',...) failed: Too many connections at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/DBSQL/DBConnection.pm line 260.

I'm in the US east coast, not sure if this makes any difference. Also, I'm using an HPC so there is also a possibility that other people are using VEP at the same time as me, as the job did run on the weekend just fine.