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The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
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Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3306 #603

Closed PlatonB closed 5 years ago

PlatonB commented 5 years ago

Elementary OS 5.0 VEP script 97 MySQL 5.7.27

Trying to annotate a simple test data set: sudo docker run -t -i -v $HOME/vep_data:/opt/vep/.vep ensemblorg/ensembl-vep

./vep --cache --merged --vcf --force_overwrite -e --dir_cache /opt/vep/.vep/ -i /opt/vep/.vep/input/VEP_input.txt -o /opt/vep/.vep/output/VEP_output.vcf

DBI connect('host=ensembldb.ensembl.org;port=3306','anonymous',...) failed: Can't connect to MySQL server on 'ensembldb.ensembl.org' (111) at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Registry.pm line 1770.

-------------------- EXCEPTION --------------------
MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3306; check your settings & DBI error message: Can't connect to MySQL server on 'ensembldb.ensembl.org' (111)
STACK Bio::EnsEMBL::Registry::load_registry_from_db /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Registry.pm:1770
STACK Bio::EnsEMBL::VEP::BaseVEP::registry /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:252
STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:120
STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:118
STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194
STACK toplevel ./vep:223
Date (localtime)    = Wed Sep 18 17:05:26 2019
Ensembl API version = 97
---------------------------------------------------

exit

Some actions from the corresponding debugging guide: mysql --host=ensembldb.ensembl.org --port=3306 --user=anonymous ERROR 2003 (HY000): Can't connect to MySQL server on 'ensembldb.ensembl.org' (111)

ping -c 5 ensembldb.ensembl.org

PING ensembldb.ebi.ac.uk (193.62.193.10) 56(84) bytes of data.
64 bytes from ensembldb.ebi.ac.uk (193.62.193.10): icmp_seq=1 ttl=239 time=136 ms
64 bytes from ensembldb.ebi.ac.uk (193.62.193.10): icmp_seq=2 ttl=239 time=143 ms
64 bytes from ensembldb.ebi.ac.uk (193.62.193.10): icmp_seq=3 ttl=239 time=113 ms
64 bytes from ensembldb.ebi.ac.uk (193.62.193.10): icmp_seq=4 ttl=239 time=140 ms
64 bytes from ensembldb.ebi.ac.uk (193.62.193.10): icmp_seq=5 ttl=239 time=120 ms

--- ensembldb.ebi.ac.uk ping statistics ---
5 packets transmitted, 5 received, 0% packet loss, time 4005ms
rtt min/avg/max/mdev = 113.167/131.004/143.928/11.970 ms
aparton commented 5 years ago

Hi,

Thank you for this report, we’ve had some issues with our public human variation database since Wednesday and we are currently investigating. I’ll let you know when we have a fix in place.

In the meantime, you can still run VEP in offline mode - https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#offline https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#offline

Kind Regards, Andrew

On 18 Sep 2019, at 18:49, PlatonB notifications@github.com wrote:

Elementary OS 5.0 VEP script 97 MySQL 5.7.27

Trying to annotate a simple test data set: sudo docker run -t -i -v $HOME/vep_data:/opt/vep/.vep ensemblorg/ensembl-vep

./vep --cache --merged --vcf --force_overwrite -e --dir_cache /opt/vep/.vep/ -i /opt/vep/.vep/input/VEP_input.txt -o /opt/vep/.vep/output/VEP_output.vcf

DBI connect('host=ensembldb.ensembl.org;port=3306','anonymous',...) failed: Can't connect to MySQL server on 'ensembldb.ensembl.org' (111) at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Registry.pm line 1770.

-------------------- EXCEPTION -------------------- MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3306; check your settings & DBI error message: Can't connect to MySQL server on 'ensembldb.ensembl.org' (111) STACK Bio::EnsEMBL::Registry::load_registry_from_db /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Registry.pm:1770 STACK Bio::EnsEMBL::VEP::BaseVEP::registry /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:252 STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:120 STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:118 STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194 STACK toplevel ./vep:223 Date (localtime) = Wed Sep 18 17:05:26 2019 Ensembl API version = 97

exit

Some actions from the corresponding debugging guide: mysql --host=ensembldb.ensembl.org --port=3306 --user=anonymous ERROR 2003 (HY000): Can't connect to MySQL server on 'ensembldb.ensembl.org' (111)

ping -c 5 ensembldb.ensembl.org

PING ensembldb.ebi.ac.uk (193.62.193.10) 56(84) bytes of data. 64 bytes from ensembldb.ebi.ac.uk (193.62.193.10): icmp_seq=1 ttl=239 time=136 ms 64 bytes from ensembldb.ebi.ac.uk (193.62.193.10): icmp_seq=2 ttl=239 time=143 ms 64 bytes from ensembldb.ebi.ac.uk (193.62.193.10): icmp_seq=3 ttl=239 time=113 ms 64 bytes from ensembldb.ebi.ac.uk (193.62.193.10): icmp_seq=4 ttl=239 time=140 ms 64 bytes from ensembldb.ebi.ac.uk (193.62.193.10): icmp_seq=5 ttl=239 time=120 ms

--- ensembldb.ebi.ac.uk ping statistics --- 5 packets transmitted, 5 received, 0% packet loss, time 4005ms rtt min/avg/max/mdev = 113.167/131.004/143.928/11.970 ms — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Ensembl/ensembl-vep/issues/603?email_source=notifications&email_token=AH56GN7KXTVA36K5UKI7WVLQKJS35A5CNFSM4IYB3E2KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HMGXATQ, or mute the thread https://github.com/notifications/unsubscribe-auth/AH56GN2SUEFTWXH5XYCJFJ3QKJS35ANCNFSM4IYB3E2A.

PlatonB commented 5 years ago

In version 98, this error no longer occurs. Issue #616 is actual now.

PlatonB commented 5 years ago

Bug is reproducing again.

aparton commented 5 years ago

Hi,

I've had a quick look and I can successfully connect to both 97 and 98 databases on ensembldb.ensembl.org - could you please send me the VEP version you're using and your VEP command?

Kind Regards, Andrew

PlatonB commented 5 years ago

98.

sudo docker run -t -i -v $HOME/vep_data:/opt/vep/.vep:Z ensemblorg/ensembl-vep

./vep --cache --merged --vcf --force_overwrite -e --dir_cache /home/platon/vep_data/ -i /home/platon/vep_data/input/test_input.txt -o /home/platon/vep_data/output/test_output.vcf

aparton commented 5 years ago

Hi,

Thanks for the report, unfortunately I've been unable to reproduce the error however.

Could you please confirm that you're still seeing the 'Cannot connect to the Ensembl MySQL server at ...' error message? You may have been unfortunate enough to query the public database during a blip that has since been fixed.

Kind Regards, Andrew

PlatonB commented 5 years ago

There's no such problem today.

aparton commented 5 years ago

Hi,

I'm going to close this issue now, if this issue crops up again please feel free to reopen it and we can investigate further.

Kind Regards, Andrew

matmu commented 4 years ago

I issue came up again today:

 DBD::mysql::st execute failed: Lost connection to MySQL server during query at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line 481.

-------------------- EXCEPTION --------------------
MSG: Detected an error whilst executing SQL 'SELECT  v.variation_id, v.name AS v_name, v.class_attrib_id AS v_class_attrib_id, v.source_id AS v_source_id, v.somatic AS v_somatic, v.flipped AS v_flipped, vs.name AS vs_name, s2.name AS vs_source_name, v.minor_allele, v.minor_allele_freq, v.minor_allele_count, v.clinical_significance, v.evidence_attribs 
FROM (( (variation v, source s1) 
  LEFT JOIN variation_synonym vs ON v.variation_id = vs.variation_id ) 
  LEFT JOIN source s2 ON vs.source_id = s2.source_id ) 
 WHERE v.name = ?  AND

        s1.source_id = v.source_id

': DBD::mysql::st execute failed: Lost connection to MySQL server during query at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line 481.

STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch /opt/vep/src/ensembl-vep/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:482
STACK Bio::EnsEMBL::Variation::DBSQL::VariationAdaptor::fetch_by_name /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/DBSQL/VariationAdaptor.pm:554
STACK Bio::EnsEMBL::VEP::Parser::ID::create_VariationFeatures /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser/ID.pm:162
STACK Bio::EnsEMBL::VEP::Parser::next /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm:175
STACK Bio::EnsEMBL::VEP::InputBuffer::next /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/InputBuffer.pm:210
STACK Bio::EnsEMBL::VEP::Runner::_buffer_to_output /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:396
STACK Bio::EnsEMBL::VEP::Runner::next_output_line /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:364
STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:202
STACK toplevel /opt/vep/src/ensembl-vep/vep:224
Date (localtime)    = Wed Apr 15 12:20:20 2020
Ensembl API version = 99
---------------------------------------------------
The command '/bin/sh -c perl INSTALL.pl         --AUTO fcp         --ASSEMBLY GRCh38         --PLUGINSDIR /opt/vep/.vep/Plugins/         --CACHEDIR /opt/vep/.vep/         --PLUGINS all         --SPECIES homo_sapiens_merged &&     vep -id rs699       --cache       --nearest symbol       -o 'STDOUT'       --merged       --no_stats       > /dev/null' returned a non-zero code: 2
aparton commented 4 years ago

Hi @matmu,

Thanks for this report. This error message is normally seen when our database servers are under increased load, and we are currently running in a reduced functionality mode as described here: http://www.ensembl.info/2020/02/18/reduced-functionality-16th-25th-march-2020/

If you try again at another time when our database server is less busy then it should resolve your problem. If not, please let me know and I'll investigate further.

Kind Regards, Andrew

vasicek58 commented 3 years ago

Hi! I'm getting a similar issue when running Haplosaurus in a local conda environment created by Snakemake. It is also caused by the server being too busy?

Possible precedence issue with control flow operator at .snakemake/conda/bcad596f5f1c6c97eee4dfe3aaf9194a/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
DBI connect('host=ensembldb.ensembl.org;port=3306','anonymous',...) failed: Can't connect to MySQL server on 'ensembldb.ensembl.org' (110) at .snakemake/conda/bcad596f5f1c6c97eee4dfe3aaf9194a/share/ensembl-vep-104.3-1/Bio/EnsEMBL/Registry.pm line 1771.
-------------------- EXCEPTION --------------------
MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3306; check your settings & DBI error message: Can't connect to MySQL server on 'ensembldb.ensembl.org' (110)
STACK Bio::EnsEMBL::Registry::load_registry_from_db .snakemake/conda/bcad596f5f1c6c97eee4dfe3aaf9194a/share/ensembl-vep-104.3-1/Bio/EnsEMBL/Registry.pm:1771
STACK Bio::EnsEMBL::VEP::BaseVEP::registry /.snakemake/conda/bcad596f5f1c6c97eee4dfe3aaf9194a/share/ensembl-vep-104.3-1/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:252
STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection .snakemake/conda/bcad596f5f1c6c97eee4dfe3aaf9194a/share/ensembl-vep-104.3-1/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:120
STACK Bio::EnsEMBL::VEP::Haplo::Runner::init .snakemake/conda/bcad596f5f1c6c97eee4dfe3aaf9194a/share/ensembl-vep-104.3-1/modules/Bio/EnsEMBL/VEP/Haplo/Runner.pm:140
STACK Bio::EnsEMBL::VEP::Haplo::Runner::run .snakemake/conda/bcad596f5f1c6c97eee4dfe3aaf9194a/share/ensembl-vep-104.3-1/modules/Bio/EnsEMBL/VEP/Haplo/Runner.pm:196
STACK toplevel .snakemake/conda/bcad596f5f1c6c97eee4dfe3aaf9194a/bin/haplo:100
Date (localtime)    = Tue Oct 26 11:50:52 2021
Ensembl API version = 104
---------------------------------------------------
dglemos commented 3 years ago

Could you try running the query again?

vasicek58 commented 3 years ago

Apologies for the long silence, it turned out to be an issue on our side. Thanks for your reply!

daniel-hui commented 2 years ago

Sorry to necro this thread but I am having this issue now. The exact command I used 6 months ago, which was working then, is giving this error now. I tried it last Friday and today, so perhaps it is not just due to Ensembl's database servers being under load this whole time. Here is the command with paths changed:

for i in {1..22}; do bsub -o vep_all_chromosomes/base_rv_pick_allele_reg_tab_chr"$i".o -e vep_all_chromosomes/base_rv_pick_allele_reg_tab_chr"$i".e "export PERL5LIB=$PERL5LIB:$HOME/cpanm/lib/perl5 ; time ~/tools/ensembl-vep/vep --cache --pick_allele -i descriptives/A6K/chr"$i"_notSVM_A6K.vcf.gz --fork 4 --compress_output gzip --tab --symbol --regulatory --biotype --af --af_1kg --af_gnomad --variant_class --custom gerp_conservation_scores.homo_sapiens.GRCh38.bw,GERP,bigwig --plugin SpliceAI,snv=spliceai_scores.raw.snv.hg38.vcf.gz,indel=spliceai_scores.raw.indel.hg38.vcf.gz --plugin REVEL,new_tabbed_revel_grch38.tsv.gz --plugin Mastermind,mastermind_cited_variants_reference-2021.08.03-grch38.vcf.gz --custom clinvar.vcf.gz,ClinVar,vcf,exact,0,CLNSIG,CLNREVSTAT,CLNDN -o vep_all_chromosomes/base_rv_pick_allele_reg_tab_chr"$i""; done

Error:

DBI connect('host=ensembldb.ensembl.org;port=3306','anonymous',...) failed: Can't connect to MySQL server on 'ensembldb.ensembl.org' (110) at /home/dahui/tools/ensembl-vep/Bio/EnsEMBL/Registry.pm line 1771.

-------------------- EXCEPTION --------------------
MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3306; check your settings & DBI error message: Can't connect to MySQL server on 'ensembldb.ensembl.org' (110)
STACK Bio::EnsEMBL::Registry::load_registry_from_db /home/dahui/tools/ensembl-vep/Bio/EnsEMBL/Registry.pm:1771
STACK Bio::EnsEMBL::VEP::BaseVEP::registry /home/dahui/tools/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:252
STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /home/dahui/tools/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:120
STACK Bio::EnsEMBL::VEP::Runner::init /home/dahui/tools/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:123
STACK Bio::EnsEMBL::VEP::Runner::run /home/dahui/tools/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:199
STACK toplevel /home/dahui/tools/ensembl-vep/vep:232
Date (localtime)    = Mon Jun  6 12:27:09 2022
Ensembl API version = 104
---------------------------------------------------

Thanks.

nuno-agostinho commented 2 years ago

Hey @daniel-hui, good morning! Are you still having these issues?

cksruthi commented 2 years ago

Hi. I am getting a similar error while running VEP.

DBI connect('host=ensembldb.ensembl.org;port=3306','anonymous',...) failed: Can't connect to MySQL server on 'ensembldb.ensembl.org:3306' (110) at /home/sruthi/Softwares/ensembl-vep-release-105/Bio/EnsEMBL/Registry.pm line 1771.

-------------------- EXCEPTION -------------------- MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3306; check your settings & DBI error message: Can't connect to MySQL server on 'ensembldb.ensembl.org:3306' (110) STACK Bio::EnsEMBL::Registry::load_registry_from_db /home/sruthi/Softwares/ensembl-vep-release-105/Bio/EnsEMBL/Registry.pm:1771 STACK Bio::EnsEMBL::VEP::BaseVEP::registry /home/sruthi/Softwares/ensembl-vep-release-105/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:252 STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /home/sruthi/Softwares/ensembl-vep-release-105/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:120 STACK Bio::EnsEMBL::VEP::Runner::init /home/sruthi/Softwares/ensembl-vep-release-105/modules/Bio/EnsEMBL/VEP/Runner.pm:123 STACK Bio::EnsEMBL::VEP::Runner::run /home/sruthi/Softwares/ensembl-vep-release-105/modules/Bio/EnsEMBL/VEP/Runner.pm:199 STACK toplevel /home/sruthi/Softwares/ensembl-vep-release-105/vep:232 Date (localtime) = Thu Jul 28 09:40:05 2022 Ensembl API version = 105

The command used was:

vep --cache --merged --dir_cache ~/Softwares/vepcache/ --fork 4 --input_file inputfile --output_file outputfile --everything --exclude_predicted --total_length --show_ref_allele --check_existing --exclude_null_alleles --clin_sig_allele 1 --flag_pick --force_overwrite --no_stats --vcf --buffer_size 2000

I have tried running this multiple times since yesterday and have been getting the same error.

nuno-agostinho commented 2 years ago

Hey @cksruthi!

Due to maintenance work, the Ensembl services were temporarily unavailable for some time during Tuesday and Wednesday: https://www.ensembl.info/2022/07/20/disruption-to-ensembl-services-4/

Unfortunately, the Ensembl database is still down and we are working to fix it as soon as possible. I am sorry for the inconvenience.

Kind regards, Nuno

cksruthi commented 2 years ago

@nuno-agostinho Thank you very much for the quick response.

dhruti89 commented 2 years ago

@nuno-agostinho Is the Ensembl database still down? I am still getting this error.

nuno-agostinho commented 2 years ago

Hey @dhruti89!

Unfortunately, the Ensembl database is still down and we are investigating this issue.

In the meanwhile, please try setting VEP's --host argument to the Ensembl database mirrors from USA (useastdb.ensembl.org) or Asia (asiadb.ensembl.org): http://www.ensembl.org/info/data/mysql.html

We are trying to get the Ensembl database back online soon. Sorry for the inconvenience.

Best regards, Nuno

dhruti89 commented 2 years ago

Thanks @nuno-agostinho for the quick revert and the workaround

fridells51 commented 2 years ago

@nuno-agostinho Are the database connectivity issues still persisting? Same VEP command was working yesterday, and today it's not. I've tried every available configuration of hosts and ports in the page you linked 2 days ago.

nuno-agostinho commented 2 years ago

Hey @fridells51,

I'm sorry to hear that. All Ensembl servers should be working now. You can test the connection to our database with the following MySQL command:

mysql -h ensembldb.ensembl.org -u anonymous

What is the VEP output that you are getting?

Thanks, Nuno

fridells51 commented 2 years ago

Hi Nuno,

Thanks for the reply. I solved the issue. Yesterday, I was on a file transfer node that can handle running commands from the command line. Today, I was trying to submit the job to the slurm controller using SBATCH and trying to run the job interactively on a compute node. Unfortunately, I don't have the HPC experience or expertise to diagnose why the database connection could not be resolved on these nodes, but I'll take it up with the HPC support. Thanks for your attention.

nuno-agostinho commented 2 years ago

Hi @fridells51,

In your case, I would suggest to check if you have all the dependencies you need to run VEP installed when running the job in HPC.

If your HPC supports running Singularity/Docker containers, you can also use the official VEP image that comes with all the dependencies already set up.

Feel free to reach me if you need help from our side!

Best regards, Nuno

daniel-hui commented 2 years ago

Hi @nuno-agostinho,

I tried again today and am still having the same issue. I tried mysql -h ensembldb.ensembl.org -u anonymous and it gives the error ERROR 2003 (HY000): Can't connect to MySQL server on 'ensembldb.ensembl.org' (110), I tried setting -h to useastdb.ensembl.org and asiadb.ensembl.org and it still gave the error. Would you know some other steps to try next? Thanks.

nakib103 commented 2 years ago

Hello @daniel-hui,

Thanks for your query!

I can see the database is up - 

% mysql -h ensembldb.ensembl.org -u anonymous --silent 
mysql>

Were you able to connect to the database before or is it your first time connecting? It might be worthwhile to check if your network is blocking this connection.

Best regards, Nakib

Duong-NguyenTrinhTrung commented 1 year ago

Hi @nuno-agostinho

I am sorry for bringing this back again. I have experience this problem yesterday and it is still today.

"DBI connect('host=ensembldb.ensembl.org;port=3306','anonymous',...) failed: Lost connection to MySQL server at 'reading initial communication packet', system error: 104 at /home/username/veptool/share/ensembl-vep-106.1-0/Bio/EnsEMBL/Registry.pm line 1771." Could I bother you to check it? Thanks in advance!

nuno-agostinho commented 1 year ago

Hi @Duong-NguyenTrinhTrung,

Can you try again today? Could you also try connecting to one of the mirrors in http://www.ensembl.org/info/data/mysql.html (useastdb.ensembl.org or asiadb.ensembl.org) using the argument --host in VEP?

Thank you!

All the best, Nuno

Duong-NguyenTrinhTrung commented 1 year ago

Hi @nuno-agostinho

Thanks for the reply. I have tried 2 alternative mirrors which different ports but still could not connect. The error message is:

DBI connect('host=asiadb.ensembl.org;port=5306','anonymous',...) failed: Lost connection to MySQL server at 'reading authorization packet', system error: 104 at /home/ljw303/veptool/share/ensembl-vep-106.1-0/Bio/EnsEMBL/Registry.pm line 1771.

To be clear, could you take a look to see if my VEP command is not appropriate?

vep -i VEP.input --host asiadb.ensembl.org --port 5306 -o VEP.output --cache --dir_cache path_to_cache --dir_plugins. /path_to_plugins/ --plugin dbNSFP,/path_to_plugins/dbNSFP4.2a.gz,SIFT_score,SIFT4G_score,Polyphen2_HDIV_score,Polyphen2_HVAR_score,LRT_score,LRT_pred,LRT_Omega. --force_overwrite

nuno-agostinho commented 1 year ago

Hey @Duong-NguyenTrinhTrung, your command seems fine.

What happens if you run the following commands?

mysql -h ensembldb.ensembl.org -u anonymous --silent
mysql -h useastdb.ensembl.org -u anonymous --silent
mysql -h asiadb.ensembl.org -u anonymous --silent

Best, Nuno

Duong-NguyenTrinhTrung commented 1 year ago

Hi @nuno-agostinho,

When I run the commands you suggested:

mysql -h ensembldb.ensembl.org -u anonymous --silent mysql -h useastdb.ensembl.org -u anonymous --silent mysql -h asiadb.ensembl.org -u anonymous --silent

I got an error message saying: "-bash: mysql: command not found". It is weird and I have no idea about this error. I supposed that I have mysql installed as I have run VEP for many times last month.

Furthermore, I install VEP via conda and this is my conda package (command: conda list): VEP_conda_packages.txt

Could you help me to take a look? Many thanks!

nuno-agostinho commented 1 year ago

Hi @Duong-NguyenTrinhTrung,

It's indeed weird that you were able to use the databases before and now they are not working.

VEP via conda is not an official distribution and we cannot offer support for it. I would recommend instead using our official VEP image for Docker or Singularity.

Please tell me if you have any further issues with this approach.

Thanks, Nuno

Duong-NguyenTrinhTrung commented 1 year ago

Hi @nuno-agostinho,

Thanks for your reply. The conda approach worked well for me over the last month. Are you sure that there is no problem with the database on your side? I am using a node in HPC and conda is the best way for me to install VEP.

Duong-NguyenTrinhTrung commented 1 year ago

Hi @nuno-agostinho,

I have installed mysql-client and test the connection to all the databases but none was successful (image attached)

mysql -h ensembldb.ensembl.org -u anonymous --silent mysql -h useastdb.ensembl.org -u anonymous --silent mysql -h asiadb.ensembl.org -u anonymous --silent

image

Could you take a look at it? Thanks!

nuno-agostinho commented 1 year ago

Hey @Duong-NguyenTrinhTrung,

We haven't had reports from other users having these specific issues and all seems fine in our end. This leads me to believe that there are issues with firewall permissions or other problems on the network that you are trying to connect from.

Have you tried to connect to these databases outside of your institute/company network (or turning off your VPN if that's your case)?

I would suggest to contact your IT team to discuss these issues. Please do tell me if these issues persist.

Best, Nuno

sruthisrini commented 1 year ago

Hello,

I got this error today

DBD::mysql::st execute failed: Table 'seq_region' is marked as crashed and should be repaired at /Users/sruthisrinivasan/perl5/ensembl-vep/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm line 261. DBD::mysql::st execute failed: Table 'seq_region' is marked as crashed and should be repaired at /Users/sruthisrinivasan/perl5/ensembl-vep/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm line 261.

So far, I was not getting errors like these and the output files were generating. Is this because of the server problem?

nakib103 commented 1 year ago

Hello @sruthisrini

Thanks for reporting it to us, we are already looking into it. We will let you once we have a update.

Best regards, Nakib

nakib103 commented 1 year ago

@sruthisrini

The issue has been fixed. Can you check again?

sruthisrini commented 1 year ago

@nakib103 It is working now. Thanks for fixing soon!

sruthisrini commented 1 year ago

Hello,

I got this error today and this is the first time I am getting this error while running the below code: /vep -i input.vcf -o output.vcf --cache --force_overwrite --tab --no_check_variants_order --force --plugin GeneSplicer,/genesplicer,/GeneSplicer/human --plugin SpliceAI,snv=spliceai_scores.raw.snv.hg38.vcf.gz,indel=spliceai_scores.raw.indel.hg38.vcf.gz,cutoff=0.5 --sift b --polyphen p

install_driver(mysql) failed: Can't load '/Users/sruthisrinivasan/perl5/perlbrew/perls/5.26.2/lib/site_perl/5.26.2/darwin-thread-multi-2level/auto/DBD/mysql/mysql.bundle' for module DBD::mysql: dlopen(/Users/sruthisrinivasan/perl5/perlbrew/perls/5.26.2/lib/site_perl/5.26.2/darwin-thread-multi-2level/auto/DBD/mysql/mysql.bundle, 0x0001): Library not loaded: '/usr/local/opt/mysql/lib/libmysqlclient.21.dylib'
  Referenced from: '/Users/sruthisrinivasan/perl5/perlbrew/perls/5.26.2/lib/site_perl/5.26.2/darwin-thread-multi-2level/auto/DBD/mysql/mysql.bundle'
  Reason: tried: '/usr/local/opt/mysql/lib/libmysqlclient.21.dylib' (no such file), '/usr/local/lib/libmysqlclient.21.dylib' (no such file), '/usr/lib/libmysqlclient.21.dylib' (no such file), '/usr/local/Cellar/mysql/8.1.0/lib/libmysqlclient.21.dylib' (no such file), '/usr/local/lib/libmysqlclient.21.dylib' (no such file), '/usr/lib/libmysqlclient.21.dylib' (no such file) at /Users/sruthisrinivasan/perl5/perlbrew/perls/5.26.2/lib/5.26.2/darwin-thread-multi-2level/DynaLoader.pm line 197.
 at (eval 34) line 3.
Compilation failed in require at (eval 34) line 3.
Perhaps a required shared library or dll isn't installed where expected
 at /Users/sruthisrinivasan/perl5/ensembl-vep/Bio/EnsEMBL/Registry.pm line 1771.

I did all the below installations:

#XCode and GCC
gcc -v

#Perlbrew
curl -L http://install.perlbrew.pl | bash
echo 'source $HOME/perl5/perlbrew/etc/bashrc' >> ~/.bash_profile
source ~/perl5/perlbrew/etc/bashrc
cd '/Users/sruthisrinivasan/perl5' 
perlbrew install -j 5 --as 5.26.2 --thread --64all -Duseshrplib perl-5.26.2 --notest
perlbrew switch 5.26.2
perlbrew install-cpanm

#Homebrew
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
(echo; echo 'eval "$(/usr/local/bin/brew shellenv)"') >> /Users/sruthisrinivasan/.zprofile
eval "$(/usr/local/bin/brew shellenv)"
brew

#xz
brew install xz

#MySQL
brew install mysql
cpanm DBI
cpanm DBD::mysql

#Installing BioPerl
curl -O https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz
tar zxvf BioPerl-1.6.924.tar.gz
echo 'export PERL5LIB=${PERL5LIB}:##PATH_TO##/bioperl-1.6.924' >> ~/.bash_profile

#Final Dependancies
cpanm Test::Differences Test::Exception Test::Perl::Critic Archive::Zip PadWalker Error Devel::Cycle Role::Tiny::With Module::Build
export DYLD_LIBRARY_PATH=/usr/local/mysql/lib/:$DYLD_LIBRARY_PATH
export PERL5LIB=$PERL5LIB:$HOME/perl5

Could you please let me know how to solve this issue?

chan-98 commented 9 months ago

Hello, went through this issue and I'm still unable to use the tool. I'm running it from inside docker:

docker run -it --rm -u `id -u`:`id -g` -v $PWD:/opt/vep/.vep ensemblorg/ensembl-vep bash

I have no name!@42c04059f3b2:/opt/vep/.vep$ vep -i S1.combined.vcf -o S1.combined.vep.vcf --species homo_sapiens --cache
DBI connect('host=ensembldb.ensembl.org;port=3306','anonymous',...) failed: Can't connect to MySQL server on 'ensembldb.ensembl.org:3306' (110) at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Registry.pm line 1771.

-------------------- EXCEPTION --------------------
MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3306; check your settings & DBI error message: Can't connect to MySQL server on 'ensembldb.ensembl.org:3306' (110)
STACK Bio::EnsEMBL::Registry::load_registry_from_db /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Registry.pm:1771
STACK Bio::EnsEMBL::VEP::BaseVEP::registry /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:283
STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:120
STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:123
STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:200
STACK toplevel /opt/vep/src/ensembl-vep/vep:46
Date (localtime)    = Wed Feb 28 10:12:31 2024
Ensembl API version = 111
---------------------------------------------------

Getting the same error still. I'm running this tool for the first time, Please guide me.

nakib103 commented 9 months ago

Hello @chan-98,

Thanks for your query!

I cannot reproduce your issue. For example, this works fine for me -

$ vep --force --id "rs699" --database  --db_version 111

It might be worthwhile to check if your network is not blocking this connection, for example you are behind a firewall.

Best regards, Nakib

THT-sleepy commented 8 months ago

Hello, I went this issue today, could you help?

Here is my command: ./vep -i examples/homo_sapiens_GRCh38.vcf --cache --force_overwrite

Here is the error message: DBI connect('host=ensembldb.ensembl.org;port=3306','anonymous',...) failed: Unknown MySQL server host 'ensembldb.ensembl.org' (-3) at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Registry.pm line 1771.

-------------------- EXCEPTION -------------------- MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3306; check your settings & DBI error message: Unknown MySQL server host 'ensembldb.ensembl.org' (-3) STACK Bio::EnsEMBL::Registry::load_registry_from_db /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Registry.pm:1771 STACK Bio::EnsEMBL::VEP::BaseVEP::registry /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:283 STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:120 STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:123 STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:200 STACK toplevel ./vep:46 Date (localtime) = Mon Mar 25 06:32:21 2024 Ensembl API version = 111

nakib103 commented 8 months ago

Hello @THT-sleepy,

Thanks for the query!

I cannot re-produce the issue. I can successfully VEP running using the public database (ensembldb.ensembl.org) -

$ vep --id "rs699" --force --database -o STDOUT
## ENSEMBL VARIANT EFFECT PREDICTOR v111.0
## Output produced at 2024-03-25 13:58:30
## Connected to homo_sapiens_core_111_38 on ensembldb.ensembl.org
## Using API version 111, DB version 111
...
#Uploaded_variation Location    Allele  Gene    Feature Feature_type    Consequence cDNA_position   CDS_position    Protein_position    Amino_acids Codons  Existing_variation  Extra
rs699   1:230710048 G   ENSG00000135744 ENST00000366667 Transcript  missense_variant    843 776 259 M/T aTg/aCg -   IMPACT=MODERATE;STRAND=-1
rs699   1:230710048 G   ENSG00000244137 ENST00000412344 Transcript  downstream_gene_variant -   -   -   -IMPACT=MODIFIER;DISTANCE=650;STRAND=-1
...

It might be worthwhile to check if your network is not blocking this connection, for example you are behind a firewall. Alternatively, you can try using --offline, then VEP would not try to connect to the database. You would be fine as long as you do not need to run any option that specifically need database connection.

Best regards, Nakib

THT-sleepy commented 8 months ago

Hello @nakib103

Thank you for your help, I reran it in my own laptop(previously using cloud server, but I don't know how to change firewall setting of it) and it went well. I think you're right.

Best Huatao