connect to MySQL server on 'genome-mysql.cse.ucsc.edu'
Williams, Daniel
Hello, I'm trying to connect to genome-mysql.cse.ucsc.edu using the instructions given on the wiki at "http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format". However, I keep getting the error
"ERROR 2003 (HY000): Can't connect to MySQL server on 'genome-mysql.cse.ucsc.edu' (110)"
However, I can ping the server. Is there a step I am missing, or is the server down? I also tried unsuccessfully to log in with a MySQL client.
Thanks!
Dan
Jonathan Casper
Hello Dan,
Thank you for your question about our public MySQL server. The server is up and running; what steps are you taking to connect to it? If you're able to run mysql from the command line, what is the result of the following command?
mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A
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Jonathan Casper
UCSC Genome Bioinformatics Group
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Jonathan Casper
Hello Dan,
I've confirmed that the genome-mysql server is up, and I was able to access it from outside of our campus just fine. Unfortunately support for mysql client issues is a bit outside the scope of this mailing list, but I can make a few more suggestions. First, try connecting to one of the Ensembl public mysql servers (listed at http://www.ensembl.org/info/data/mysql.html) to see if this is specifically about our server or about any mysql connection you attempt. If you're attempting to connect from an institution, it's possible that your IT staff have external mysql connections blocked by default for security reasons. Then make sure your mysql client is trying to connect to the default mysql port on our server (3306). You might also try using a fresh install of the most recent version of your client, just in case there are some version incompatibilities.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
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Jonathan Casper
UCSC Genome Bioinformatics Group
Jonathan,
Thanks for the quick reply. I ran the command you requested, and the output is:
ERROR 2003 (HY000): Can't connect to MySQL server on ERROR 2003 (HY000): Can't connect to MySQL server on 'genome-mysql.soe.ucsc.edu' (110) (110)
I tried this from a Linux cluster and from my Windows desktop. I can "ping" the MySQL server from both locations.
Dan