Unable to connect to genome-mysql.cse.ucsc.edu

[Xavi Armengol]

Dear all, 

I'm trying to connect to the ucsc mysql server (genome-mysql.cse.ucsc.edu), from the OSX terminal and mysql client, using the following syntax: 

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A

I'm getting the following response: 

ERROR 2013 (HY000): Lost connection to MySQL server at 'reading initial communication packet', system error: 54

I've also tried without -A option, with same results. 

I have discarded the possibility of some local network restrictions, because I'm able to connect to other MySQL remote servers, using similar method and same default port. 

I have been searching on the Internet for this error with no success, so I would like to know if do you know what could be the cause of this error. 

Thank you very much!

-- 

Xavi Armengol

[Brian Lee]

Dear Xavi,

Thank you for using the UCSC Genome Browser and reporting that you are having trouble connecting to the public mysql server.

A test when your email came in and a current retest of the server indicates it has been working. Here is an example you could try:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -ANe 'select * from kgXref limit 5;' hg19

Our administrators have examined our public mysql server and ensured there should not be a problem and even made minor enhancements. Can you try your queries again, and also see if you can access other mysql servers beyond ours? We have seen another user report a similar error when a 'stateful firewall' was involved from the institution that was making the query, and perhaps that may be happening here. Another way to test if the firewall is involved is to try the query from a connection off campus.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

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[Brian Lee]

Please note that any reference to our resources under the .cse. domain should be updated to the .soe. domain.  For example, our public MySQL server genome-mysql.cse.ucsc.edu should now be accessed at the address of genome-mysql.soe.ucsc.edu instead.

[Peidong Gao]

Hi 
I just found I have same issues, my problem is we are building php web and require to connect mysql.cse.ucsc.edu to get reference
I can successfully connect to the UCSC MySQL server from the terminal using the following command:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu hg19 -e 'SELECT chrom, txStart, txEnd, strand, name, name2, exonStarts, exonEnds FROM refGene WHERE chrom="chr2" limit 5;'

However, when I attempt the same connection from within a PHP script, I receive the following error:
Error: Can't connect to server on 'genome-mysql.cse.ucsc.edu' (13)

Any suggestions?

Thanks for all the help and time!!!

William

[Jairo Navarro Gonzalez]

Hello,

We have deprecated the .cse. domain and machines, so the servers you are trying to connect do not exist anymore. There was a temporary redirect for a few years, but those might have been removed now. Please access the MySQL servers using the following address:

http://genome-mysql.soe.ucsc.edu/

More information about MySQL access can be found on the following help page:

https://genome.ucsc.edu/goldenPath/help/mysql.html

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.

If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

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[Jairo Navarro Gonzalez]

Hello,

You may also be interested in using the REST API to query the genome for your script:

https://genome.ucsc.edu/goldenPath/help/api.html

For example, you can get track data using the following URL in JSON format:

https://api.genome.ucsc.edu/getData/track?genome=hg38;track=gold;chrom=chr1;start=47000;end=48000

If you provide us with more information about what you are trying to achieve with the PHP script, we can give feedback on the best way to query the Genome Browser.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

[Peidong Gao]

Hi,

I have tried both genome-mysql.cse.ucsc.edu and genome-mysql.soe.ucsc.edu domons. They can all access MySQL in my server using R or in shell.

The problem is when I try to use my test php files to run the R script, is come with the error message no matter what domain name.

R script executed successfully.
Output:
Error during MySQL connection: Failed to connect to database: Error: Can't connect to server on 'genome-mysql.cse.ucsc.edu' (13)
R script executed successfully.
Output:
Error during MySQL connection: Failed to connect to database: Error: Can't connect to server on 'genome-mysql.soe.ucsc.edu' (13)

Thanks!!!!!

[Jairo Navarro Gonzalez]

Hello,

Sometimes, PHP scripts cannot handle an account without a password (genome).
Can you try to access MySQL using the following credentials:

account:    genomep
password:  password

Let us know if that resolves the problem.

If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser