Unable to connect to UCSC genome database via linux command line

[Amy Harden (MED - Postgraduate Researcher)]

Hello,

 

This may be an issue with the other programmes I’m using, so if so I apologise.

 

I am using RNAFramework and Bowtie2 to generate reference indexes for RNA-seq structure analysis etc.

A command that is used is the rf-index command which queries the UCSC genome database to obtain the reference sequence https://rnaframework-docs.readthedocs.io/en/latest/rf-index/.

I have had no issue using this in the last few months, however starting last week I now get the message/error after running

$ rf-index -g hg19 -a refGene -b2

 

“[+] Connecting to UCSC genome database (genome-mysql.cse.ucsc.edu:3306)...

 

  [!] Error: Connection to UCSC genome database failed.

             Please check the genome assembly and try again.”

 

Googling this error etc. hasn’t helped so far, so I thought I’d email and ask if there’s an obvious quick fix that I am missing.

I have run this exact same command before successfully, so I am not sure why it no longer works when nothing, to my knowledge, has changed on my end.

 

Any help would be much appreciated, and please let me know if you need more information.

 

Many thanks,

Amy

[Hiram Clawson]

Good Afternoon Amy:

You can test the MySQL connection with the command line mysql client.

Try this on your shell command line:

$ mysql -h genome-mysql.cse.ucsc.edu -P 3306 -u genomep -p'password' -e 'show
tables;' hg19

See if that provides a table listing from the database hg19.

--Hiram

On 11/11/24 12:16 PM, 'Amy Harden (MED - Postgraduate Researcher)' via UCSC