Question: rerun orthomcl when I updata mysql
gravatar for 1291016966
3.9 years ago by
12910169660 wrote:

Hello, Good moorning everyone!My name is myshu. I have some problems occured when I run orthomcl after I update my MySQL..

The command I typed is : orthomclInstallSchema orthomcl.config And the error is :

DBI connect('orthomcl_AF_Aspergillus_2:3307','root',...) failed: Can't connect to MySQL server on '3307' (22) at /analysis/software_han/orthomclSoftware-v2.0.9/bin/../lib/perl/OrthoMCLEngine/Main/ line 56.

Do you know how to deal with it???

best wishes~, myshu

tool orthomcl mysql • 1.4k views
ADD COMMENTlink modified 3.9 years ago by Philipp Bayer6.6k • written 3.9 years ago by 12910169660
gravatar for Philipp Bayer
3.9 years ago by
Philipp Bayer6.6k
Philipp Bayer6.6k wrote:

It tries to connect to the MySQL server but it doesn't find the server where it thinks it is.
There's a good chance your MySQL server is off after the update, or the port is wrong - try this:

service mysql status

what does it print? if it's off, you may have to restart the server using sudo service mysql start.

Can you log in using the user credentials in your orthomcl.config?

mysql -u YOUR_USER -p

(enter password)

Type this:

mysql> SHOW VARIABLES LIKE 'port';

Does it print:

| Variable_name | Value |
| port          | 3306  |
1 row in set (0.16 sec)

By default, mysql runs on port 3306, but your above command indicates that your orthomcl.config looks for port 3307. Try changing the value to 3306.

ADD COMMENTlink written 3.9 years ago by Philipp Bayer6.6k
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