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Old 06-14-2013, 01:22 PM   #1
kai3192
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Exclamation ERROR in DBI connect orthomclInstallSchema

Hello,
I am using orthomcl ... at the step 5 (orthomclInstallSchema) in the manual (http://orthomcl.org/common/downloads.../UserGuide.txt) it gives me an error saying 'DBI connect('orthomcl:localhost:3307','orthomcl',...) failed: Access denied for user 'orthomcl'@'localhost' (using password: YES) at /home/kaivalya3192/orthomclSoftware-v2.0.8/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 56
[email protected]:~/orthomclSoftware-v2.0.8/bin$' ...

Can somebody please help me ???

Thank you...

Last edited by kai3192; 06-14-2013 at 01:59 PM. Reason: Typing Error
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Old 06-16-2013, 02:15 AM   #2
SES
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It appears you don't have permissions on the database. You will need to create a database and give a user permissions on that. Then, create a simple config file like the one printed when you run orthomclInstallSchema with no arguments. In that config file you will include the database name, user and password and names for the tables to create. If you run the program again with the config file as the only argument, it should work. Let us know if that does not solve your problem.
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Old 06-17-2013, 07:12 AM   #3
kai3192
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I should create a config file in orthomcl means that I need to edit the preexisting file orthomcl.config.template right ??
I did edit that and entered the same database name and password as for the database i created in mysql... i also entered same user name a nd have granted the privileges for that user name in mysql for the same database....

IT IS STILL GIVing me an error 'DBI connect('orthomcl:3307','kaivalya3192',...) failed: Can't connect to MySQL server on '3307' (22) at /home/kaivalya3192/orthomclSoftware-v2.0.8/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 56'
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Old 06-17-2013, 07:22 AM   #4
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Quote:
Originally Posted by kai3192 View Post
IT IS STILL GIVing me an error 'DBI connect('orthomcl:3307','kaivalya3192',...) failed: Can't connect to MySQL server on '3307' (22) at /home/kaivalya3192/orthomclSoftware-v2.0.8/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 56'
Okay, now this is a different error and it indicates your serving is not running. Start the daemon (mysqld or mysqld_safe) and then try to connect. By the way, you can use the following command to see if the daemon is running.

Code:
ps aux | grep mysqld
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Old 06-17-2013, 07:52 AM   #5
kai3192
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When I use the script u just gave me it says

mysql 1033 0.0 0.5 492532 43256 ? Ssl 10:21 0:02 /usr/sbin/mysqld
1000 5070 0.0 0.0 8108 924 pts/1 R+ 21:19 0:00 grep --color=auto mysqld
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Old 06-17-2013, 08:01 AM   #6
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does this mean that the Daemon is working ??
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Old 06-17-2013, 08:04 AM   #7
SES
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At this point, I recommend you try to connect to the database from the command line. If you are able to do so, that would suggest there is a typo in your config file or possibly something wrong with your DBI installation/configuration.
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Old 06-17-2013, 08:10 AM   #8
kai3192
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I was able to connect to the database using commandline using the user root, but not using the user kaivalya3192
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Old 06-17-2013, 08:16 AM   #9
SES
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Quote:
Originally Posted by kai3192 View Post
I was able to connect to the database using commandline using the user root, but not using the user kaivalya3192
I think that points to your issue because the DBI module is just an interface, and you'll have to be able to connect using the credentials you provide.
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Old 06-17-2013, 08:17 AM   #10
GenoMax
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Original post indicated that the user is/needs to be "orthomcl". Isn't that still valid?
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Old 06-17-2013, 08:24 AM   #11
kai3192
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Thank you so much... It just worked and I was able to run the OrthomclInstallSchema....

BUT NOW I am getting an error in the 9th step orthomclLoadBlast saying 'DBD::mysql::st execute failed: The used command is not allowed with this MySQL version at orthomclLoadBlast line 39, <F> line 14.'
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Old 06-17-2013, 01:35 PM   #12
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I am using ubuntu.... and I have installed MySQL version 5.5 server.... I aslo tried reinstalling by building the source and then typing DENABLED--local-infile=1 while using the c-make command...

After installation it still does not work...
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Old 06-18-2013, 04:46 AM   #13
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Quote:
Originally Posted by kai3192 View Post
I am using ubuntu.... and I have installed MySQL version 5.5 server.... I aslo tried reinstalling by building the source and then typing DENABLED--local-infile=1 while using the c-make command...

After installation it still does not work...
If you see the server running and you can connect and create databases, then you probably have a working installation. That error is most likely a Perl DBI error, so I would suggest you take a look at the DBI test suite and see if everything is installed correctly. Or, install a more recent DBI version.

So, try to get the database access working again and then re-install Perl DBI and see if that doesn't solve your problems. Good luck.
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Old 06-25-2013, 10:51 PM   #14
gyuxutong
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Quote:
Originally Posted by kai3192 View Post
Thank you so much... It just worked and I was able to run the OrthomclInstallSchema....
I encounter the same question you mentioned. Could you give me a help to pass the first step, running the OrthomclInstallSchema. Thank you.
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Old 09-10-2013, 07:01 AM   #15
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Quote:
Originally Posted by kai3192 View Post
Thank you so much... It just worked and I was able to run the OrthomclInstallSchema....

BUT NOW I am getting an error in the 9th step orthomclLoadBlast saying 'DBD::mysql::st execute failed: The used command is not allowed with this MySQL version at orthomclLoadBlast line 39, <F> line 14.'
Hello. Thanks god i found your thread.

I am still stuck in your first problem. Even if i put "root" and my root password in the .config file, i cannot connect. I have the same message error that you had.

Did you do some extra things or it just worked like that?

Thanks.
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Old 09-10-2013, 07:09 AM   #16
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Quote:
Originally Posted by amaruquyllur View Post
Hello. Thanks god i found your thread.

I am still stuck in your first problem. Even if i put "root" and my root password in the .config file, i cannot connect. I have the same message error that you had.

Did you do some extra things or it just worked like that?

Thanks.
Did you follow the advice earlier in the thread? That is, can you connect to the database from the command line to confirm mysql is running (and that you have created a user that can connect)? Also, you shouldn't be using the root user for normal operations.
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Old 09-10-2013, 07:20 AM   #17
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Quote:
Originally Posted by amaruquyllur View Post
Yes:

- I can connect to mysql as root.
- I created the user "orthomcl".
- I can connect with the user "ortomcl" as well.
- I have granted all permissions to"orthomcl".

Yet the same error... I am wondering why...
Okay, have you installed an updated version of the Perl driver for mysql (DBD::mysql)? You will need to make sure you can connect via DBD::mysql, and if you can, that reduces the source of problems to the configuration file or the orthomcl script.
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Old 09-10-2013, 07:31 AM   #18
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Yes, i updated DBD::mysql today.

According to the orthoMCL User Guide, both DBD::mysql and DBI are running OK (i get no output when i type the commands on my terminal).

P.S. i edited my last post, maybe that can help.
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Old 09-10-2013, 07:33 AM   #19
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mysql> show grants for 'orthomcl'@'localhost';
+------------------------------------------------------------------------------------------------------------------+
| Grants for [email protected] |
+------------------------------------------------------------------------------------------------------------------+
| GRANT USAGE ON *.* TO 'orthomcl'@'localhost' IDENTIFIED BY PASSWORD '***' |
| GRANT SELECT, INSERT, UPDATE, DELETE, CREATE, DROP, INDEX, CREATE VIEW ON `orthomcl`.* TO 'orthomcl'@'localhost' |
+------------------------------------------------------------------------------------------------------------------+
2 rows in set (0.00 sec)


Yet the same error when i type:

$ orthomclInstallSchema orthomcl.config
DBI connect('orthomcl:3307','orthomcl',...) failed: Can't connect to MySQL server on '3307' (60) at /***/orthomclSoftware-v2.0.9/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 56.
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Old 09-10-2013, 07:44 AM   #20
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Are you administering this machine locally?

If you are using a firewall you may need to make adjustments to allow connects to port 3307 (the message seems to indicate inability to do that above).
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