If you still have issues with MySQL try the following in perl:

system("mysqlimport -u USERNAME -pPASS orthomcl /pathto/SimilarSequences --local");

or from command line:

mysqlimport -u USERNAME -pPASS orthomcl /pathto/SimilarSequences --local

I am also creating an automated application where you have to give in your genome files and a main file takes care of all the steps.

I am having the same problem. Did you find a solution? Thanks, G.

Hi,

Try adding :mysqllocalinfile=1 to the end of the dbConnectString in orthomcl.config file, it was default 0 on my system so orthomcl was not able to load the blast results.

Example: dbConnectString=dbi:mysql:orthomcl:mysqllocalinfile=1

Let me know if this works well.

Gd luck. Reetu

Hi, I'm having the same problems with mysql and orthomcl. I added :mysqllocalinfile=1 to the end of the dbConnectString in orthomcl.config file, but it did not work for me.

In addition, I also used local-infile=1 in the confi file of mysql using sudo nano /etc/mysql/my.cnf, but still does not wok:

[mysqld]

local-infile=1

[mysql]

local-infile = 1

. other thing was to modify client by adding loose-local-infile=1 [client] loose-local-infile=1

but I have the same error again.

If anyone knows another solution, would be helpful

thanks a lot!

Hi, thanks a lot for your answer.

the mysql version is 5.5 in ubuntu and the perl DBI is libclass-dbi-sweet perl 0.10-1 (I installed it using Ubuntu Software Center)

I check the /etc/my.cnf and appears this information related with InnoDB:

* InnoDB
 #
 # InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
 # Read the manual for more InnoDB related options. There are many!

and i do not see the option "InnoDBbufferPool_size"

about my orthomcl scripts, i have them in the same directory.

I keep on getting the same error.

best regards,

I got it!!

What you should append on the dbConnectString is ";mysqllocalinfile=1"! This is how the DBI module understands the --local-infile setting...

Just like this: dbConnectString=dbi:mysql:orthomcl;mysqllocalinfile=1

Hi all. I'm also having this problem when I try to run orthomclLoadBlast. I'm using OrthoMCL 2.0.9 on a new system running Ubuntu 13 and I'm using the most recent version of mysql server and client (5.5.35).

Editing orthomcl.config to have a dbConnectString as described above did not work for me. My database is called orthomcl_basal_metazoans so I used that instead of orthomcl. It should be a semicolon and not a colon, right? I tried both and neither worked but I'm just making sure I'm at least doing that right. Here's what that line looks like: dbConnectString=dbi:mysql:orthomcl_basal_metazoans;mysqllocalinfile=1. What am I missing?

Thanks, Kevin

I wrote to OrthoMCL help and got a helpful reply but I still don't understand. This is what I was told:

Thanks for writing. Other users have encountered this problem as well. In the Orthomcl UserGuide, under step 9, we offer this suggestion, which I hope might help:

NOTE: You might get the following error when you run this command:

"The used command is not allowed with this MySQL version."

The SQL that causes this is LOAD DATA LOCAL INFILE. MySql needs specific configuration to enable this command. See these two pages:

http://dev.mysql.com/doc/refman/5.1/en/load-data-local.html http://dev.mysql.com/doc/refman/5.0/en/loading-tables.html