While working with OrthoMCL I get to a part in which I have to upload my data in MySQL and then the program should make pairs of my data which are basically protein sequences. While running the command orthomclPairs I get the following error
DBD::mysql::st execute failed: Table 'BestQueryTaxonScore' already exists at /home/sebastian/Downloads/OrthoMCL_v_2.0/orthomclSoftware-v2.0.9/bin/orthomclPairs line 709, <F> line 14.
To me it seems my database is full of information from a previous analysis and some tables may have the same names so a good solution would be reset the database .
AM I right? How can I solve this issue?
I appreciate your help and I' m sorry if something I say does not make sense but I am very new to "computers".
Without any familiarity with this OrthoMCL software, it's perfectly obvious from the error message that the script attempted to create a table that was already present.
If you're setting up to work on a new problem, perhaps there's a way to create a new database. In MySQL parlance, a new database will let you create tables with the same name in it.
Or, as you say, you might "reset" your existing database. But that's OrthoMCL parlance, not MySQL parlance.
So the answer to my question is this:
Drop the database everytime you've ran the program (i.e. everytime you have uploaded the parsed BLAST search).
The database can be droped as follows:
mysql -u user -p DATABASE NAME (login with privileges)
Then this
drop database YOUR_DATABASE (this will delete all the tables for this database)
Then this
create database YOUR_DATABASE; (adds back the database namespace)
then just installschema outside MySQL
I hope it' s helpful for other working with MyOrthomcl.