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stajichlab / OrthoMCL

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problem at the step 4 with mysql-5.6.21 #8

Open emlee413 opened 5 years ago

emlee413 commented 5 years ago

Problem at the step 4.

orthomclSoftware-v2.0.9/bin$ ./orthomclInstallSchema ../my_orthomcl_dir/orthomcl.config

DBI connect('orthomcl:mysql_local_infile=1:localhost:3307;mysql_read_default_file=/home/mylab/bin/mysql/mysql.cnf','orthomcl',...) failed: Access denied for user 'orthomcl'@'localhost' (using password: YES) at /home/mylab/bin/orthomclSoftware-v2.0.9/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 56.

Do you have any suggestion on how to solve this? I'm really in basic level of orthoMCL. Thanks.

hyphaltip commented 5 years ago

this is not an official orthomcl source repo so I suggest contacting their team - but seems like your password is incorrect in the connections - I assume you configured orthomcl.config to have the username and password that works for your mysql connection?

I would also suggest a more standalone tool like OrthoFinder https://github.com/davidemms/OrthoFinder/releases for orthology which does not require a database behind it.

emlee413 commented 5 years ago

I will try also OrthoFinder. I'm seriously considering using that. Anyway after getting your comment , I tried to change my dbLogin. That works! Thank you so much.