Need Help With SyMap Building And MySQL

Question

[novice]

Hello,

I have assembled a draft genome of S.Pombe and would like to align it to the reference genome to study variations. It looks like SyMap would be best fit for this purpose, but I'm having a problem.

SyMap tells me there's a MySQL server already running so I should either shut it down or point SyMap to another server. Since I work on an HPC that allows me limited permissions, I cannot shutdown the MySQL server. So I've been trying to build my own local MySQL server. With zero knowledge about MySQL, this has been frustrating.

I tried to follow this guide to build MySQL as a non-root user with the addition of the flag MYSQL_TCP_PORT=3307 to the cmake command to have the local server run on a different port than the original's (3306). Whenever I get to the step where I have to execute mysql_install_db, it says:

2015-10-31 20:52:02 [WARNING] mysql_install_db is deprecated. Please consider switching to mysqld --initialize
2015-10-31 20:52:02 [ERROR]   Child process: /home/rajeha/software/mysql/bin/mysqldterminated prematurely with errno= 32
2015-10-31 20:52:02 [ERROR]   Failed to execute /home/rajeha/software/mysql/bin/mysqld --bootstrap --datadir=/home/rajeha/software/mysql/data --lc-messages-dir=/usr/share/mysql --lc-messages=en_US
-- server log begin --
2015-11-01T01:52:02.964453Z 0 [Warning] --bootstrap is deprecated. Please consider using --initialize instead
2015-11-01T01:52:02.969334Z 0 [ERROR] Invalid old_passwords mode: 1. Valid values are 2 and 0

2015-11-01T01:52:02.969376Z 0 [ERROR] Aborting

-- server log end --

If I try to run the server with mysql_safe, it says:

./bin/mysqld_safe: line 130: /var/log/mysqld.log: Permission denied
./bin/mysqld_safe: line 164: /var/log/mysqld.log: Permission denied
151031 20:53:12 mysqld_safe mysqld from pid file /home/rajeha/software/mysql/the.pid ended
./bin/mysqld_safe: line 130: /var/log/mysqld.log: Permission denied

I know this could be due to various reasons but I really don't know what other information to include. Please tell me what could be helpful to know.

I would appreciate your help. Thanks.

Answer 1

[Philipp Bayer]

(First of all, this question may give better answers on StackOverflow)

They changed the MySQL installation commands in a recent version, quoting from the manual:

shell> bin/mysql_install_db --user=mysql    # Before MySQL 5.7.6
shell> bin/mysqld --initialize --user=mysql # MySQL 5.7.6 and up
shell> bin/mysql_ssl_rsa_setup

So you'd have to replace mysql_install_db by mysqld --initialize

Also, check whether the mysql.conf file you use has a command for "old_passwords" and set that to 2 if it's there.

In your later command when it complains about "permission denied", it tries to write to a system-wide log-file you do not have access to. The config-file in your MySQL directory should have a few settings for paths to config files (like "general_log_file") you should replace by paths you can write to.

Source: http://dev.mysql.com/doc/refman/5.7/en/binary-installation.html

[novice]

Thanks for the reply. I cannot seem to find the mysql.conf file or the config-file you mentioned. Do you know where they are?

Running find, I found the file /packaging/deb-vivid/extra/mysql.conf.cnf with one line [mysql], beside the header comments. I added "old_passwords=2" to it but running the bin/mysqld script still gave an error that old passwords is equal to 1.