Lỗi could not open required defaults file my.ini năm 2024

Hi everyone. I know this may be a more general problem but I don't know where to ask. I'm trying to run Stacks but this error keeps appearing:

Failed to open required defaults file: usr/miniconda3/envs/genomevol/share/stacks/sql/mysql.cnf

I've tried updating mysql, installing mysql-server instead of mysql-client, remove everything related to mysql and reinstalling it, but nothing works. Also mysql.cnf does exist in etc/mysql/conf.d/, but when I call mysql alone, it says

ERROR 1045 (28000): Access denied for user 'user'@'localhost' (using password: NO)

I don't know what else to do, I'm really new in bioinformatics and I'm not sure what's happening.

I would appreciate any help you can give me.

mysql ubuntu offtopic • 1.4k views

Before sosetup i run sudo soup after that automated Setup sosetup -f sosetup_master is showing this error. mysql: [ERROR] Could not open required defaults file: /etc/mysql/debian.cnf

Please wait while... setting OS timezone to UTC... setting OSSEC timezone to UTC... restarting OSSEC... enabling securityonion.service in systemd... stopping services... Enter password: mysql: [ERROR] Could not open required defaults file: /etc/mysql/debian.cnf mysql: [ERROR] Fatal error in defaults handling. Program aborted!

I have a new install of Linux Mint 19 (within the last two months), installed mysql and "Adminer" database manager to verify that mysql is working with my "normal" userid. When I run cqrlog debug=1 I get the following output:

**** DEBUG LEVEL 1 **** SSL libraries: /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0 Loading libmysqlclient: /usr/lib/x86_64-linux-gnu/libmariadbclient.so.18.0.0 ************************** MySQL version: 10. ************************** ********************************** MySQL version assigned: 5.6 ********************************** Loaded 93636 LoTW users Loaded 98114 eQSL users Loaded 48268 SCP calls * User home directory: /home/bob/ Program home directory: /home/bob/.config/cqrlog/ Data directory: /home/bob/.config/cqrlog/database/ Memebers directory: /usr/share/cqrlog/members/ ZIP code directory: /usr/share/cqrlog/zipcodes/ Binary dir: /usr/bin/ Share dir: /usr/share/cqrlog/ TConnection to MySQL: 5.6 * 56 us states loaded /usr/sbin/mysqld --defaults-file=/home/bob/.config/cqrlog/database/mysql.cnf --datadir=/home/bob/.config/cqrlog/database/ --socket=/home/bob/.config/cqrlog/database/sock --port=64000 Trying to connect to database mysqld: [ERROR] Could not open required defaults file: /home/bob/.config/cqrlog/database/mysql.cnf mysqld: [ERROR] Fatal error in defaults handling. Program aborted! TMySQL56Connection : Server connect failed. Trying:1 Trying to connect to database TMySQL56Connection : Server connect failed. Trying:2 ... etc.

I tried deleting the mysql.cnf file from the database folder, and when I run cqrlog debug=1 with no config file, it reappears during execution but is still unable to be opened from the very same folder in which it was written by cqrlog.

I have a program that installs MySQL from zip file. Program can extract files from zip file to the Program Files folder and create an option file in Program Files folder for mysql called "my.ini".

After the extraction process, program is gonna initialize data folders and files via run the mysqld.exe.

The program run the mysqld.exe via Process.Start() with some arguments. The arguments are --defaults-file=C:\Program Files\MySQL\my.ini --initialize-insecure --console.

When I try to run mysqld.exe with that arguments, it throws an error like;

mysqld: [ERROR] Could not open required defaults file: C:\Program
mysqld: [ERROR] Fatal error in defaults handling. Program aborted!

My codes are like below;

        Process p = new Process();
        p.StartInfo.UseShellExecute = false;
        p.StartInfo.RedirectStandardOutput = true;
        p.StartInfo.WorkingDirectory = destPath + "\\bin";
        p.StartInfo.FileName = destPath + "\\bin\\mysqld.exe";
        p.StartInfo.Arguments = "--defaults-file=" + destPath + "\\my.ini --initialize-insecure --console";
        p.OutputDataReceived += P_OutputDataReceived;
        p.Start();
        // destPath:"C:\\Program Files\\MySQL"