If someone has option log-bin in their default configuration file mysql_install_db prints warning "2020-09-03 16:37:13 1 [Warning] Failed to load slave replication state from table mysql.gtid_slave_pos: 1017: Can't find file: './mysql/' (errno: 2 "No such file or directory")", although having such a table is not expected before mysql_install_db run.

How to Repeat.

$ ./scripts/mysql_install_db --no-defaults --basedir=. --datadir=./data --log-bin=master 

Installing MariaDB/MySQL system tables in './data' ...

2020-09-03 16:37:13 1 [Warning] Failed to load slave replication state from table mysql.gtid_slave_pos: 1017: Can't find file: './mysql/' (errno: 2 "No such file or directory")

OK

...

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Suggested Fix

Ignore log-bin option in --bootstrap mode.