Thank you for using the UCSC Genome Browser and sending your inquiry.
We have fixed the issue that was referenced in the thread you shared. To better diagnose your issues, could you send us the following information:
1) The Linux operating system you are using to run GBiC.
2) Have you updated your GBiC script recently (within the last few months)
3. Does the script contain a line that sets the "sql_mode" to "empty", and not to "strict", in your MySQL configuration?
The specific code change can be seen on the following git commit:
I hope this is helpful. If you have any further questions, please reply to genome...@soe.ucsc.edu.
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Thanks so much! Your response gave me the information I needed to fix the error. I ran the following commands:
sed -Ei '/^.(mysqld|server).$/a sql_mode=' $MYCNF
sudo /etc/init.d/mariadb restart
To answer your questions:
Here are the contents of my.cnf:
# The MariaDB configuration file
# The MariaDB/MySQL tools read configuration files in the following order:
# 0. "/etc/mysql/my.cnf" symlinks to this file, reason why all the rest is read.
# 1. "/etc/mysql/mariadb.cnf" (this file) to set global defaults,
# 2. "/etc/mysql/conf.d/*.cnf" to set global options.
# 3. "/etc/mysql/mariadb.conf.d/*.cnf" to set MariaDB-only options.
# 4. "~/.my.cnf" to set user-specific options.
# If the same option is defined multiple times, the last one will apply.
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
# If you are new to MariaDB, check out https://mariadb.com/kb/en/basic-mariadb-articles/
# This group is read both by the client and the server
# use it for options that affect everything
# Port or socket location where to connect
# port = 3306
socket = /run/mysqld/mysqld.sock
# Import all .cnf files from configuration directory