FortiGate Next Generation Firewall utilizes purpose-built security processors and threat intelligence security services from FortiGuard labs to deliver top-rated protection and high performance, including encrypted traffic.
This article describes how to run a file system check automatically.
This feature adds the option to perform an automatic file system check if the FortiGate shuts down ungracefully.

By default, automatic file system check is disabled.
When disabled, the next time an administrator logs in after an ungraceful shutdown, a warning message will advise them to manually run a file system check.

GUI warning.

CLI warning.
WARNING: File System Check Recommended! Unsafe reboot may have caused inconsistency in disk drive.
It is strongly recommended that you check file system consistency before proceeding.
Please run 'execute disk scan 17'
Note: The device will reboot and scan during startup. This may take up to an hour.

From GUI.

1) Go to System -> Settings.

2) In the 'Start Up' settings section, enable 'Auto file system check', as illustrated below:

3) Select 'Apply'.

From CLI.
# config system global
    set autorun-log-fsck enable

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Technical Tip: Run a File System Check automatically