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The last time I ran a full scan with Malwarebytes it was 1 hour and 18 minutes. I wouldn't run MBAM instead of an antivirus program. It is meant to work in tandem with antivirus.
Check your antivirus scheduling settings. I know that some have an option to shut down after the scan is finished. Run the scan right before you go to bed and the computer will be off when you wake up.
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