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When Craft tries to apply an update, it tries to back up the database. Although that's great in general, backing up a large database using PHP requires a lot of memory and resources that might not be available in the hosting environment or the client does not have enough access to make any related adjustments.

Is there a setting of some kind that would prevent Craft CMS from backing up the database when updating? I already use a command line script to backup the database before applying an update.

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Yes you can use the backupDbOnUpdate config setting:

https://craftcms.com/docs/config-settings#backupDbOnUpdate

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