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I am trying to back up my Ubuntu partition using the Backups app to an external USB hard drive. I have formatted the drive (NTFS) and mounted it to /media. I can access the mounted drive and write and read to and from it using the file browser and from terminal. However, it doesn't show up and offer the disk as a possible location to backup to in the Backups app. Any suggestions?

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You can't backup the system partition with deja-dup (the name of the backup tool), this tool can be used for backing up your personal stuff. When you want to backup the Ubuntu system partition, you can use Clonezilla. Download the ISO file and create a bootable media from it.
Boot from the CD/DVD/USB media you created - here you see how to perform everything :

Clonezilla : How to backup (operating system) partitions

Clonezilla : How to restore (operating system) partitions

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