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I've been experiencing a huge issue with my system recently, where something unknown is eating all of my available drive space in the root fs. Even if I delete files, it will almost instantaneously be back to "0 Bytes Available" again (as reported by Gnome).

Running the Disk Usage Analyzer, it seems the problem is within ~. For example, I had over 6GB free on the root fs. Disk Analyzer shows ~ as 5.7GB but the largest file within ~ is only 175MB and everything added up wouldn't even be 200MB total. So what in ~ is taking up this phantom space? A run of "du -h" lists the small files, and then just plain "." with a size of 5.8GB! I don't know what this is, or if it's safe to delete it (if that's even possible).

I've been running this system without issue for quite some time now, until this started popping up. Without available disk space, I can't launch apps and Gnome is completely messed up upon restart - it won't start due to lack of space.

On a different yet possibly related issue, I also have another EXT4 data partition which Gnome and the system is also listing as having "0 bytes" free space but I know this is incorrect. GParted reports 33GB free. This isn't as big of an issue because it's not affecting the root partition and system usability, but I thought I'd mention it as it very well could be related and needs fixing too.

Thanks for any assistance!

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    Directory refs to "." are short-hand for the current directory. It would be a Bad Idea to delete that. Are your reports showing information for hidden files? e.g., are you seeing how large those files and directories with names that start with "." are?
    – user459652
    Oct 19, 2015 at 1:26
  • Read the manual page of lsof. A process writes into this file but the file is deleted. One possibility.
    – A.B.
    Oct 19, 2015 at 5:04

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One possibility is that some deleted file is still being written to and is expanding:

Deleting a large file does not free up space

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