File disappeared but appears with "locate"?

[linux_dream]

Hi people,
I just noticed that one of my files (sfbooker.bin) disappeared as if I had removed it. When I type locate "sfbooker" I see

/usr/local/share/scid/books/sfbooker.bin

which is where the file is supposed to be.
However when I go there either with PCmanFM or with the terminal and type "ls", I see absolutely no file in /usr/local/share/scid/books.

I have typed "sudo updatedb" and retried the "locate sfbooker" and it still returns

/usr/local/share/scid/books/sfbooker.bin

.

So I don't understand what's going on. Have I lost my file? If so, how is that possible? The file was set in such a way that only root could modify/delete it and I never deleted it. And if it's deleted, why does it appear with the locate command?

I tried the live CD (via an usb stick) of Lubuntu 14.04 and mounted my everyday's Lubuntu partition. The file sfbooker.bin is still invisible... I also ran fsck (via the live cd) this morning and no error was reported.

[bab1]

Hi people,
I just noticed that one of my files (sfbooker.bin) disappeared as if I had removed it. When I type locate "sfbooker" I see

/usr/local/share/scid/books/sfbooker.bin

which is where the file is supposed to be.
However when I go there either with PCmanFM or with the terminal and type "ls", I see absolutely no file in /usr/local/share/scid/books.

I have typed "sudo updatedb" and retried the "locate sfbooker" and it still returns

/usr/local/share/scid/books/sfbooker.bin

.

So I don't understand what's going on. Have I lost my file? If so, how is that possible? The file was set in such a way that only root could modify/delete it and I never deleted it. And if it's deleted, why does it appear with the locate command?

I tried the live CD (via an usb stick) of Lubuntu 14.04 and mounted my everyday's Lubuntu partition. The file sfbooker.bin is still invisible... I also ran fsck (via the live cd) this morning and no error was reported.

Post the output of

stat /usr/local/share/scid/books/sfbooker.bin

[linux_dream]

Post the output of

stat /usr/local/share/scid/books/sfbooker.bin

stat: cannot stat ‘/usr/local/share/scid/books/sfbooker.bin’: No such file or directory

[philinux]

Linux_dream,

You may need to run sudo updatedb then rerun locate. Locate could be looking at the old database.

[bab1]

Post the output of

stat /usr/local/share/scid/books/sfbooker.bin

This tells me that the file no longer exists.

[linux_dream]

Linux_dream,

You may need to run sudo updatedb then rerun locate. Locate could be looking at the old database.

Well as I wrote in the first post, I've already done this (now maybe 10 times since then, and the file still appears with the locate command.)

This tells me that the file no longer exists.

Okay. I would like to understand linux though. Why does "locate sfbooker" still points at an empty folder, even after I typed "sudo updatedb"?
And what are the possible reasons a file could disappear on its own like that one?
That is very scary... I mean, I feel like any file could simply disappear, even if it's in read-only and can only be modified with "sudo"...

[steeldriver]

Is /usr/local (or any of the directories below it - /usr/local/share, /usr/local/share/scid, /usr/local/share/scid/books) on a separate partition/filesystem?

[linux_dream]

Is /usr/local (or any of the directories below it - /usr/local/share, /usr/local/share/scid, /usr/local/share/scid/books) on a separate partition/filesystem?

No, same partition. I only have 2 Windows partitions, 1 swap and 1 Lubuntu (ext4 file system).

[linux_dream]

Mystery solved:
The file is indeed deleted (probably due to that I shut down my computer the hard way due to a a freeze).
Why did locate still point at an empty folder despite having typed "sudo updatedb"? Well because apparently sudo updatedb only adds locations of new files but doesn't remove old ones.
So I had to delete a file

dd if=/dev/zero of=/var/lib/mlocate/mlocate.db

or

sudo bash -c "cat $>  /var/lib/mlocate/mlocate.db"

. And then "sudo updatedb" again.
Then "locate sfbooker" does not return anything as expected.
Problem solved.