Run the following command as root user.
Try finding other files owned by the user.
This will list all files owned by this user that could be affecting the quota reported by Cpanel.
Cpanel/WHM sometimes has problems with the user quota files causing all users accounts to have unlimited disk space available or 0 megs of disk space in use.
*To enable user quota support on a file system, add “usrquota” to the fourth field containing the word “defaults”.
If you need both user quota and group quota support on a file system?, then edit /etc/fstab
... /dev/hda2 /home ext3 defaults,usrquota,grpquota 1 1
chmod 600 /partition/aquota.user
Re-boot or re-mount file partition with quotas.
From the Linux Man Pages:
quotacheck – scan a filesystem for disk usage, create, check and repair quota files.
quotacheck -vgum /partition
quotacheck reports its operation as it progresses. Normally it operates silently. If the option is specified twice, also the current directory is printed (note that printing can slow down the scan measurably).
Only user quotas listed in /etc/mtab or on the filesystems specified are to be checked. This is the default action.
Only group quotas listed in /etc/mtab or on the filesystems specified are to be checked.
Don’t try to remount filesystem read-only. See comment with option -M.
Check all mounted non-NFS filesystems in /etc/mtab
quotacheck should only be run by super-user. Non-privileged users are presumably not allowed to read all the directories on the given filesystem.
aquota.user or aquota.group : located at filesystem root with quotas (version 2 quota, non-XFS filesystems)
quota.user or quota.group :located at filesystem root with quotas (version 1 quota, non-XFS filesystems)
/etc/mtab names and locations of mounted filesystems
Example Steps for /home partition:
1. First check whether quota is enabled for /home partition.
# vi /etc/fstab
LABEL=/home /home ext3 defaults,usrquota 1 2
2. Remount the /home partition
# mount -o remount /home
3. Create a file called aquota.user for which we need to run quotacheck.
# quotacheck -c /home
4. Enable quota
# quotaon /home
This will enable quota on /home. Now you can edit the quota of a user using.
5) Run /scripts/fixquotas this will solve the quota issue of cpanel accounts.
6) After this `repquota -a` should print out the soft/hard limits with grace periods for all users. If quotas are still not reporting anything in WHM and/or CPanel, check
# repquota -a
7) /var/cpanel/cpanel.config for disablequotacache=0
If that is set to 0, try setting it to 1 and see if that fixes it.
# vi /var/cpanel/cpanel.config ; /scripts/fixquotas
8 If a user’s quota shows more space being used than is in their home directory chances are there are stray files on the system owned by their UID. To find these files, run the following as root:
# find -user username > /tmp/username.txt
Hope this helps.