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It may be that mysql is attempting to use /tmp. I had a similar issue before where a mysql process was apparently using /tmp although if I did an "ls -la /tmp" it didn't appear to be.
Solution was to have mysql write to a different temporary directory, which I created by adding:
tmpdir=/home/mysql
in my.cnf; creating the mysql directory in /home/ and giving it mysql.mysql owner.group ownership; then restarting mysql.
Don't know if that's your issue, but the similarity appears to be there.
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