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Malware scan can be time consuming process not only due to vhosts/* size, but also because of IM malware scan is run with the lowest cpu nice priority=19 and low ionice priority (ionice class best-effort, ionice priority=6). For sure that can the reason for IM malware scan to slow down, if your server is under load, and that is only because your server primary mission services (httpd, mysqld) are given higher priority.
Feel free to readjust cpu nice or ionice priority for IM malware scan process by using `renice`, `ionice` tools respectively in a case you want to get IM malware scan process results earlier.
If you think IM scan is stuck (you can check that with `strace -p`), please open zendesk ticket and provide us with server access so we can find the reason and fix it.
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