Maldet is a malware detector and scanner for Linux, designed for shared hosting environments. If maldet not installed on the server then we can follow below steps on the server to install it.
Installation steps:-
# wget http://www.rfxn.com/downloads/maldetect-current.tar.gz
# tar -xvf maldetect-current.tar.gz
# ls -l | grep maldetect
# cd maldetect-1.6.4/
# ls
# ./install.sh

Once it is installed we can scan a particular cpanel account using below command:-

maldet -a /home/user/
Replace the user with the cpanel account user that we want to scan for infected files.

We can write the output to a test files using below command
maldet -a /home/user/ > infectedlist.txt