Servers connected to the Internet see a constant number of attacks and scans throughout the day. While a firewall and regular system updates are a good first defense to keep the system secure, you should also regularly check that no attacker came in. The tools described in this tutorial are made for these reason tests, they scan for malware, viruses, and rootkits. They should be run regularly, e.g. every night, and send you reports by e-mail. You can also use Chkrootkit, Rkhunter, and ISPProtect to scan a system if you have suspicious activities such as high load, suspicious processes or if the server suddenly starts sending malware.


All these scanners must be run as root users. Log in as root before running:

sudo -s


on Ubuntu to become root user.


chkrootkit - Linux Rootkit Scanner


Chkrootkit is a classic rootkit scanner. It checks your server for suspicious rootkit processes and checks for a list of known rootkit files.


Either install the package that comes with your distribution (on Debian and Ubuntu you would run

apt-get install chkrootkit


), or download the sources from and install manually:

wget --passive-ftp
tar xvfz chkrootkit.tar.gz
cd chkrootkit-*/
make sense


Afterwards, you can move the chkrootkit directory somewhere else, e.g. to /usr/local/chkrootkit:

cd ..

mv chkrootkit-<version>/ /usr/local/chkrootkit


and create a symlink for easy access:

ln -s /usr/local/chkrootkit/chkrootkit /usr/local/bin/chkrootkit


To check your server with chkrootkit, run the command:



A common false positive report is:

Checking `bindshell'...                                     INFECTED (PORTS:  465)


Don't worry when you get this message on an email server, this is the SMTPS (Secure SMTP) port of your mail system and a well known false positive.


You can even run chkrootkit by a cron job and get the results emailed to you. First, find out the path where chkrootkit is installed on your server with:

which chkrootkit



root@server1:/tmp/chkrootkit-0.52# which chkrootkit



Chkrootkit is installed in the path /usr/sbin/chkrootkit, we need this path in the cron line below:


crontab -e


To create a cron job like this:

0 3 * * * /usr/sbin/chkrootkit 2>&1 | mail -s "chkrootkit output of my server" you@yourdomain.tld)


That would run chkrootkit every night at 3:00. Replace the path to chkrootkit with the path you received from the above command and exchange the email address with your actual address.


Lynis - Universal Security Auditing Tool and Rootkit Scanner


Lynis (formerly rkhunter) is a security auditing tool for Linux and BSD based systems. It performs detailed auditing of many security aspects and configurations of your system. Download the latest Lynis sources from

cd /tmp
tar xvfz lynis-2.7.1.tar.gz
mv lynis /usr/local/
ln -s /usr/local/lynis/lynis /usr/local/bin/lynis


This will install Lynis to the directory /usr/local/lynis and creates a symlink for easy access. Now run

lynis update info


to check if you use the latest version.


Now you can scan your system for rootkits by running:

lynis audit system


Lynis will perform a few checks and then stops to give you some time to read the results. Press [ENTER] to continue with the scan.


In the end, it will show you a summary of the scan.


To run Lynis non-interactively, start it with the --quick option:

lynis --quick


To run Lynis automatically at night, create a cron job like this:

0 3 * * * /usr/local/bin/lynis --quick 2>&1 | mail -s "lynis output of my server"


This will run Lynis every night a 3:00h. Replace the email address with your real address.


ISPProtect - Website Malware Scanner


ISPProtect is a malware scanner for web servers, it scans for malware in website files and CMS systems like Wordpress, Joomla, Drupal etc. If you run a web hosting server, then the hosted websites are the most attacked part of your server and it is recommended to do sanity checks on them regularly. ISPProtect contains 5 scanning engines:

Signature-based malware scanner.

Heuristic malware scanner.

A scanner to show the installation directories of outdated CMS systems.

A scanner that shows you all the outdated WordPress plugins of the whole server.

A database content scanner which checks MySQL databases for potentially malicious content.

ISPProtect is not free software, but there is a free trial that can be used without registration to check your server for malware or clean an infected system. The free license key to use the full version of the software once on your server is simply 'trial'.


ISPProtect requires PHP and ClamAV to be installed on the server, this should be the case on most hosting systems. ClamAV is used by ISPProtect in the first scan level with ISPProtect's own Malware signature set. In case you don't have a command line PHP installed yet, execute:

apt-get install php7.0-cli clamav


on Debian 9 or:

apt-get install php7.2-cli clamav


on Ubuntu 18.04 LTS or:

yum install php


on Fedora and CentOS.


Run the following commands to install ISPProtect.

mkdir -p /usr/local/ispprotect
chown -R root:root /usr/local/ispprotect
chmod -R 750 /usr/local/ispprotect
cd /usr/local/ispprotect
tar xzf ispp_scan.tar.gz
rm -f ispp_scan.tar.gz
ln -s /usr/local/ispprotect/ispp_scan /usr/local/bin/ispp_scan


To start ISPProtect, run:



The scanner automatically checks for updates, then asks for the key (enter the word "trial" here) and then asks for the path of the websites, normally that's /var/www.


Please enter scan key: <-- trial
Please enter path to scan: <-- /var/www


The scanner will now start the scan. Scanning progress is shown. The names of the infected files are shown on the screen at the end of the scan and the results are stored in file in the ISPProtect install directory for later use:


To update ISPProtect, run the command:

ispp_scan --update


To run ISPProtect automatically as a nightly cronjob, create a cron file with nano:

nano /etc/cron.d/ispprotect


and insert the following line:

0 3  * * *   root /usr/local/ispprotect/ispp_scan --update && /usr/local/ispprotect/ispp_scan --path=/var/www --email-results=root@localhost --non-interactive --scan-key=AAA-BBB-CCC-DDD


Replace "root@localhost" with your email address, the scan report is sent to this address. Then exchange "AAA-BBB-CCC-DDD" with your license key. You can get a license key here.


A full list of command line options of ISPProtect ispp_scan command can be obtained with:

ispp_scan --help


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