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Updated on 17.5.2022

How to scan CentOS server for malware

Linux malware

Some unexpected behaviour on a Linux server could be a result of malware infection, while other malicious software might not alert to their presence. Scanning your system for different types of unwanted programs can help identify issues, or at least give you the peace of mind for having a clean server.

There are multiple options for making sure your cloud server is clean of any malware, this guide goes over a couple of scanning software you can utilise for checking your system.

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ClamAV is a popular open-source antivirus engine available on a multitude of platforms including the majority of Linux distributions. Install it on CentOS 7 with the following command.

sudo yum install clamav clamav-update clamav-scanner-systemd clamav-server-systemd

Afterwards, you’ll need to edit the configuration a little by commenting out the Example text from two files, the simplest way to do so is to use sed for some fast editing with these commands.

sudo sed -i -e "s/^Example/#Example/" /etc/freshclam.conf
sudo sed -i -e "s/^Example/#Example/" /etc/clamd.d/scan.conf

With the required modules installed and configured, next, you should update the virus database for ClamAV.

First, stop the related processes to allow for the update the proceed.

sudo systemctl stop clamav-freshclam

Then use the command below to run the updater application.

sudo freshclam

When you’ve finished updating the virus definitions, start and enable the services.

sudo systemctl start clamav-freshclam
sudo systemctl enable clamav-freshclam

Then do a test scan to your home directory just to make sure the scanning works as it should use the following command.

sudo clamscan -r /home

Granted that your home directory didn’t contain any viruses or other types of malware, the scan should come back empty.

So how do you know it works?

For this, you can download an anti-virus test file, which is a small completely harmless program that most anti-virus software report as infected, though with an obvious test file name EICAR-AV-Test. Use the following command to download the test file to your home directory.

wget -P ~/

Now scan your home folder again with the same command as above, you should receive notice of one infected file at the end summary after the scan is completed. When you’ve confirmed that ClamAV finds the test file correctly, use the command below to scan it again and remove the infected file once found.

sudo clamscan --infected --remove --recursive /home

Be careful when using the –remove parameter. First, run a broader scan without it, and then more localized scan when removing files or remove them manually.

To perform a complete scan of your cloud server, use the this command.

sudo clamscan --infected --recursive --exclude-dir="^/sys" /

The scan goes through each directory in your system root recursively, but skips /sys just to avoid unnecessary warning printouts, as the virtual file system consists of some unreadable files, which could not contain viruses anyway.


Rkhunter is a common option for scanning your system for rootkits and general vulnerabilities. It can be easily installed from the package manager on CentOS using the following command.

sudo yum install rkhunter

Once installed and before scanning, you’ll need to update the file properties database.

sudo rkhunter --propupd

This lets the scanner to know the current state of certain files to prevent some false alarms. After the update, simply run the scanner with the following.

sudo rkhunter --checkall

The scanner goes through some system commands, checks for actual rootkits and some malware, network and local host settings, and then gives you the summary as well as recording the findings to a log file.

Afterwards, you can get a condensed look at the scan log with this command.

sudo cat /var/log/rkhunter/rkhunter.log | grep -i warning

Go through the output to get some tips on what you could do to improve your system security.

Janne Ruostemaa

  1. Sorry, I have no sudo, now what?

  2. ClamAV taking 100% CPU .. any setting to fix it at 50% MAX?

  3. Hello, thank for the article.

    How to configure a Cron Job for both modules?


  4. I have a .sql file. How can I scan it. Thank you in advance .

  5. Fernando Zamora

    Hi, thanks for sharing, you save my server… one webshell was installed so I removed it and the backdoor too, thanks!

  6. Hello guys
    I have cloud server where network has been blocked. I can manage it only by console.
    Unknown service scans 5432 port of random ip adresses from random ports. I must find and remove malware to unblock my server.

    Does anybody know how to fix it?

  7. Hi janne, does this clamAv antivirus scan our Azure cloud storage in schedule basis ?

  8. top guide, thank you!


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