When Linux antivirus lets you down: How to remove malware from a website manually - Page 2 - Manual search cookbook

Manual search cookbook

In Linux and some Unix-like systems, it is hard to find more useful commands for searching files than find and grep. 

Finally, you can use a command like this to identify what PHP scripts are currently running in the background and possibly impacting website performance.

lsof +r 1 -p `ps axww | grep httpd | grep -v grep | awk '{ if(!str) { str=$1 } else { str=str","}} END{print str}'` | grep vhosts | grep php 

Malicious code analysis

Now that we know how to search for possibly malicious files, let's dive a bit deeper and list what exactly we are looking for and where.

1. Check the upload, cache, tmp, backup, log, and images directories.

You need to check all directories that are used for file uploading. For example, with Joomla you should look for .php files in the ./images folder. There is a high chance that if you find something, it will be malicious. For WordPress it is worth checking the wp-content/uploads, backup and theme cache directories.

find ./images -name '*.ph*' 

2. Looking for files with weird names

Here are examples of strange file names to look out for: php, fyi.php, n2fd2.php. You should also look for unusual patterns in file names. For example:

• File names comprising an odd and unreadable mixture of letters, numbers and symbols, e.g. srrfwz.php, ath.php, kirill.php, b374k.php.php, tryag.php.
• ​Because many users rename files by appending the digit '1', look out for normal-looking file names that append numbers other than 1 to filename parts, e.g. index9.php, wp3-login.php.
  

3. Looking for files with unusual extensions.

4. Looking for files with non-standard attributes or creation dates.

5. Looking for doorways using a large number of .html or .php files.​

find ./ -xdev -type d -print0 | while IFS= read -d '' dir; do echo "$(find "$dir" -maxdepth 1 -print0 | grep -zc .) $dir"; done | sort -rn | head -50 

 (Check this thread to find more details on the commands for checking directory file counts.)

Server logs can help​

Integrity checks

It is much easier to analyze attack vectors and look for malware scripts on websites if some security precautions were already made beforehand. Integrity checks help to identify the changes on the file system in a timely manner, and detect malicious activities quickly. The easiest and most effective way to perform such checks is by using version control systems such as git, SVN, or CVS. For example, with git, if you correctly configure the .gitignore file, the process of integrity checking comes down to executing two commands:

git status # check all changed files
git diff # find malicious code

This guarantees that you have a backup copy of your files, and allows you to quickly restore the website to a previous state. Experienced server administrators can also use inotify, tripwire, auditd and similar tools to track file and folder access and changes.

Unfortunately, it is not always possible to configure the version control system or any site integrity check services on a server. In the case of shared hosting, it is not possible to use a version control system or system services. To overcome this problem you can use CMS extensions, in the form of a plugin or a stand-alone script, to track file changes. Some CMSs (e.g. Bitrix or DLE) already have built-in integrity checks.

If the website is using custom scripts or is built with static HTML files, you can use the following shell command to make a snapshot of currently stored files:

ls -lahR > original_file.txt

If any malware threats occur you can create another snapshot and then compare them using any comparison software you like, for example, WinDiff, AraxisMerge Tool, BeyondCompare, the diff command (on Linux) or even compare snapshots online. 

Conclusion

In cases where antivirus solutions fail to clean a hacked website, it is useful to know how to do it yourself on the command line, with heuristics, and using built-in OS and CMS tools and features. Even with high-rate detection malware scanners such as ImunifyAV, being able to confirm the detection rates manually is an important, confidence-building skill.

ImunifyAV is the completely free antivirus and anti-malware scanner. Upgrade to ImunifyAV+ to access the built-in, one-click, fully automated cleanup feature, or get it as part of Imunify360's complete and comprehensive website security solution, which includes an intelligent WAF, IDS and IPS, Proactive Defense, automated kernel patch management and more.