ClamAV and MalDet - Are these quarantined or infected?

Learning about hardening my VPS, I installed ClamAV and MalDet, using both for a few months. Tonight, I decided that, instead of just checking home I'd check the entire VPS other than "/sys".

This was the result:

/usr/local/maldetect.bk11949/sigs/rfxn.ndb: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/sigs/hex.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/sigs/rfxn.hdb: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/sigs/md5.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/sigs/rfxn.yara: {HEX}gzbase64.inject.unclassed.15.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/sigs/md5v2.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/tmp/.lmdup.666.11852/maldetect-current.tar.gz: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/tmp/.lmdup.666.11852/maldetect-1.6/files/sigs/rfxn.ndb: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/tmp/.lmdup.666.11852/maldetect-1.6/files/sigs/hex.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/tmp/.lmdup.666.11852/maldetect-1.6/files/sigs/rfxn.hdb: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/tmp/.lmdup.666.11852/maldetect-1.6/files/sigs/md5.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/tmp/.lmdup.666.11852/maldetect-1.6/files/sigs/rfxn.yara: {HEX}gzbase64.inject.unclassed.15.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/tmp/.lmdup.666.11852/maldetect-1.6/files/sigs/md5v2.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/tmp/.lmdup.666.11852/maldetect-1.6/files/clean/gzbase64.inject.unclassed: {HEX}gzbase64.inject.unclassed.15.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/clean/gzbase64.inject.unclassed: {HEX}gzbase64.inject.unclassed.15.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/sigs.old/rfxn.ndb: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/sigs.old/hex.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/sigs.old/rfxn.hdb: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/sigs.old/md5.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/sigs.old/rfxn.yara: {HEX}gzbase64.inject.unclassed.15.UNOFFICIAL FOUND
/usr/local/maldetect.bk11949/sigs.old/md5v2.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect/sigs/rfxn.ndb: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect/sigs/hex.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect/sigs/rfxn.hdb: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect/sigs/md5.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect/sigs/rfxn.yara: {HEX}gzbase64.inject.unclassed.15.UNOFFICIAL FOUND
/usr/local/maldetect/sigs/md5v2.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/maldetect/clean/gzbase64.inject.unclassed: {HEX}gzbase64.inject.unclassed.15.UNOFFICIAL FOUND
/usr/local/src/maldetect-1.5/files/sigs/rfxn.ndb: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/src/maldetect-1.5/files/sigs/hex.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/src/maldetect-1.5/files/sigs/rfxn.hdb: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/src/maldetect-1.5/files/sigs/md5.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/src/maldetect-1.5/files/sigs/md5v2.dat: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/local/src/maldetect-1.5/files/clean/gzbase64.inject.unclassed: {HEX}gzbase64.inject.unclassed.15.UNOFFICIAL FOUND
/usr/local/src/maldetect-current.tar.gz: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/share/clamav/rfxn.ndb: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/share/clamav/rfxn.hdb: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/usr/share/clamav/rfxn.yara: {HEX}gzbase64.inject.unclassed.15.UNOFFICIAL FOUND
/var/lib/clamav/rfxn.ndb: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/var/lib/clamav/rfxn.hdb: YARA.Safe0ver_Shell__Safe_Mod_Bypass_By_Evilc0der_php.UNOFFICIAL FOUND
/var/lib/clamav/rfxn.yara: {HEX}gzbase64.inject.unclassed.15.UNOFFICIAL FOUND

Known viruses: 6109455
Engine version: 0.99.2
Scanned directories: 8699
Scanned files: 62104
Infected files: 41
Data scanned: 2514.92 MB
Data read: 4509.22 MB (ratio 0.56:1)
Time: 606.692 sec (10 m 6 s)

So... now I'm scared since I don't look at these as anything but bad news.

Please advise.

YARA is a tool used by various malware protections used for creating description of malware families based on textual of binary patters. The detected malware, "Safe0ver Shell -Safe Mod Bypass By Evilc0der.php" seems to a PHP webshell, an exploit tool that is most likely used to gain shell access on vulnerable servers running PHP.

However, the locations where the malware was found are on directories where either CalmAV or MalDet stores their signature files. Also, to be active, the detected malware should be in the original form (MIME type application/x-httpd-php), which it is not. The signature files must contain enough information about the malware in order to detect it, which may cause false positives when the signature files are scanned with a malware detection tool.

The output seems to be from ClamAV. ClamAV is originally designed to scan emails (and websites) instead of whole filesystems. This increases the rate of false positives even further.

You can exclude these directories. For that

• clamscan has option

  --exclude=REGEX, --exclude-dir=REGEX
      Don't scan file/directory names matching regular expression.
      These options can be used multiple times
  

• clamdscan uses clamd.conf - Configuration file for Clam AntiVirus Daemon. The configuration file location can be set by option --config-file=FILE and the configuration file takes ExcludePath REGEX directives.

• Linux Malware Detect has a file to list paths to ignore:

  .: 8 [ IGNORE OPTIONS ]
  
  There are four ignore files available and they break down as follows:
  
  /usr/local/maldetect/ignore_paths
  A line spaced file for paths that are to be execluded from search results
   Sample ignore entry:
   /home/user/public_html/cgi-bin