BitNinja allows to scan the server with a malware detection tool; this can be done with a single command:
bitninjacli --module=MalwareScanner --scan=/your_path
While the scan is ongoing, you can check the real-time detection log:
tail -f /var/log/bitninja/mod.malware_detection.log
If there is a need, you can cancel the malware scan:
bitninjacli --module=MalwareScanner --cancel
To use the malware scanner in a more advanced way, you can adjust the configuration file(/etc/bitninja/MalwareDetection/config.ini).
More information about the malware scanner configuration can be found here.