https://www.virtualmin.com/node/39491

Scan a message as root:

spamassassin -D -t -p /home/processengineeringllc/homes/eiasillo/.spamassassin/user_prefs < /home/processengineeringllc/homes/eiasillo/Maildir/.spam/cur/1454619898.14251_0.www

Scan a message as a user:

su -s /bin/sh -c "spamassassin -D -t -p /home/processengineeringllc/homes/eiasillo/.spamassassin/user_prefs < /home/processengineeringllc/homes/eiasillo/Maildir/.spam/cur/1454565258.32109_0.www" - eiasillo

Train the Bayesian filter as a user:

su -s /bin/sh -c "sa-learn -D --spam --no-sync /home/processengineeringllc/homes/eiasillo/Maildir/.spam/{cur,new}" - eiasillo

Update rules (taken from /etc/cron.daily/spamassassin):

su - debian-spamd -c "sa-update --gpghomedir /var/lib/spamassassin/sa-update-keys"