Store SPAM and HAM messages in two different folders, for example ‘train_spam’ and ‘train_ham’.

Train Spamassassin for one mailbox using the messages from that folders:

cd /var/qmail/mailnames/DOMAIN/spam/Maildir/

sa-learn –spam .train_spam/*
Output will look similar to this:
Learned tokens from 727 message(s) (13758 message(s) examined)

sa-learn –ham .train_ham/*
Output will look similar to this:
Learned tokens from 573 message(s) (11408 message(s) examined)

Copy the spam assassin files into every email account on the server. Keep in mind that if anyone was doing their own spam/ham sorting this will override it (whitelist/blacklist will be left alone).

find /var/qmail/mailnames/ -mindepth 2 -maxdepth 2 -type d -exec /bin/cp -f /var/qmail/mailnames/DOMAIN/spam/.spamassassin/bayes_* {}/.spamassassin/ \;