Hi source,
zmtrainsa is run via cron job "45 23 * * * /opt/zimbra/bin/zmtrainsa --cleanup >> /opt/zimbra/log/spamtrain.log 2>&1".
To run it manually, use this syntax "/opt/zimbra/bin/zmtrainsa <server> <user> <pass> <spam|ham> [folder]"
Are you already running it in this manner?