CR-V 2007 to 2011

I left the lights on on my 2006 CRV petrol manual and flattened the battery. I took the battery out and recharged it. On reconnecting the battery the alarm went off almost continuously but didnt go off when I plipped the key fob and in fact nothing seemed to turn the alarm off, manual locking and unlocking doors, operating central locking manually or by key fob etc and the alarm carried on going for 20 mins or so. I could start and drive the car so the immobiliser wasnt acting. The alarm would then stop and restart every 10 mins or so untill I disconnected the battery. on reconnecting the alarm would go off at random times even whilst driving?? It has settled down a bit …