Its very hard to say what is causing such thoughts, being on anti-depressants, there are rare side effects that include a possible increase in thoughts of harming oneself or others, however in general people who are prescribed anti-depressants are prone to having thoughts of harming themselves.
As it is related to the falling asleep and waking up I'm inclined to think its a period where your thoughts wander, perhaps you're still in a dreamy state and thoughts that you wouldnt rationally or conciously consider start to come into your waking mind.
Do you have anyone you talk to about your mental health, could you bring this up with them and have a chat about how this makes you feel? Also if you are concerned that it is related to your medication still, contact the person who prescribed it.
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