Tried the early morning run as suggested, apart from feeling groggy jumped on the machine, and only managed to get to the 2nd 3 min run before I had to stop, it felt like I hit a 12ft wall.
I'd woke at 6am, no early cuppa, just got straight on it.
I honestly thought it would be easy 
Will try again tomorrow, and I will complete run 2.
Could be you just started out too fast. That happened to me the other day. I restarted the podcast and walked the 5 min. warm up again and made sure I started slower. It is easy to start off too fast, especially if you're feeling good and ready to go. I don't run on a treadmill though...so I'm not sure if there is a set speed the thing is programmed at. I think that we are variables that cannot be predicted at this early stage of our running careers. Our bodies, some mornings, are ready to do the work and other days maybe the magic beans aren't there. We have to adjust our speed accordingly, but we can still do the time.
I think our bodies are learning to deal with this new activity. Just because two days ago, I was able to jog 10 minutes or 28 minutes at an 8 min. kilometer speed doesn't mean I can go 10 min. at an 8 min. clip today. Maybe I need to slow down to an 8.5 min pace. It could be that I didn't sleep well. I could be coming down with a cold. Maybe I didn't eat enough calories yesterday and I don't have ready fuel for my muscles. Doesn't matter -- just slow it down, pace your breathing and do the time. Kick that "failure" right out of your mind! Think: I can, I want, I will do it.
We've all been right where you are. The key is, to keep going out there (or on the treadmill) and to plug away at the minutes and the miles. You can do it. 
Run when it suits you, both with your schedule and your body. I love running, but you could not pay me to wake up at 6 a.m. and run. I just can't do it. So I found a time that works for me - after working for a few hours, I take a break just before lunch and run - and I've stuck with the programme and reached week 8 with the normal ups and downs. I would probably be able to wrap up with work earlier than 7-8 p.m. if I were done running in the morning, but I know I wouldn't be able to do the run consistently and would give up entirely after some time. So it's a trade-off. But this way I get a nice couple of hours break from work so I'm re-energised when it's time to get back to the desk.
Ah Shivani, you sound more like you normal self today, I hope that means you're feeling better. x
I am a morning runner but not without half a cup of tea or at the very least a small glass of water when I first awake.
Drink first, get dressed, use the bathroom, head out the door. First thing I do when I get back....have another drink.
Never get dehydrated, you muscles won't thank you.
You haven't failed you got on the machine. You can absolutely do it keep going ☺☺
Drink something maybe ? Do you warm up?
Leaping out of bed and straight into that routine, maybe not sensible?
I think I would feel really ill...
Many thanks for all the comments and advice, it's much appreciated.
I kicked the failure out of my mind, got in from work and thought I'm going to try again, and hey presto! I did it Week 4 Run 2 done at the 2nd attempt. It was ok til the last 2 minutes but slowed right down and made it through!
I think you are all right, I got up, no cuppa, no drink, just got dressed up and went for it. When I try a morning run again I'll make sure I actually wake up first!
When I got to the end of my run, I went to increase the incline for the 5 min cool down and found it was still on 2...no wonder it hurt at the end.
I will take an extra day off and do run 3 on Friday. Thanks again everyone
W5R2 2nd attempt DONE! 
Week 4, run 1 (attempt 2)
Week 4 Runs 1 and 2 Done, Future Looks Bleak
Week 4 Run 2 done !!!!
Post run update: to failed run week 4 run 1
