Ok, i just solved the problem, This problem is with adding ssh key. So the correct commands for heroku deploying is
nihan@heel:~$ heroku login
Enter your Heroku credentials.
Email: debashis.dip@gmail.com
Password (typing will be hidden):
Authentication successful.
nihan@heel:~$ cd dev/flask-app
nihan@heel:~/dev/flask-app$ heroku keys:clear
Removing all SSH keys... done
nihan@heel:~/dev/flask-app$ heroku keys:add
Found existing public key: /home/nihan/.ssh/id_rsa.pub
Uploading SSH public key /home/nihan/.ssh/id_rsa.pub... done
nihan@heel:~/dev/flask-app$ ssh-add ~/.ssh/id_rsa <---- This was the missing key
Enter passphrase for /home/nihan/.ssh/id_rsa:
Identity added: /home/nihan/.ssh/id_rsa (/home/nihan/.ssh/id_rsa)
nihan@heel:~/dev/flask-app$ git push heroku master
Because my ssh never knew which key to use it somehow have heroku the wrong information and that's why heroku was denying.