In my case, I was trying to clone a private repository in our group Github account to me laptop:
Yuqians-MacBook-Air:regenerateSNID yuqianliu$ git clone https://github.com/nyusngroup/velocity_CCSNe.git
Cloning into 'velocity_CCSNe'...
fatal: https://github.com/nyusngroup/velocity_CCSNe.git/info/refs?service=git-upload-pack not found: did you run git update-server-info on the server?
I found two ways can solve this.
(1) Use http instead of https. It asks me the name and password of our group Github account. After I entered the information, I can clone it.
Yuqians-MacBook-Air:regenerateSNID yuqianliu$ git clone http://github.com/nyusngroup/velocity_CCSNe.git
Cloning into 'velocity_CCSNe'...
Username for 'http://github.com':nyusngroup
Password for 'http://nyusngroup@github.com':
(2) Add my Github account to the collaborators of the private repository in our group Github account, as pointed by Monkey King's answer above.