After being unable to clone a private github repo inside a TeamCity command line build step, even when making sure the ssh-agent was running with the correct key, I found this answer: Team City Git "Host key verification failed"
How to do what this answer suggests? How do I run my TeamCity job under a different account than "System"?
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Chuque
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If you are running TeamCity agents as a Service on Windows, then go to Server Manager -> Configuration -> Services. Find your TeamCity agent there, right click to see Properties, and go to Log On tab, where you can change default Local System account to anything you want:

Peska
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I'm actually running TeamCity with an EC2 agent pool, which are running Linux. – Chuque Apr 12 '18 at 22:16