After resolved this issue http://devnet.jetbrains.com/message/5502730#5502730,
It takes several hours to checkout submodule for the first build with github VCS Root and it does not finished.
Here is the build log
[18:55:37]Checking for changes
[18:55:39]Publishing internal artifacts
[18:55:39][Publishing internal artifacts] Sending build.start.properties.gz file
[18:55:39]Clearing temporary directory: C:\TeamCity\buildAgent\temp\buildTmp
[18:55:39]Clean build enabled: removing old files from C:\TeamCity\buildAgent\work\d5bd6e88e6d8f4c6
[18:55:39]Checkout directory: C:\TeamCity\buildAgent\work\d5bd6e88e6d8f4c6
[18:55:39]Updating sources: agent side checkout (running for 6m:33s)
[18:55:39][Updating sources] Will perform clean checkout. Reason: Checkout directory is empty or doesn't exist
[18:55:39][Updating sources] Cleaning C:\TeamCity\buildAgent\work\d5bd6e88e6d8f4c6
[18:55:39][VCS Root: https://github.com/myteam/myrepo.git] revision: 9ce7c339672bb2a7b113f0513231e9d7cb198c98
I don't have any idea to investigate the manner.
Please let us know if threr is any information.