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Symptoms

Running your Unreal Engine project in Docker fails with the following error: 
Running: /usr/bin/env -- "chmod" "+x" "/project/Intermediate/Staging/MultiplayerTest1Server.sh"
chmod: changing permissions of '/project/Intermediate/Staging/MultiplayerTest1Server.sh': Operation not permitted
Took 0.0064401s to run env, ExitCode=1
ERROR: Failed to chmod "/project/Intermediate/Staging/MultiplayerTest1Server.sh"
       (see /home/ue4/Library/Logs/Unreal Engine/LocalBuildLogs/Log.txt for full exception trace)
AutomationTool executed for 0h 2m 46s
AutomationTool exiting with ExitCode=1 (Error_Unknown)
RunUAT ERROR: AutomationTool was unable to run successfully. Exited with code: 1

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Explanation

This is happening because there are files in the Intermediate folder that are owned by a different user. This can happen if you build the Linux target on your host machine and then try to run it in Docker.

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Solution

Delete the whole Intermediate folder and try again.