What operating system is this?
We had a similar/same issue on one of our deployments. I wrote a discussion topic on the ArcGIS for Server forms here that you may find valuable: https://community.esri.com/message/646889-arcgis-for-server-error-failed-to-start-the-server-machine-premature-end-of-file
Corruption with "server.xml" also cause the same issue so consider it also, you can check at the following path :"C:\Program Files\ArcGIS\Server\framework\runtime\tomcat\conf". in case you are in a cluster you can copy it from one of the another cluster machines.
Had this same issue - :"C:\Program Files\ArcGIS\Server\framework\runtime\tomcat\conf" was corrupted after some Windows Server 2008R2 patches. Copying from another server site solved the issue.
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