Hi,
the error caused by default 10s writeTimeout inherited from OkHttp library. While readTimeout is configurable by sonar.ws.timeout param, the writeTimout is not currently configurable. In some cases, depends on the analysis report size and /or your infrastructure setup, 10s is not enough to upload an analysis report that causes socket timeout error and DirectoryNotEmptyException. I have implemented a fix and committed it to SonarSource github: https://github.com/SonarSource/sonarqube/pull/3252/files