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Can not mkdir/file when app started from script

I use Docker Toolbox 1.12.3 on Windows.My image contains java app. If I start my app right from Dockerfile:

CMD java -server $JAVA_OPTS -cp $CLASSPATH com.bagri.server.hazelcast.BagriCacheServer

then the app writes logs properly. But, if I start the app from bash script which creates log dirs and then starts the app then no dirs created and no log files.
What is wrong with the script approach?

Thanks, Denis.