We are working on run time code coverage calculation of a web application. For this purpose we are using Emma (a free open source code coverage tool).
To find the coverage of an application the application should run under emma tool like
It seems most likely that this is due to using on-the-fly instrumentation approach. Even if you get it to somehow run, your coverage reports will have lot of irrelevant entries for all the classes loaded by jboss including its own libraries and other applications.
I feel you should instead instrument only your specific application jar offline and deploy the instrumented jar.