Mmm, that's helpful, thanks. I'm working in Eclipse and I'm actually getting a different error when I try to run the application from Eclipse compared to when I run from the console namely: Exception in thread "main" java.lang.UnsatisfiedLinkError: libNautyWrapper: file not found at java.lang.Runtime._load(libgcj.so.7) at java.lang.Runtime.loadLibrary(libgcj.so.7) at java.lang.System.loadLibrary(libgcj.so.7) at sequence.RunApplication.(RunApplication.java:3) at java.lang.Class.initializeClass(libgcj.so.7) at java.lang.Class.forName(libgcj.so.7) at gnu.java.lang.MainThread.run(libgcj.so.7) They both seem to take ...