new FileInputStream(new File("./FIFO")) call on Unix blocks current thread forever if the file is FIFO (named pipe). Whenever this happen it actually means that your application (NetBeans in my case) is unusable (especially if it is called from AWT thread). I din't find any workaround how to prevent from it or how to recover from it. There is no way how to identify such fifo files, FileChannel isn't selectable, such blocked thread can't be killed by Thread.interrupt call.