不能运行NetBeans的JavaFX外JAR(Can't run javafx JAR o

我这里有一个问题，我的JavaFX应用程序的jar，通过Netbeans的生成。其实一切都运行得很好，如果我的Netbeans里面运行。然而，当我使用命令行并尝试运行原先由NetBeans中创建我的应用程序的罐子，使用下面的命令：

java -jar SequenceAlign.jar

我在终端得到的错误很多。错误有以下几种：

java.lang.NullPointerException

file:/Users/tsukanomon/NetBeansProjects/SequenceAlign/dist/SequenceAlign.jar!/sequencealign/bioGUI.fxml

   at sequencealign.bioGUIController.getMatrixSubNames(bioGUIController.java:110)
    at sequencealign.bioGUIController.populateComboSubMatrix(bioGUIController.java:99)
    at sequencealign.bioGUIController.initialize(bioGUIController.java:137)
    at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2152)
    at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2028)
    at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2742)
    at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2721)
    at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2707)
    at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2694)
    at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2683)
    at sequencealign.SequenceAlign.start(SequenceAlign.java:21)
    at com.sun.javafx.application.LauncherImpl$5.run(LauncherImpl.java:319)
    at com.sun.javafx.application.PlatformImpl$5.run(PlatformImpl.java:206)
    at com.sun.javafx.application.PlatformImpl$4.run(PlatformImpl.java:173)
    at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:76)
     Exception in Application start method

 java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at  sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at com.javafx.main.Main.launchApp(Main.java:642)
at com.javafx.main.Main.main(Main.java:805)
 Caused by: java.lang.RuntimeException: Exception in Application start method
at com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:403)
at com.sun.javafx.application.LauncherImpl.access$000(LauncherImpl.java:47)
at com.sun.javafx.application.LauncherImpl$1.run(LauncherImpl.java:115)
at java.lang.Thread.run(Thread.java:722)
Caused by: java.lang.NullPointerException
at sequencealign.bioGUIController.getMatrixSubNames(bioGUIController.java:110)
at sequencealign.bioGUIController.populateComboSubMatrix(bioGUIController.java:99)
at sequencealign.bioGUIController.initialize(bioGUIController.java:137)
at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2152)
at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2028)
at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2742)
at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2721)
at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2707)
at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2694)
at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2683)
at sequencealign.SequenceAlign.start(SequenceAlign.java:21)
at com.sun.javafx.application.LauncherImpl$5.run(LauncherImpl.java:319)
at com.sun.javafx.application.PlatformImpl$5.run(PlatformImpl.java:206)
at com.sun.javafx.application.PlatformImpl$4.run(PlatformImpl.java:173)
at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:76)
 2013-05-15 02:14:38.924 java[48780:2517] [JRSAppKitAWT markAppIsDaemon]:Process manager          already initialized: can't fully enable headless mode.   java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at com.javafx.main.Main$2.run(Main.java:881)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:241)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:721)
at java.awt.EventQueue.access$200(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:682)
at java.awt.EventQueue$3.run(EventQueue.java:680)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:691)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
 Caused by: java.awt.HeadlessException
at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:207)
at java.awt.Window.<init>(Window.java:535)
at java.awt.Frame.<init>(Frame.java:420)
at java.awt.Frame.<init>(Frame.java:385)
at javax.swing.SwingUtilities$SharedOwnerFrame.<init>(SwingUtilities.java:1759)
at javax.swing.SwingUtilities.getSharedOwnerFrame(SwingUtilities.java:1834)
at javax.swing.JOptionPane.getRootFrame(JOptionPane.java:1697)
at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:863)
at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:667)
at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:638)
... 19 more

我的规格有：